Starting phenix.real_space_refine
on Wed Mar 12 02:40:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iaz_35323/03_2025/8iaz_35323.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iaz_35323/03_2025/8iaz_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_35323/03_2025/8iaz_35323.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iaz_35323/03_2025/8iaz_35323.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iaz_35323/03_2025/8iaz_35323.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iaz_35323/03_2025/8iaz_35323.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'GLU:plan': 3}
          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: 4.87, per 1000 atoms: 0.66
  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: 1.99
  Conformation dependent library (CDL) restraints added in 374.6 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: 3.18
  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: 2.74

  Time building geometry restraints manager: 2.31 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: 11604
        3.86 -     7.73: 60
        7.73 -    11.59: 9
       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=" 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
  angle pdb=" C2'  DG C   4 "
        pdb=" C1'  DG C   4 "
        pdb=" N9   DG C   4 "
      ideal   model   delta    sigma   weight residual
     113.50  121.84   -8.34 1.50e+00 4.44e-01 3.09e+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: 1288
       0.070 -    0.140: 113
       0.140 -    0.210: 18
       0.210 -    0.279: 6
       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:             0.660
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.840
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  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:13.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
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   7962  Z= 0.351
  Angle     :  0.796  19.318  11674  Z= 0.452
  Chirality :  0.047   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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.004   0.001   TRP A 140 
 HIS   0.005   0.001   HIS A  99 
 PHE   0.014   0.002   PHE A 360 
 TYR   0.014   0.002   TYR A  44 
 ARG   0.004   0.000   ARG A 130 

*********************** 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  : 0.485 
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: 1.2274
  time to fit residues: 82.2328
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  : 0.471 
-------------------------------------------------------------------------------
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 48 optimal weight:    9.9990
   chunk 43 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 44 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 51 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 373 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.191733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.159866 restraints weight = 6937.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 0.35
r_work: 0.3342 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3248
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3248 r_free = 0.3248    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      200 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      208 |
|-----------------------------------------------------------------------------|
r_final: 0.3235
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7962  Z= 0.180
  Angle     :  0.635  10.488  11674  Z= 0.333
  Chirality :  0.038   0.257   1428
  Planarity :  0.004   0.042    736
  Dihedral  : 26.493 179.053   3352
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.02 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 29.45 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.44), residues: 382
  helix:  2.83 (0.39), residues: 174
  sheet: -0.05 (0.85), residues: 41
  loop : -2.32 (0.40), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  73 
 HIS   0.003   0.001   HIS A  99 
 PHE   0.010   0.001   PHE A 118 
 TYR   0.008   0.001   TYR A  33 
 ARG   0.003   0.000   ARG A  95 

*********************** 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
  62 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 40
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
REVERT: A   51 MET cc_start: 0.8128 (ttm) cc_final: 0.7855 (ttm)
REVERT: A  127 ARG cc_start: 0.8429 (ptt180) cc_final: 0.8064 (ptt-90)
REVERT: A  210 LYS cc_start: 0.8203 (mtpm) cc_final: 0.7769 (mmtm)
REVERT: A  256 LYS cc_start: 0.8282 (ttmm) cc_final: 0.7953 (mttp)
REVERT: A  329 GLU cc_start: 0.8302 (pm20) cc_final: 0.7626 (pm20)
REVERT: A  357 ASP cc_start: 0.7490 (p0) cc_final: 0.7098 (p0)
  outliers start: 22
  outliers final: 8
  residues processed: 61
  average time/residue: 1.1317
  time to fit residues: 73.2934
Evaluate side-chains
  44 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 36
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
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   94 THR
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain A residue  287 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:    0.8980
   chunk 29 optimal weight:    6.9990
   chunk 6 optimal weight:    0.0670
   chunk 11 optimal weight:    4.9990
   chunk 41 optimal weight:    7.9990
   chunk 17 optimal weight:    4.9990
   chunk 42 optimal weight:    9.9990
   chunk 34 optimal weight:   10.0000
   chunk 39 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 48 optimal weight:   10.0000
   overall best weight:    2.5924

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.178636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.143578 restraints weight = 7102.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 0.39
r_work: 0.3116 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3097
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      208 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      206 |
|-----------------------------------------------------------------------------|
r_final: 0.3096
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   7962  Z= 0.308
  Angle     :  0.730  10.206  11674  Z= 0.382
  Chirality :  0.043   0.295   1428
  Planarity :  0.004   0.045    736
  Dihedral  : 26.586 177.792   3341
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.81 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 28.86 %
    Favored  : 66.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.43), residues: 382
  helix:  2.38 (0.39), residues: 175
  sheet:  0.03 (0.82), residues: 41
  loop : -2.42 (0.40), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 140 
 HIS   0.005   0.001   HIS A  99 
 PHE   0.018   0.002   PHE A  35 
 TYR   0.011   0.002   TYR A  33 
 ARG   0.007   0.001   ARG A 130 

*********************** 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: 17
    poor density    : 40
  time to evaluate  : 0.418 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6717 (ttpt)
REVERT: A   51 MET cc_start: 0.8170 (ttm) cc_final: 0.7840 (ttm)
REVERT: A  127 ARG cc_start: 0.8567 (ptt180) cc_final: 0.8210 (ptt-90)
REVERT: A  138 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8576 (mt)
REVERT: A  210 LYS cc_start: 0.8302 (mtpm) cc_final: 0.7825 (mttm)
REVERT: A  385 GLU cc_start: 0.6541 (pt0) cc_final: 0.6229 (pm20)
  outliers start: 17
  outliers final: 9
  residues processed: 54
  average time/residue: 1.2104
  time to fit residues: 69.0975
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  : 0.470 
-------------------------------------------------------------------------------
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  138 LEU
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  287 ILE
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 46 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 47 optimal weight:    7.9990
   chunk 0 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 44 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 35 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    2.5186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.177764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.142044 restraints weight = 7049.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 0.48
r_work: 0.3203 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3118
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      206 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      204 |
|-----------------------------------------------------------------------------|
r_final: 0.3118
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   7962  Z= 0.295
  Angle     :  0.718   9.750  11674  Z= 0.375
  Chirality :  0.043   0.284   1428
  Planarity :  0.004   0.041    736
  Dihedral  : 26.530 178.720   3339
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.07 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 26.82 %
    Favored  : 67.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.43), residues: 382
  helix:  2.40 (0.39), residues: 174
  sheet:  0.19 (0.82), residues: 41
  loop : -2.49 (0.40), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 140 
 HIS   0.004   0.001   HIS A  99 
 PHE   0.015   0.002   PHE A  35 
 TYR   0.012   0.002   TYR A  33 
 ARG   0.004   0.001   ARG A 130 

*********************** 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
  54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 35
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6731 (ttpt)
REVERT: A   51 MET cc_start: 0.8204 (ttm) cc_final: 0.7891 (ttm)
REVERT: A  127 ARG cc_start: 0.8559 (ptt180) cc_final: 0.8186 (ptt-90)
REVERT: A  210 LYS cc_start: 0.8279 (mtpm) cc_final: 0.7795 (mttm)
REVERT: A  283 LYS cc_start: 0.7116 (tttp) cc_final: 0.6799 (ttpt)
REVERT: A  355 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7898 (tp)
  outliers start: 19
  outliers final: 11
  residues processed: 51
  average time/residue: 1.3645
  time to fit residues: 73.2330
Evaluate side-chains
  45 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 32
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
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   82 VAL
Chi-restraints excluded: chain A residue   94 THR
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  280 VAL
Chi-restraints excluded: chain A residue  287 ILE
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  383 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 47 optimal weight:    8.9990
   chunk 8 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 44 optimal weight:   10.0000
   chunk 34 optimal weight:    7.9990
   chunk 13 optimal weight:    0.5980
   chunk 16 optimal weight:    4.9990
   chunk 7 optimal weight:    0.7980
   chunk 54 optimal weight:    5.9990
   overall best weight:    1.4582

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3933 r_free = 0.3933 target = 0.182033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.146265 restraints weight = 6931.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 0.45
r_work: 0.3101 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3066
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      204 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      203 |
|-----------------------------------------------------------------------------|
r_final: 0.3066
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7962  Z= 0.205
  Angle     :  0.661   9.147  11674  Z= 0.346
  Chirality :  0.040   0.264   1428
  Planarity :  0.004   0.039    736
  Dihedral  : 26.425 179.254   3339
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.54 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 28.28 %
    Favored  : 67.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.44), residues: 382
  helix:  2.61 (0.39), residues: 174
  sheet:  0.30 (0.84), residues: 41
  loop : -2.49 (0.40), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 336 
 HIS   0.004   0.001   HIS A  99 
 PHE   0.010   0.002   PHE A 118 
 TYR   0.011   0.001   TYR A  33 
 ARG   0.004   0.000   ARG A  95 

*********************** 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
  49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 35
  time to evaluate  : 0.504 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6614 (ttpt)
REVERT: A  127 ARG cc_start: 0.8588 (ptt180) cc_final: 0.8236 (ptt-90)
REVERT: A  210 LYS cc_start: 0.8236 (mtpm) cc_final: 0.7753 (mttm)
REVERT: A  283 LYS cc_start: 0.7025 (tttp) cc_final: 0.6715 (ttpt)
REVERT: A  355 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7801 (tp)
REVERT: A  385 GLU cc_start: 0.7242 (pm20) cc_final: 0.6963 (pt0)
  outliers start: 14
  outliers final: 7
  residues processed: 46
  average time/residue: 1.2210
  time to fit residues: 59.4949
Evaluate side-chains
  43 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 34
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
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  162 THR
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain A residue  287 ILE
Chi-restraints excluded: chain A residue  355 LEU
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 22 optimal weight:    5.9990
   chunk 31 optimal weight:    0.6980
   chunk 28 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 47 optimal weight:    8.9990
   chunk 9 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 54 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 46 optimal weight:    7.9990
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3855 r_free = 0.3855 target = 0.175474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.138782 restraints weight = 7050.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 0.78
r_work: 0.3188 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3083
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      203 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3082 r_free = 0.3082    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      204 |
|-----------------------------------------------------------------------------|
r_final: 0.3082
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   7962  Z= 0.337
  Angle     :  0.757   9.347  11674  Z= 0.395
  Chirality :  0.045   0.299   1428
  Planarity :  0.004   0.041    736
  Dihedral  : 26.542 179.296   3339
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.85 %
    Favored  : 91.88 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 26.82 %
    Favored  : 67.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.43), residues: 382
  helix:  2.24 (0.39), residues: 174
  sheet:  0.13 (0.81), residues: 41
  loop : -2.59 (0.40), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 140 
 HIS   0.004   0.001   HIS A  99 
 PHE   0.016   0.002   PHE A  35 
 TYR   0.011   0.002   TYR A  33 
 ARG   0.005   0.001   ARG A 130 

*********************** 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
  54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 36
  time to evaluate  : 0.509 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6743 (ttpt)
REVERT: A  210 LYS cc_start: 0.8299 (mtpm) cc_final: 0.7793 (mttm)
REVERT: A  385 GLU cc_start: 0.7306 (pm20) cc_final: 0.6964 (pt0)
  outliers start: 18
  outliers final: 9
  residues processed: 51
  average time/residue: 1.3439
  time to fit residues: 72.2757
Evaluate side-chains
  41 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 31
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
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   94 THR
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  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 8 optimal weight:    2.9990
   chunk 43 optimal weight:    9.9990
   chunk 54 optimal weight:    5.9990
   chunk 37 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 48 optimal weight:   10.0000
   chunk 31 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3872 r_free = 0.3872 target = 0.176931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.140166 restraints weight = 7014.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 0.52
r_work: 0.3228 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3150
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3150 r_free = 0.3150    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      204 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3150 r_free = 0.3150    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      205 |
|-----------------------------------------------------------------------------|
r_final: 0.3150
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   7962  Z= 0.285
  Angle     :  0.721   9.214  11674  Z= 0.377
  Chirality :  0.043   0.287   1428
  Planarity :  0.004   0.040    736
  Dihedral  : 26.526 179.412   3339
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.33 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 26.53 %
    Favored  : 68.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.43), residues: 382
  helix:  2.32 (0.39), residues: 174
  sheet:  0.14 (0.81), residues: 41
  loop : -2.61 (0.40), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 336 
 HIS   0.004   0.001   HIS A  99 
 PHE   0.012   0.002   PHE A  35 
 TYR   0.012   0.002   TYR A  33 
 ARG   0.005   0.001   ARG A 130 

*********************** 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
  49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 32
  time to evaluate  : 0.549 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6723 (ttpt)
REVERT: A  138 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8631 (mt)
REVERT: A  210 LYS cc_start: 0.8257 (mtpm) cc_final: 0.7752 (mttm)
REVERT: A  329 GLU cc_start: 0.8243 (pm20) cc_final: 0.7687 (pm20)
REVERT: A  385 GLU cc_start: 0.7180 (pm20) cc_final: 0.6812 (pt0)
  outliers start: 17
  outliers final: 10
  residues processed: 47
  average time/residue: 1.3427
  time to fit residues: 66.6783
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  : 0.515 
-------------------------------------------------------------------------------
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   82 VAL
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  138 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 43 optimal weight:    9.9990
   chunk 54 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 50 optimal weight:    8.9990
   chunk 33 optimal weight:    7.9990
   overall best weight:    2.9986

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

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.175480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.139383 restraints weight = 7052.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 0.81
r_work: 0.3198 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3060
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      205 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      206 |
|-----------------------------------------------------------------------------|
r_final: 0.3060
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.2310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   7962  Z= 0.342
  Angle     :  0.769   9.720  11674  Z= 0.401
  Chirality :  0.045   0.305   1428
  Planarity :  0.004   0.041    736
  Dihedral  : 26.638 179.935   3339
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  7.33 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 25.36 %
    Favored  : 69.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.43), residues: 382
  helix:  2.30 (0.40), residues: 168
  sheet:  0.16 (0.81), residues: 41
  loop : -2.71 (0.40), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 140 
 HIS   0.004   0.001   HIS A  99 
 PHE   0.016   0.002   PHE A  35 
 TYR   0.012   0.002   TYR A  33 
 ARG   0.006   0.001   ARG A 130 

*********************** 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
  53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 36
  time to evaluate  : 0.566 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6769 (ttpt)
REVERT: A  210 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7776 (mttm)
  outliers start: 17
  outliers final: 10
  residues processed: 49
  average time/residue: 1.2080
  time to fit residues: 63.0255
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  : 0.510 
-------------------------------------------------------------------------------
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   82 VAL
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  210 LYS
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   chunk 48 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9990
   chunk 33 optimal weight:    6.9990
   chunk 54 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.179015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.144713 restraints weight = 7078.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 0.45
r_work: 0.3067 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3009
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3009 r_free = 0.3009    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      206 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3009 r_free = 0.3009    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      206 |
|-----------------------------------------------------------------------------|
r_final: 0.3009
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.2278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7962  Z= 0.262
  Angle     :  0.699   9.264  11674  Z= 0.365
  Chirality :  0.042   0.280   1428
  Planarity :  0.004   0.039    736
  Dihedral  : 26.484 178.666   3339
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.28 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 26.82 %
    Favored  : 68.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.43), residues: 382
  helix:  2.46 (0.39), residues: 171
  sheet:  0.15 (0.81), residues: 41
  loop : -2.49 (0.41), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 336 
 HIS   0.004   0.001   HIS A  99 
 PHE   0.010   0.002   PHE A 360 
 TYR   0.012   0.002   TYR A  33 
 ARG   0.004   0.000   ARG A  95 

*********************** 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
  49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 33
  time to evaluate  : 0.531 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6733 (ttpt)
REVERT: A  210 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7784 (mttm)
REVERT: A  256 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8115 (mttp)
  outliers start: 16
  outliers final: 10
  residues processed: 45
  average time/residue: 1.2879
  time to fit residues: 61.3200
Evaluate side-chains
  44 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 31
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
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   82 VAL
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue   95 ARG
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  210 LYS
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain A residue  256 LYS
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 52 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 44 optimal weight:   10.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.178945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.143937 restraints weight = 7042.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 0.47
r_work: 0.3256 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3161
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      206 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      206 |
|-----------------------------------------------------------------------------|
r_final: 0.3161
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.2290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7962  Z= 0.267
  Angle     :  0.706   8.972  11674  Z= 0.368
  Chirality :  0.042   0.280   1428
  Planarity :  0.004   0.040    736
  Dihedral  : 26.467 177.763   3339
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.33 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 27.41 %
    Favored  : 67.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.43), residues: 382
  helix:  2.35 (0.39), residues: 174
  sheet:  0.14 (0.80), residues: 41
  loop : -2.61 (0.40), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 336 
 HIS   0.004   0.001   HIS A  99 
 PHE   0.011   0.002   PHE A  35 
 TYR   0.012   0.002   TYR A  33 
 ARG   0.004   0.001   ARG A  95 

********************** 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
  47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 31
  time to evaluate  : 0.490 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6715 (ttpt)
REVERT: A  210 LYS cc_start: 0.8219 (mtpm) cc_final: 0.7717 (mttm)
REVERT: A  256 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8004 (mttp)
  outliers start: 16
  outliers final: 11
  residues processed: 44
  average time/residue: 1.2546
  time to fit residues: 58.4852
Evaluate side-chains
  44 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 31
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
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   82 VAL
Chi-restraints excluded: chain A residue   94 THR
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  256 LYS
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 54 optimal weight:    5.9990
   chunk 4 optimal weight:    0.3980
   chunk 49 optimal weight:    8.9990
   chunk 36 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0050
   chunk 44 optimal weight:   10.0000
   chunk 50 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.8800

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

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.181822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.146841 restraints weight = 7094.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 0.49
r_work: 0.3265 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3108
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3108 r_free = 0.3108    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      206 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3108 r_free = 0.3108    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      207 |
|-----------------------------------------------------------------------------|
r_final: 0.3108
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7962  Z= 0.162
  Angle     :  0.640   8.248  11674  Z= 0.334
  Chirality :  0.038   0.251   1428
  Planarity :  0.004   0.038    736
  Dihedral  : 26.384 178.026   3339
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.81 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 28.28 %
    Favored  : 68.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.44), residues: 382
  helix:  2.83 (0.40), residues: 171
  sheet:  0.38 (0.82), residues: 41
  loop : -2.47 (0.41), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 336 
 HIS   0.003   0.001   HIS A  99 
 PHE   0.007   0.001   PHE A 200 
 TYR   0.013   0.001   TYR A  33 
 ARG   0.004   0.001   ARG A  95 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4091.14 seconds
wall clock time: 70 minutes 38.56 seconds (4238.56 seconds total)