Starting phenix.real_space_refine
on Sat May 10 23:52:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iaz_35323/05_2025/8iaz_35323.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iaz_35323/05_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_35323/05_2025/8iaz_35323.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iaz_35323/05_2025/8iaz_35323.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iaz_35323/05_2025/8iaz_35323.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iaz_35323/05_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-5687/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: 5.19, per 1000 atoms: 0.70
  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: 2.20
  Conformation dependent library (CDL) restraints added in 440.7 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: 2.84
  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: 2.65

  Time building geometry restraints manager: 2.53 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:             0.820
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.940
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:9.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.160
-------------------------------------------------------------------------------
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   7966  Z= 0.323
  Angle     :  0.804  19.318  11680  Z= 0.453
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15517 (  278)
  hydrogen bonds       : angle       4.60152 (  653)
  metal coordination   : bond        0.00755 (    4)
  metal coordination   : angle       4.95686 (    6)
  covalent geometry    : bond        0.00607 ( 7962)
  covalent geometry    : angle       0.79583 (11674)

*********************** 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: 1.1051
  time to fit residues: 73.9341
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  : 0.473 
-------------------------------------------------------------------------------
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 = 0.159864 restraints weight = 6937.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 0.35
r_work: 0.3344 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3250
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    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 = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      210 |
|-----------------------------------------------------------------------------|
r_final: 0.3238
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
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   7966  Z= 0.149
  Angle     :  0.645  10.488  11680  Z= 0.334
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05947 (  278)
  hydrogen bonds       : angle       3.42612 (  653)
  metal coordination   : bond        0.00983 (    4)
  metal coordination   : angle       4.88499 (    6)
  covalent geometry    : bond        0.00298 ( 7962)
  covalent geometry    : angle       0.63550 (11674)

*********************** 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  : 0.489 
Fit side-chains
   revert: symmetry clash
REVERT: A   51 MET cc_start: 0.8129 (ttm) cc_final: 0.7858 (ttm)
REVERT: A  127 ARG cc_start: 0.8428 (ptt180) cc_final: 0.8062 (ptt-90)
REVERT: A  210 LYS cc_start: 0.8202 (mtpm) cc_final: 0.7768 (mmtm)
REVERT: A  256 LYS cc_start: 0.8280 (ttmm) cc_final: 0.7952 (mttp)
REVERT: A  329 GLU cc_start: 0.8300 (pm20) cc_final: 0.7627 (pm20)
REVERT: A  357 ASP cc_start: 0.7496 (p0) cc_final: 0.7097 (p0)
  outliers start: 22
  outliers final: 8
  residues processed: 61
  average time/residue: 1.1015
  time to fit residues: 71.2892
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  : 0.480 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 29 optimal weight:    6.9990
   chunk 6 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 41 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   chunk 42 optimal weight:    8.9990
   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:    3.6788

-------------------------------------------------------------------------------
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 = 0.3871 r_free = 0.3871 target = 0.176471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.140297 restraints weight = 7092.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 0.83
r_work: 0.3133 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3022
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      210 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3020 r_free = 0.3020    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      207 |
|-----------------------------------------------------------------------------|
r_final: 0.3020
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056   7966  Z= 0.310
  Angle     :  0.822  10.887  11680  Z= 0.425
  Chirality :  0.048   0.321   1428
  Planarity :  0.005   0.045    736
  Dihedral  : 26.725 177.754   3341
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.33 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 26.82 %
    Favored  : 67.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.01 (0.42), residues: 382
  helix:  2.11 (0.39), residues: 175
  sheet: -0.03 (0.82), residues: 41
  loop : -2.48 (0.40), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 140 
 HIS   0.005   0.001   HIS A  99 
 PHE   0.022   0.003   PHE A  35 
 TYR   0.011   0.002   TYR A 171 
 ARG   0.006   0.001   ARG A 130 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09682 (  278)
  hydrogen bonds       : angle       3.62665 (  653)
  metal coordination   : bond        0.01192 (    4)
  metal coordination   : angle       5.45280 (    6)
  covalent geometry    : bond        0.00667 ( 7962)
  covalent geometry    : angle       0.81281 (11674)

*********************** 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
  59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 39
  time to evaluate  : 0.462 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6836 (ttpt)
REVERT: A  138 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8660 (mt)
REVERT: A  210 LYS cc_start: 0.8377 (mtpm) cc_final: 0.7878 (mttm)
REVERT: A  385 GLU cc_start: 0.6624 (pt0) cc_final: 0.6314 (pm20)
  outliers start: 20
  outliers final: 10
  residues processed: 54
  average time/residue: 1.2484
  time to fit residues: 71.1586
Evaluate side-chains
  43 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 31
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
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   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  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:    4.9990
   chunk 54 optimal weight:    5.9990
   chunk 44 optimal weight:    9.9990
   chunk 29 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 35 optimal weight:    0.1980
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.3784

-------------------------------------------------------------------------------
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 = 0.3929 r_free = 0.3929 target = 0.182109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.146684 restraints weight = 7044.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 0.48
r_work: 0.3124 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3094
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      207 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3093 r_free = 0.3093    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      206 |
|-----------------------------------------------------------------------------|
r_final: 0.3093
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7966  Z= 0.159
  Angle     :  0.650   9.479  11680  Z= 0.336
  Chirality :  0.039   0.260   1428
  Planarity :  0.004   0.038    736
  Dihedral  : 26.399 179.659   3339
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.81 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 27.99 %
    Favored  : 67.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.41 (0.43), residues: 382
  helix:  2.63 (0.39), residues: 174
  sheet:  0.07 (0.82), residues: 41
  loop : -2.45 (0.40), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 140 
 HIS   0.004   0.001   HIS A  99 
 PHE   0.010   0.001   PHE A 118 
 TYR   0.011   0.001   TYR A  33 
 ARG   0.003   0.000   ARG A  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06288 (  278)
  hydrogen bonds       : angle       3.32706 (  653)
  metal coordination   : bond        0.00731 (    4)
  metal coordination   : angle       4.59831 (    6)
  covalent geometry    : bond        0.00323 ( 7962)
  covalent geometry    : angle       0.64203 (11674)

*********************** 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
  53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 36
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6476 (ttpt)
REVERT: A  210 LYS cc_start: 0.8236 (mtpm) cc_final: 0.7761 (mttm)
REVERT: A  254 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8153 (mtm180)
REVERT: A  329 GLU cc_start: 0.8351 (pm20) cc_final: 0.7756 (pm20)
  outliers start: 17
  outliers final: 10
  residues processed: 49
  average time/residue: 1.2419
  time to fit residues: 64.4214
Evaluate side-chains
  46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 34
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
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  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
Chi-restraints excluded: chain A residue  385 GLU
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:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 39 optimal weight:    6.9990
   chunk 2 optimal weight:    0.7980
   chunk 44 optimal weight:   10.0000
   chunk 34 optimal weight:    8.9990
   chunk 13 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 54 optimal weight:    6.9990
   overall best weight:    3.3588

-------------------------------------------------------------------------------
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 = 0.3853 r_free = 0.3853 target = 0.175093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.139276 restraints weight = 7008.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 0.72
r_work: 0.3165 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3069
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    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 = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      204 |
|-----------------------------------------------------------------------------|
r_final: 0.3069
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   7966  Z= 0.285
  Angle     :  0.795  10.141  11680  Z= 0.410
  Chirality :  0.046   0.311   1428
  Planarity :  0.005   0.042    736
  Dihedral  : 26.639 178.724   3339
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.59 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 25.66 %
    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:  0.00 (0.43), residues: 382
  helix:  2.16 (0.39), residues: 174
  sheet:  0.10 (0.82), residues: 41
  loop : -2.57 (0.40), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   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   0.005   0.001   ARG A  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09239 (  278)
  hydrogen bonds       : angle       3.56375 (  653)
  metal coordination   : bond        0.00960 (    4)
  metal coordination   : angle       4.89753 (    6)
  covalent geometry    : bond        0.00612 ( 7962)
  covalent geometry    : angle       0.78767 (11674)

*********************** 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
  54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 32
  time to evaluate  : 0.468 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6845 (ttpt)
REVERT: A  138 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8658 (mt)
REVERT: A  210 LYS cc_start: 0.8307 (mtpm) cc_final: 0.7804 (mttm)
  outliers start: 22
  outliers final: 11
  residues processed: 50
  average time/residue: 1.4047
  time to fit residues: 73.9010
Evaluate side-chains
  42 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 29
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
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  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  280 VAL
Chi-restraints excluded: chain A residue  287 ILE
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:    4.9990
   chunk 31 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 47 optimal weight:    8.9990
   chunk 9 optimal weight:    0.3980
   chunk 19 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 46 optimal weight:    6.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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 = 0.3932 r_free = 0.3932 target = 0.182378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.147019 restraints weight = 7089.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 0.46
r_work: 0.3271 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3173
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      204 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      206 |
|-----------------------------------------------------------------------------|
r_final: 0.3173
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7966  Z= 0.149
  Angle     :  0.640   8.059  11680  Z= 0.332
  Chirality :  0.038   0.255   1428
  Planarity :  0.004   0.038    736
  Dihedral  : 26.326 179.219   3339
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.81 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 27.11 %
    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:  2.77 (0.40), residues: 171
  sheet:  0.67 (0.85), residues: 39
  loop : -2.46 (0.40), residues: 172

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   0.010   0.001   PHE A 118 
 TYR   0.011   0.001   TYR A  33 
 ARG   0.003   0.000   ARG A  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05956 (  278)
  hydrogen bonds       : angle       3.26028 (  653)
  metal coordination   : bond        0.00580 (    4)
  metal coordination   : angle       4.22433 (    6)
  covalent geometry    : bond        0.00301 ( 7962)
  covalent geometry    : angle       0.63320 (11674)

*********************** 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
  51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 35
  time to evaluate  : 0.543 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6471 (ttpt)
REVERT: A  210 LYS cc_start: 0.8223 (mtpm) cc_final: 0.7754 (mttm)
REVERT: A  254 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8060 (mtm180)
REVERT: A  329 GLU cc_start: 0.8277 (pm20) cc_final: 0.7762 (pm20)
REVERT: A  385 GLU cc_start: 0.7349 (pm20) cc_final: 0.7058 (pt0)
  outliers start: 16
  outliers final: 9
  residues processed: 49
  average time/residue: 1.1680
  time to fit residues: 60.7488
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  : 0.469 
-------------------------------------------------------------------------------
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  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 8 optimal weight:    4.9990
   chunk 43 optimal weight:    9.9990
   chunk 54 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 48 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 41 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.3908 r_free = 0.3908 target = 0.179985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.143743 restraints weight = 6986.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 0.46
r_work: 0.3263 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3126
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      206 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3125 r_free = 0.3125    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      206 |
|-----------------------------------------------------------------------------|
r_final: 0.3125
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
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      :  0.004   0.044   7966  Z= 0.192
  Angle     :  0.685   8.066  11680  Z= 0.355
  Chirality :  0.040   0.272   1428
  Planarity :  0.004   0.041    736
  Dihedral  : 26.369 179.265   3339
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.59 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 26.82 %
    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:  0.36 (0.43), residues: 382
  helix:  2.57 (0.39), residues: 174
  sheet:  0.44 (0.83), residues: 41
  loop : -2.58 (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   0.011   0.002   PHE A  35 
 TYR   0.011   0.001   TYR A  33 
 ARG   0.004   0.001   ARG A  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07157 (  278)
  hydrogen bonds       : angle       3.33538 (  653)
  metal coordination   : bond        0.00662 (    4)
  metal coordination   : angle       4.16539 (    6)
  covalent geometry    : bond        0.00400 ( 7962)
  covalent geometry    : angle       0.67912 (11674)

*********************** 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
  51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 34
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6652 (ttpt)
REVERT: A  144 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8642 (mttt)
REVERT: A  210 LYS cc_start: 0.8245 (mtpm) cc_final: 0.7759 (mttm)
REVERT: A  254 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8078 (mtm180)
REVERT: A  385 GLU cc_start: 0.7338 (pm20) cc_final: 0.7036 (pt0)
  outliers start: 17
  outliers final: 10
  residues processed: 49
  average time/residue: 1.3641
  time to fit residues: 70.4204
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  : 0.464 
-------------------------------------------------------------------------------
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  144 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 43 optimal weight:   10.0000
   chunk 54 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   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:    2.9788

-------------------------------------------------------------------------------
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 = 0.3858 r_free = 0.3858 target = 0.175634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.143113 restraints weight = 7048.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 0.60
r_work: 0.3113 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3046
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      206 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      207 |
|-----------------------------------------------------------------------------|
r_final: 0.3046
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   7966  Z= 0.257
  Angle     :  0.764   9.258  11680  Z= 0.395
  Chirality :  0.044   0.296   1428
  Planarity :  0.004   0.043    736
  Dihedral  : 26.543 179.855   3339
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.59 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 25.66 %
    Favored  : 68.80 %
  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:  2.27 (0.39), residues: 175
  sheet:  0.15 (0.81), residues: 41
  loop : -2.64 (0.40), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 140 
 HIS   0.005   0.001   HIS A  99 
 PHE   0.015   0.002   PHE A  35 
 TYR   0.011   0.002   TYR A  33 
 ARG   0.006   0.001   ARG A 130 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08603 (  278)
  hydrogen bonds       : angle       3.47864 (  653)
  metal coordination   : bond        0.00767 (    4)
  metal coordination   : angle       4.44047 (    6)
  covalent geometry    : bond        0.00549 ( 7962)
  covalent geometry    : angle       0.75716 (11674)

*********************** 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
  52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 33
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6805 (ttpt)
REVERT: A  210 LYS cc_start: 0.8276 (mtpm) cc_final: 0.7773 (mttm)
REVERT: A  256 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8063 (mttp)
REVERT: A  385 GLU cc_start: 0.7125 (pm20) cc_final: 0.6813 (pt0)
  outliers start: 19
  outliers final: 12
  residues processed: 48
  average time/residue: 1.2548
  time to fit residues: 63.7403
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  : 0.508 
-------------------------------------------------------------------------------
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  254 ARG
Chi-restraints excluded: chain A residue  256 LYS
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 35 optimal weight:    3.9990
   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:    9.9990
   chunk 19 optimal weight:    0.8980
   chunk 33 optimal weight:    0.3980
   chunk 54 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    2.0184

-------------------------------------------------------------------------------
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
A 211 ASN
A 310 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.179995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.145355 restraints weight = 7057.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 0.43
r_work: 0.3216 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3045
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      207 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      207 |
|-----------------------------------------------------------------------------|
r_final: 0.3045
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7966  Z= 0.197
  Angle     :  0.699   8.796  11680  Z= 0.362
  Chirality :  0.041   0.275   1428
  Planarity :  0.004   0.040    736
  Dihedral  : 26.439 179.433   3339
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.07 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 25.95 %
    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:  0.22 (0.43), residues: 382
  helix:  2.45 (0.39), residues: 174
  sheet:  0.26 (0.81), residues: 41
  loop : -2.62 (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   0.010   0.002   PHE A 360 
 TYR   0.012   0.002   TYR A  33 
 ARG   0.004   0.000   ARG A  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07371 (  278)
  hydrogen bonds       : angle       3.38942 (  653)
  metal coordination   : bond        0.00643 (    4)
  metal coordination   : angle       4.25263 (    6)
  covalent geometry    : bond        0.00412 ( 7962)
  covalent geometry    : angle       0.69295 (11674)

*********************** 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
  54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 35
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6730 (ttpt)
REVERT: A  210 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7794 (mttm)
REVERT: A  211 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8532 (t0)
REVERT: A  254 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8191 (mtm180)
REVERT: A  256 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8101 (mttp)
REVERT: A  385 GLU cc_start: 0.7280 (pm20) cc_final: 0.6973 (pt0)
  outliers start: 19
  outliers final: 11
  residues processed: 51
  average time/residue: 1.2952
  time to fit residues: 69.8811
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  : 0.469 
-------------------------------------------------------------------------------
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  211 ASN
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  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:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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
A 211 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.179295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.145357 restraints weight = 7041.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 0.45
r_work: 0.3276 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3137
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      207 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      207 |
|-----------------------------------------------------------------------------|
r_final: 0.3137
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.2217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.107   7966  Z= 0.244
  Angle     :  0.988  59.198  11680  Z= 0.564
  Chirality :  0.042   0.278   1428
  Planarity :  0.004   0.041    736
  Dihedral  : 26.440 179.426   3339
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.33 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 26.82 %
    Favored  : 68.51 %
  Cbeta Deviations :  0.27 %
  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:  0.21 (0.43), residues: 382
  helix:  2.44 (0.39), residues: 174
  sheet:  0.27 (0.81), residues: 41
  loop : -2.63 (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   0.011   0.002   PHE A 360 
 TYR   0.012   0.002   TYR A  33 
 ARG   0.005   0.000   ARG A  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07457 (  278)
  hydrogen bonds       : angle       3.38472 (  653)
  metal coordination   : bond        0.00645 (    4)
  metal coordination   : angle       4.23987 (    6)
  covalent geometry    : bond        0.00487 ( 7962)
  covalent geometry    : angle       0.98398 (11674)

********************** 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
  49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 33
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6659 (ttpt)
REVERT: A  254 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8132 (mtm180)
REVERT: A  256 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8038 (mttp)
REVERT: A  385 GLU cc_start: 0.7204 (pm20) cc_final: 0.6921 (pt0)
  outliers start: 16
  outliers final: 11
  residues processed: 46
  average time/residue: 1.3090
  time to fit residues: 63.7553
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  : 0.475 
-------------------------------------------------------------------------------
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  254 ARG
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:    6.9990
   chunk 4 optimal weight:    6.9990
   chunk 49 optimal weight:    8.9990
   chunk 36 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   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:    1.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.3900 r_free = 0.3900 target = 0.179200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.143797 restraints weight = 7029.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 0.43
r_work: 0.3248 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3142
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      207 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      207 |
|-----------------------------------------------------------------------------|
r_final: 0.3142
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.107   7966  Z= 0.244
  Angle     :  0.988  59.198  11680  Z= 0.564
  Chirality :  0.042   0.278   1428
  Planarity :  0.004   0.041    736
  Dihedral  : 26.440 179.426   3339
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.33 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 27.11 %
    Favored  : 68.51 %
  Cbeta Deviations :  0.27 %
  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:  0.21 (0.43), residues: 382
  helix:  2.44 (0.39), residues: 174
  sheet:  0.27 (0.81), residues: 41
  loop : -2.63 (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   0.011   0.002   PHE A 360 
 TYR   0.012   0.002   TYR A  33 
 ARG   0.005   0.000   ARG A  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07457 (  278)
  hydrogen bonds       : angle       3.38472 (  653)
  metal coordination   : bond        0.00645 (    4)
  metal coordination   : angle       4.23987 (    6)
  covalent geometry    : bond        0.00487 ( 7962)
  covalent geometry    : angle       0.98398 (11674)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4013.84 seconds
wall clock time: 70 minutes 2.26 seconds (4202.26 seconds total)