Starting phenix.real_space_refine
on Wed Sep 17 05:15:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zb9_39898/09_2025/8zb9_39898.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zb9_39898/09_2025/8zb9_39898.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.31
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zb9_39898/09_2025/8zb9_39898.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zb9_39898/09_2025/8zb9_39898.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zb9_39898/09_2025/8zb9_39898.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zb9_39898/09_2025/8zb9_39898.cif"
  }
  resolution = 3.31
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.039
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: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    3075      2.51       5
     N     848      2.21       5
     O     939      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4904
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2455
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 312, 2455
          Classifications: {'peptide': 312}
          Link IDs: {'PTRANS': 18, 'TRANS': 293}
          Chain breaks: 4
    Chain: "a"
      Number of atoms: 2449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 310, 2449
          Classifications: {'peptide': 310}
          Link IDs: {'PTRANS': 18, 'TRANS': 291}
          Chain breaks: 3
  Time building chain proxies: 1.21, per 1000 atoms: 0.25
  Number of scatterers: 4904
  At special positions: 0
  Unit cell: (86.7, 103.7, 64.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O     939      8.00
     N     848      7.00
     C    3075      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=11, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   4 " - pdb=" SG  CYS A  15 " distance=2.28
    Simple disulfide: pdb=" SG  CYS A  55 " - pdb=" SG  CYS A 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 179 " - pdb=" SG  CYS A 224 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 280 " - pdb=" SG  CYS A 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 313 " - pdb=" SG  CYS A 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a  55 " - pdb=" SG  CYS a 143 " distance=1.97
    Simple disulfide: pdb=" SG  CYS a 179 " - pdb=" SG  CYS a 224 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a 280 " - pdb=" SG  CYS a 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a 291 " - pdb=" SG  CYS a 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a 313 " - pdb=" SG  CYS a 316 " distance=1.97

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.47
  Conformation dependent library (CDL) restraints added in 123.7 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1130

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 10 sheets defined
      16.1% alpha, 17.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 27
    Processing helix  chain 'A' and resid 40 through 52
    Processing helix  chain 'A' and resid 61 through 82
      removed outlier: 5.341A  pdb=" N   ASP A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   GLU A  74 " --> pdb=" O   SER A  70 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ILE A  75 " --> pdb=" O   ARG A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 146
      No H-bonds generated for 'chain 'A' and resid 144 through 146'
    Processing helix  chain 'A' and resid 180 through 184
      removed outlier: 3.814A  pdb=" N   ILE A 183 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 24 through 27
    Processing helix  chain 'a' and resid 40 through 53
      removed outlier: 3.570A  pdb=" N   GLY a  53 " --> pdb=" O   SER a  49 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 61 through 82
      removed outlier: 5.317A  pdb=" N   ASP a  73 " --> pdb=" O   ARG a  69 " (cutoff:3.500A)
      removed outlier: 5.412A  pdb=" N   GLU a  74 " --> pdb=" O   SER a  70 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ILE a  75 " --> pdb=" O   ARG a  71 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 144 through 146
      No H-bonds generated for 'chain 'a' and resid 144 through 146'
    Processing helix  chain 'a' and resid 180 through 184
      removed outlier: 4.044A  pdb=" N   ILE a 183 " --> pdb=" O   ASP a 180 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LEU a 184 " --> pdb=" O   GLY a 181 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'a' and resid 180 through 184'
    Processing helix  chain 'a' and resid 227 through 231
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 15
      removed outlier: 3.567A  pdb=" N   GLU A  12 " --> pdb=" O   ASN A   7 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ASN A   7 " --> pdb=" O   GLU A  12 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LYS A  14 " --> pdb=" O   ALA A   5 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ALA A   5 " --> pdb=" O   LYS A  14 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   GLN a   2 " --> pdb=" O   ILE A   6 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57
      removed outlier: 7.247A  pdb=" N   GLY A  56 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 89
      removed outlier: 6.860A  pdb=" N   SER A  87 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 155
    Processing sheet with id=AA5, first strand: chain 'A' and resid 321 through 323
      removed outlier: 3.569A  pdb=" N   LYS A 276 " --> pdb=" O   SER A 322 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA A 218 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   LEU A 216 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ARG A 277 " --> pdb=" O   HIS A 214 " (cutoff:3.500A)
      removed outlier: 10.307A  pdb=" N   HIS A 214 " --> pdb=" O   ARG A 277 " (cutoff:3.500A)
      removed outlier: 5.455A  pdb=" N   ILE A 213 " --> pdb=" O   HIS A 205 " (cutoff:3.500A)
      removed outlier: 6.079A  pdb=" N   HIS A 205 " --> pdb=" O   ILE A 213 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   PHE A 200 " --> pdb=" O   SER A 197 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   LYS A 192 " --> pdb=" O   ASN A 189 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   GLY A 185 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLY a 185 " --> pdb=" O   GLY a 196 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LYS a 192 " --> pdb=" O   ASN a 189 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   PHE a 200 " --> pdb=" O   SER a 197 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   TRP a 201 " --> pdb=" O   LEU a 216 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   LEU a 216 " --> pdb=" O   TRP a 201 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   GLY a 203 " --> pdb=" O   HIS a 214 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   THR a 210 " --> pdb=" O   VAL a 207 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   LEU a 216 " --> pdb=" O   VAL a 275 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ALA a 218 " --> pdb=" O   LEU a 273 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 285 through 287
      removed outlier: 3.567A  pdb=" N   ILE A 286 " --> pdb=" O   TRP A 311 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'a' and resid 34 through 35
    Processing sheet with id=AA8, first strand: chain 'a' and resid 56 through 57
      removed outlier: 7.456A  pdb=" N   GLY a  56 " --> pdb=" O   VAL a 149 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'a' and resid 86 through 87
    Processing sheet with id=AB1, first strand: chain 'a' and resid 285 through 287
      removed outlier: 3.794A  pdb=" N   CYS a 313 " --> pdb=" O   ILE a 286 " (cutoff:3.500A)

    110 hydrogen bonds defined for protein.
    303 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.71

  Time building geometry restraints manager: 0.63 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: 926
        1.32 -     1.45: 1458
        1.45 -     1.58: 2587
        1.58 -     1.71: 0
        1.71 -     1.85: 60
  Bond restraints: 5031
  Sorted by residual:
  bond pdb=" CA  GLN a   2 "
       pdb=" C   GLN a   2 "
    ideal  model  delta    sigma   weight residual
    1.525  1.465  0.059 1.28e-02 6.10e+03 2.15e+01
  bond pdb=" CA  PRO A  93 "
       pdb=" C   PRO A  93 "
    ideal  model  delta    sigma   weight residual
    1.522  1.476  0.046 9.90e-03 1.02e+04 2.14e+01
  bond pdb=" CA  CYS a   4 "
       pdb=" C   CYS a   4 "
    ideal  model  delta    sigma   weight residual
    1.531  1.482  0.049 1.15e-02 7.56e+03 1.85e+01
  bond pdb=" CA  GLN A  91 "
       pdb=" C   GLN A  91 "
    ideal  model  delta    sigma   weight residual
    1.531  1.477  0.054 1.32e-02 5.74e+03 1.67e+01
  bond pdb=" C   TYR A  97 "
       pdb=" O   TYR A  97 "
    ideal  model  delta    sigma   weight residual
    1.236  1.191  0.045 1.24e-02 6.50e+03 1.30e+01
  ... (remaining 5026 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 6417
        1.71 -     3.43: 307
        3.43 -     5.14: 60
        5.14 -     6.86: 11
        6.86 -     8.57: 4
  Bond angle restraints: 6799
  Sorted by residual:
  angle pdb=" N   PRO A  93 "
        pdb=" CA  PRO A  93 "
        pdb=" C   PRO A  93 "
      ideal   model   delta    sigma   weight residual
     110.50  101.93    8.57 1.57e+00 4.06e-01 2.98e+01
  angle pdb=" C   VAL A  96 "
        pdb=" CA  VAL A  96 "
        pdb=" CB  VAL A  96 "
      ideal   model   delta    sigma   weight residual
     111.40  103.49    7.91 1.90e+00 2.77e-01 1.73e+01
  angle pdb=" N   LEU a  13 "
        pdb=" CA  LEU a  13 "
        pdb=" C   LEU a  13 "
      ideal   model   delta    sigma   weight residual
     114.64  108.38    6.26 1.52e+00 4.33e-01 1.69e+01
  angle pdb=" N   CYS a   4 "
        pdb=" CA  CYS a   4 "
        pdb=" C   CYS a   4 "
      ideal   model   delta    sigma   weight residual
     108.18  115.92   -7.74 2.01e+00 2.48e-01 1.48e+01
  angle pdb=" N   GLN A  98 "
        pdb=" CA  GLN A  98 "
        pdb=" C   GLN A  98 "
      ideal   model   delta    sigma   weight residual
     109.94  115.97   -6.03 1.57e+00 4.06e-01 1.48e+01
  ... (remaining 6794 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.98: 2511
       16.98 -    33.97: 384
       33.97 -    50.95: 89
       50.95 -    67.93: 15
       67.93 -    84.91: 9
  Dihedral angle restraints: 3008
    sinusoidal: 1247
      harmonic: 1761
  Sorted by residual:
  dihedral pdb=" CB  CYS A   4 "
           pdb=" SG  CYS A   4 "
           pdb=" SG  CYS A  15 "
           pdb=" CB  CYS A  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   31.72   61.28     1      1.00e+01 1.00e-02 4.99e+01
  dihedral pdb=" CA  ASP a  92 "
           pdb=" C   ASP a  92 "
           pdb=" N   PRO a  93 "
           pdb=" CA  PRO a  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.90   25.10     0      5.00e+00 4.00e-02 2.52e+01
  dihedral pdb=" CB  CYS A 280 "
           pdb=" SG  CYS A 280 "
           pdb=" SG  CYS A 329 "
           pdb=" CB  CYS A 329 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  131.00  -38.00     1      1.00e+01 1.00e-02 2.03e+01
  ... (remaining 3005 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 382
       0.035 -    0.071: 206
       0.071 -    0.106: 79
       0.106 -    0.142: 26
       0.142 -    0.177: 5
  Chirality restraints: 698
  Sorted by residual:
  chirality pdb=" CA  GLN A  98 "
            pdb=" N   GLN A  98 "
            pdb=" C   GLN A  98 "
            pdb=" CB  GLN A  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.82e-01
  chirality pdb=" CA  VAL a 149 "
            pdb=" N   VAL a 149 "
            pdb=" C   VAL a 149 "
            pdb=" CB  VAL a 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.34e-01
  chirality pdb=" CA  VAL a 207 "
            pdb=" N   VAL a 207 "
            pdb=" C   VAL a 207 "
            pdb=" CB  VAL a 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.28e-01
  ... (remaining 695 not shown)

  Planarity restraints: 889
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 280 "   -0.036 5.00e-02 4.00e+02   5.53e-02 4.90e+00
        pdb=" N   PRO A 281 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A 281 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 281 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 314 "   -0.011 2.00e-02 2.50e+03   2.21e-02 4.88e+00
        pdb=" C   ARG A 314 "    0.038 2.00e-02 2.50e+03
        pdb=" O   ARG A 314 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   SER A 315 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP a  38 "    0.035 5.00e-02 4.00e+02   5.33e-02 4.55e+00
        pdb=" N   PRO a  39 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO a  39 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO a  39 "    0.030 5.00e-02 4.00e+02
  ... (remaining 886 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1354
        2.79 -     3.32: 4194
        3.32 -     3.85: 7481
        3.85 -     4.37: 8734
        4.37 -     4.90: 15828
  Nonbonded interactions: 37591
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 296 "
            pdb=" NH1 ARG A 336 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" O   LYS a 296 "
            pdb=" NH1 ARG a 336 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" OG1 THR A 302 "
            pdb=" OD1 ASP A 303 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   TYR a  34 "
            pdb=" NH1 ARG a  71 "
     model   vdw
     2.326 3.120
  nonbonded pdb=" OD1 ASP a  17 "
            pdb=" N   GLY a  18 "
     model   vdw
     2.331 3.120
  ... (remaining 37586 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 82 or resid 85 through 159 or resid 166 through  \ 
337))
  selection = (chain 'a' and (resid 1 through 94 or resid 96 through 235 or resid 238 through  \ 
337))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.130
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
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      :  0.008   0.254   5042  Z= 0.429
  Angle     :  1.103  49.213   6821  Z= 0.602
  Chirality :  0.051   0.177    698
  Planarity :  0.006   0.055    889
  Dihedral  : 16.830  84.914   1845
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 16.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.24 %
    Favored  : 85.76 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 22.65 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.11 (0.33), residues: 604
  helix:  1.07 (0.59), residues: 71
  sheet: -2.67 (0.55), residues: 89
  loop : -2.68 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG a 336 
 TYR   0.012   0.002   TYR A 260 
 PHE   0.023   0.002   PHE A 104 
 TRP   0.008   0.001   TRP A 226 
 HIS   0.009   0.002   HIS a 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00726 ( 5031)
  covalent geometry    : angle       0.87422 ( 6799)
  SS BOND              : bond        0.08155 (   11)
  SS BOND              : angle      11.86805 (   22)
  hydrogen bonds       : bond        0.22492 (  110)
  hydrogen bonds       : angle       7.49101 (  303)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 89
  time to evaluate  : 0.208 
Fit side-chains
REVERT: a    4 CYS cc_start: 0.8501 (m) cc_final: 0.8287 (m)
REVERT: a  208 ASN cc_start: 0.7951 (t0) cc_final: 0.7372 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 90
  average time/residue: 0.0615
  time to fit residues: 7.5475
Evaluate side-chains
  76 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 26 optimal weight:    0.2980
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 324 HIS
** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
a 263 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.181022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.145006 restraints weight = 5288.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3721 rms_B_bonded: 2.87
r_work: 0.3517 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5042  Z= 0.129
  Angle     :  0.612   7.384   6821  Z= 0.323
  Chirality :  0.046   0.197    698
  Planarity :  0.005   0.054    889
  Dihedral  :  4.919  22.431    664
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.60 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 22.47 %
    Favored  : 74.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.58 (0.34), residues: 604
  helix:  1.48 (0.63), residues: 72
  sheet: -2.03 (0.60), residues: 84
  loop : -2.40 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG a 314 
 TYR   0.005   0.001   TYR A 221 
 PHE   0.014   0.001   PHE A 104 
 TRP   0.007   0.001   TRP A 311 
 HIS   0.003   0.001   HIS a 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 5031)
  covalent geometry    : angle       0.60500 ( 6799)
  SS BOND              : bond        0.00635 (   11)
  SS BOND              : angle       1.78219 (   22)
  hydrogen bonds       : bond        0.03623 (  110)
  hydrogen bonds       : angle       4.76685 (  303)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 0.202 
Fit side-chains
REVERT: a  208 ASN cc_start: 0.7779 (t0) cc_final: 0.7177 (t0)
  outliers start: 19
  outliers final: 12
  residues processed: 92
  average time/residue: 0.0745
  time to fit residues: 8.9574
Evaluate side-chains
  88 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  297 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain a residue  134 ILE
Chi-restraints excluded: chain a residue  256 HIS
Chi-restraints excluded: chain a residue  262 VAL
Chi-restraints excluded: chain a residue  264 THR
Chi-restraints excluded: chain a residue  329 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 45 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 270 GLN
** a  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.181465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.144826 restraints weight = 5274.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 2.92
r_work: 0.3489 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.1630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5042  Z= 0.130
  Angle     :  0.580   7.091   6821  Z= 0.303
  Chirality :  0.044   0.140    698
  Planarity :  0.005   0.054    889
  Dihedral  :  4.644  22.254    664
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 22.28 %
    Favored  : 73.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.46 (0.34), residues: 604
  helix:  1.63 (0.62), residues: 72
  sheet: -2.15 (0.54), residues: 95
  loop : -2.26 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG a 148 
 TYR   0.007   0.001   TYR A  35 
 PHE   0.012   0.001   PHE A 104 
 TRP   0.007   0.001   TRP A 226 
 HIS   0.004   0.001   HIS a 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 5031)
  covalent geometry    : angle       0.57595 ( 6799)
  SS BOND              : bond        0.00271 (   11)
  SS BOND              : angle       1.30924 (   22)
  hydrogen bonds       : bond        0.03114 (  110)
  hydrogen bonds       : angle       4.36287 (  303)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 86
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   66 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8145 (tp30)
  outliers start: 25
  outliers final: 15
  residues processed: 104
  average time/residue: 0.0601
  time to fit residues: 8.5867
Evaluate side-chains
  90 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  288 ASP
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  313 CYS
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain a residue  229 THR
Chi-restraints excluded: chain a residue  256 HIS
Chi-restraints excluded: chain a residue  262 VAL
Chi-restraints excluded: chain a residue  264 THR
Chi-restraints excluded: chain a residue  329 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 25 optimal weight:    0.4980
   chunk 6 optimal weight:    0.0980
   chunk 55 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 9 optimal weight:    0.2980
   chunk 53 optimal weight:    0.7980
   chunk 24 optimal weight:    0.3980
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
A  82 ASN
** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.186218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.148930 restraints weight = 5213.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.3766 rms_B_bonded: 2.97
r_work: 0.3525 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.1998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5042  Z= 0.102
  Angle     :  0.551   8.319   6821  Z= 0.285
  Chirality :  0.043   0.132    698
  Planarity :  0.005   0.054    889
  Dihedral  :  4.340  21.351    664
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 24.13 %
    Favored  : 72.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.26 (0.34), residues: 604
  helix:  1.69 (0.61), residues: 72
  sheet: -1.98 (0.54), residues: 95
  loop : -2.11 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG a 314 
 TYR   0.005   0.001   TYR A 260 
 PHE   0.009   0.001   PHE A 104 
 TRP   0.006   0.001   TRP A 226 
 HIS   0.002   0.001   HIS A 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 5031)
  covalent geometry    : angle       0.54889 ( 6799)
  SS BOND              : bond        0.00274 (   11)
  SS BOND              : angle       1.08406 (   22)
  hydrogen bonds       : bond        0.02539 (  110)
  hydrogen bonds       : angle       4.00753 (  303)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 80
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   66 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7978 (tt0)
  outliers start: 21
  outliers final: 16
  residues processed: 94
  average time/residue: 0.0588
  time to fit residues: 7.5072
Evaluate side-chains
  93 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 CYS
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  104 PHE
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  313 CYS
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain a residue  102 HIS
Chi-restraints excluded: chain a residue  134 ILE
Chi-restraints excluded: chain a residue  256 HIS
Chi-restraints excluded: chain a residue  264 THR
Chi-restraints excluded: chain a residue  329 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 35 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0970
   chunk 30 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A  82 ASN
** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.180968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.144349 restraints weight = 5286.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 2.86
r_work: 0.3481 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5042  Z= 0.142
  Angle     :  0.577   7.493   6821  Z= 0.300
  Chirality :  0.044   0.130    698
  Planarity :  0.005   0.053    889
  Dihedral  :  4.457  21.105    664
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.43 %
    Favored  : 89.57 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 24.13 %
    Favored  : 71.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.21 (0.34), residues: 604
  helix:  1.73 (0.61), residues: 72
  sheet: -1.82 (0.56), residues: 95
  loop : -2.10 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG a 166 
 TYR   0.006   0.001   TYR A  35 
 PHE   0.010   0.001   PHE A 104 
 TRP   0.007   0.001   TRP A 226 
 HIS   0.005   0.001   HIS a 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 5031)
  covalent geometry    : angle       0.57381 ( 6799)
  SS BOND              : bond        0.00312 (   11)
  SS BOND              : angle       1.20780 (   22)
  hydrogen bonds       : bond        0.02896 (  110)
  hydrogen bonds       : angle       4.04858 (  303)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 82
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: a    2 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7854 (mp10)
  outliers start: 23
  outliers final: 19
  residues processed: 100
  average time/residue: 0.0637
  time to fit residues: 8.5899
Evaluate side-chains
  95 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 CYS
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  104 PHE
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  288 ASP
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  313 CYS
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain a residue  104 PHE
Chi-restraints excluded: chain a residue  256 HIS
Chi-restraints excluded: chain a residue  262 VAL
Chi-restraints excluded: chain a residue  264 THR
Chi-restraints excluded: chain a residue  329 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 19 optimal weight:    0.0070
   chunk 37 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   chunk 41 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.6200

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

Flipped N/Q/H residues before XYZ refinement:
A  82 ASN
** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.182906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.146446 restraints weight = 5322.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 2.88
r_work: 0.3520 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5042  Z= 0.119
  Angle     :  0.575   7.455   6821  Z= 0.298
  Chirality :  0.043   0.128    698
  Planarity :  0.005   0.053    889
  Dihedral  :  4.317  21.005    664
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.44 %
    Favored  : 90.56 %
  Rotamer:
    Outliers :  5.89 %
    Allowed  : 23.39 %
    Favored  : 70.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.15 (0.34), residues: 604
  helix:  1.78 (0.61), residues: 72
  sheet: -1.72 (0.55), residues: 95
  loop : -2.07 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG a  69 
 TYR   0.006   0.001   TYR A  35 
 PHE   0.009   0.001   PHE A 104 
 TRP   0.006   0.001   TRP A 226 
 HIS   0.003   0.001   HIS A 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 5031)
  covalent geometry    : angle       0.57271 ( 6799)
  SS BOND              : bond        0.00272 (   11)
  SS BOND              : angle       1.10262 (   22)
  hydrogen bonds       : bond        0.02660 (  110)
  hydrogen bonds       : angle       3.93761 (  303)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 80
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7659 (mt-10)
  outliers start: 32
  outliers final: 24
  residues processed: 103
  average time/residue: 0.0609
  time to fit residues: 8.5561
Evaluate side-chains
  98 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 74
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 CYS
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  104 PHE
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  202 MET
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  256 HIS
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  313 CYS
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain a residue   55 CYS
Chi-restraints excluded: chain a residue  102 HIS
Chi-restraints excluded: chain a residue  104 PHE
Chi-restraints excluded: chain a residue  132 SER
Chi-restraints excluded: chain a residue  229 THR
Chi-restraints excluded: chain a residue  256 HIS
Chi-restraints excluded: chain a residue  262 VAL
Chi-restraints excluded: chain a residue  264 THR
Chi-restraints excluded: chain a residue  329 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 58 optimal weight:    9.9990
   chunk 9 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  82 ASN
** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.175312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.140676 restraints weight = 5353.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 2.68
r_work: 0.3456 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   5042  Z= 0.235
  Angle     :  0.675   6.982   6821  Z= 0.354
  Chirality :  0.047   0.136    698
  Planarity :  0.005   0.054    889
  Dihedral  :  4.879  21.051    664
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.58 %
    Favored  : 87.42 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 24.68 %
    Favored  : 69.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.38 (0.34), residues: 604
  helix:  1.47 (0.61), residues: 72
  sheet: -1.81 (0.55), residues: 95
  loop : -2.24 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 314 
 TYR   0.009   0.001   TYR a  32 
 PHE   0.014   0.002   PHE A 323 
 TRP   0.008   0.001   TRP A 226 
 HIS   0.007   0.002   HIS a 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00557 ( 5031)
  covalent geometry    : angle       0.67037 ( 6799)
  SS BOND              : bond        0.00409 (   11)
  SS BOND              : angle       1.52314 (   22)
  hydrogen bonds       : bond        0.03554 (  110)
  hydrogen bonds       : angle       4.35387 (  303)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 79
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: a    2 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7957 (mp10)
  outliers start: 31
  outliers final: 25
  residues processed: 102
  average time/residue: 0.0614
  time to fit residues: 8.3229
Evaluate side-chains
  99 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 74
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  104 PHE
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  202 MET
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  256 HIS
Chi-restraints excluded: chain A residue  288 ASP
Chi-restraints excluded: chain A residue  297 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  313 CYS
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain a residue   55 CYS
Chi-restraints excluded: chain a residue  132 SER
Chi-restraints excluded: chain a residue  134 ILE
Chi-restraints excluded: chain a residue  229 THR
Chi-restraints excluded: chain a residue  256 HIS
Chi-restraints excluded: chain a residue  262 VAL
Chi-restraints excluded: chain a residue  264 THR
Chi-restraints excluded: chain a residue  313 CYS
Chi-restraints excluded: chain a residue  321 VAL
Chi-restraints excluded: chain a residue  329 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 56 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A  82 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.177877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.141956 restraints weight = 5364.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3684 rms_B_bonded: 2.82
r_work: 0.3471 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5042  Z= 0.166
  Angle     :  0.632   7.944   6821  Z= 0.328
  Chirality :  0.045   0.135    698
  Planarity :  0.005   0.054    889
  Dihedral  :  4.728  21.470    664
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.26 %
    Favored  : 88.74 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 25.23 %
    Favored  : 69.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.36 (0.33), residues: 604
  helix:  1.41 (0.60), residues: 73
  sheet: -1.82 (0.55), residues: 95
  loop : -2.20 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG a 166 
 TYR   0.006   0.001   TYR A 221 
 PHE   0.010   0.001   PHE A 323 
 TRP   0.008   0.001   TRP A 226 
 HIS   0.005   0.001   HIS a 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 5031)
  covalent geometry    : angle       0.62727 ( 6799)
  SS BOND              : bond        0.00482 (   11)
  SS BOND              : angle       1.48465 (   22)
  hydrogen bonds       : bond        0.03136 (  110)
  hydrogen bonds       : angle       4.21524 (  303)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 77
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  192 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7964 (mtmm)
REVERT: a    2 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7905 (mp10)
  outliers start: 28
  outliers final: 26
  residues processed: 98
  average time/residue: 0.0634
  time to fit residues: 8.4586
Evaluate side-chains
  99 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 72
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  104 PHE
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  192 LYS
Chi-restraints excluded: chain A residue  202 MET
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  256 HIS
Chi-restraints excluded: chain A residue  288 ASP
Chi-restraints excluded: chain A residue  297 SER
Chi-restraints excluded: chain A residue  304 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  313 CYS
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain a residue   55 CYS
Chi-restraints excluded: chain a residue  104 PHE
Chi-restraints excluded: chain a residue  132 SER
Chi-restraints excluded: chain a residue  229 THR
Chi-restraints excluded: chain a residue  256 HIS
Chi-restraints excluded: chain a residue  262 VAL
Chi-restraints excluded: chain a residue  264 THR
Chi-restraints excluded: chain a residue  313 CYS
Chi-restraints excluded: chain a residue  321 VAL
Chi-restraints excluded: chain a residue  329 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 58 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 8 optimal weight:    0.0040
   chunk 22 optimal weight:    0.2980
   chunk 3 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
A  82 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.181437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.145458 restraints weight = 5270.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3727 rms_B_bonded: 2.81
r_work: 0.3514 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.2124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5042  Z= 0.120
  Angle     :  0.582   8.873   6821  Z= 0.300
  Chirality :  0.043   0.130    698
  Planarity :  0.005   0.055    889
  Dihedral  :  4.387  20.935    664
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.60 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 25.41 %
    Favored  : 69.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.22 (0.34), residues: 604
  helix:  1.54 (0.59), residues: 73
  sheet: -1.75 (0.54), residues: 95
  loop : -2.11 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG a  69 
 TYR   0.005   0.001   TYR A 221 
 PHE   0.009   0.001   PHE A 104 
 TRP   0.006   0.001   TRP A 226 
 HIS   0.003   0.001   HIS a 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 5031)
  covalent geometry    : angle       0.57918 ( 6799)
  SS BOND              : bond        0.00349 (   11)
  SS BOND              : angle       1.08408 (   22)
  hydrogen bonds       : bond        0.02651 (  110)
  hydrogen bonds       : angle       3.97765 (  303)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 80
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 28
  outliers final: 25
  residues processed: 100
  average time/residue: 0.0614
  time to fit residues: 8.2949
Evaluate side-chains
  101 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 76
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  104 PHE
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  202 MET
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  256 HIS
Chi-restraints excluded: chain A residue  297 SER
Chi-restraints excluded: chain A residue  304 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  313 CYS
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain a residue  104 PHE
Chi-restraints excluded: chain a residue  132 SER
Chi-restraints excluded: chain a residue  134 ILE
Chi-restraints excluded: chain a residue  229 THR
Chi-restraints excluded: chain a residue  256 HIS
Chi-restraints excluded: chain a residue  262 VAL
Chi-restraints excluded: chain a residue  264 THR
Chi-restraints excluded: chain a residue  313 CYS
Chi-restraints excluded: chain a residue  329 CYS
Chi-restraints excluded: chain a residue  333 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 31 optimal weight:    4.9990
   chunk 42 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0060
   chunk 36 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 52 optimal weight:    0.3980
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
A  82 ASN
A 154 GLN
** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.182676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.146779 restraints weight = 5327.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 2.83
r_work: 0.3530 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.2355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5042  Z= 0.114
  Angle     :  0.587   8.712   6821  Z= 0.302
  Chirality :  0.043   0.147    698
  Planarity :  0.005   0.055    889
  Dihedral  :  4.252  20.460    664
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 26.15 %
    Favored  : 69.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.08 (0.34), residues: 604
  helix:  1.83 (0.59), residues: 72
  sheet: -1.61 (0.55), residues: 95
  loop : -2.05 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG a  69 
 TYR   0.005   0.001   TYR A 221 
 PHE   0.009   0.001   PHE A 104 
 TRP   0.006   0.001   TRP A 226 
 HIS   0.002   0.001   HIS a 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 5031)
  covalent geometry    : angle       0.58382 ( 6799)
  SS BOND              : bond        0.00393 (   11)
  SS BOND              : angle       1.20312 (   22)
  hydrogen bonds       : bond        0.02565 (  110)
  hydrogen bonds       : angle       3.88558 (  303)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 76
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 24
  outliers final: 22
  residues processed: 95
  average time/residue: 0.0541
  time to fit residues: 7.1360
Evaluate side-chains
  96 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 74
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  104 PHE
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  202 MET
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  234 THR
Chi-restraints excluded: chain A residue  256 HIS
Chi-restraints excluded: chain A residue  304 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  313 CYS
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain a residue   55 CYS
Chi-restraints excluded: chain a residue  104 PHE
Chi-restraints excluded: chain a residue  132 SER
Chi-restraints excluded: chain a residue  229 THR
Chi-restraints excluded: chain a residue  256 HIS
Chi-restraints excluded: chain a residue  262 VAL
Chi-restraints excluded: chain a residue  264 THR
Chi-restraints excluded: chain a residue  313 CYS
Chi-restraints excluded: chain a residue  329 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 57 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 53 optimal weight:    0.3980
   chunk 1 optimal weight:    0.2980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  82 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.183397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.146909 restraints weight = 5368.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 2.83
r_work: 0.3519 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5042  Z= 0.121
  Angle     :  0.581   8.495   6821  Z= 0.300
  Chirality :  0.043   0.143    698
  Planarity :  0.005   0.055    889
  Dihedral  :  4.239  20.301    664
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 26.52 %
    Favored  : 68.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.07 (0.34), residues: 604
  helix:  1.84 (0.59), residues: 72
  sheet: -1.57 (0.55), residues: 95
  loop : -2.05 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG a 166 
 TYR   0.005   0.001   TYR A 221 
 PHE   0.009   0.001   PHE A 104 
 TRP   0.007   0.001   TRP A 226 
 HIS   0.003   0.001   HIS a 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 5031)
  covalent geometry    : angle       0.57909 ( 6799)
  SS BOND              : bond        0.00281 (   11)
  SS BOND              : angle       1.01935 (   22)
  hydrogen bonds       : bond        0.02579 (  110)
  hydrogen bonds       : angle       3.89097 (  303)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1253.77 seconds
wall clock time: 22 minutes 12.44 seconds (1332.44 seconds total)