Starting phenix.real_space_refine
on Fri Aug 22 15:43:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i9q_35280/08_2025/8i9q_35280_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i9q_35280/08_2025/8i9q_35280.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.22
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i9q_35280/08_2025/8i9q_35280.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i9q_35280/08_2025/8i9q_35280.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i9q_35280/08_2025/8i9q_35280_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i9q_35280/08_2025/8i9q_35280_neut.cif"
  }
  resolution = 4.22
  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=   0.003 sd=   0.059
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      29      5.16       5
     C    3264      2.51       5
     N     897      2.21       5
     O     989      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5179
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "D"
      Number of atoms: 3832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 508, 3832
          Classifications: {'peptide': 508}
          Link IDs: {'PTRANS': 14, 'TRANS': 493}
    Chain: "Q"
      Number of atoms: 1347
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 167, 1347
          Classifications: {'peptide': 167}
          Link IDs: {'PTRANS': 8, 'TRANS': 158}
  Time building chain proxies: 1.20, per 1000 atoms: 0.23
  Number of scatterers: 5179
  At special positions: 0
  Unit cell: (117.52, 118.65, 110.74, 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      29     16.00
     O     989      8.00
     N     897      7.00
     C    3264      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.44
  Conformation dependent library (CDL) restraints added in 209.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1264

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 4 sheets defined
      51.4% alpha, 2.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'D' and resid 27 through 49
      removed outlier: 4.035A  pdb=" N   ILE D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 52
      No H-bonds generated for 'chain 'D' and resid 50 through 52'
    Processing helix  chain 'D' and resid 73 through 81
      removed outlier: 3.784A  pdb=" N   ILE D  77 " --> pdb=" O   ASP D  73 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   MET D  81 " --> pdb=" O   ILE D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 85 through 102
      removed outlier: 3.543A  pdb=" N   LEU D  91 " --> pdb=" O   ALA D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 107 through 126
      removed outlier: 3.674A  pdb=" N   ILE D 111 " --> pdb=" O   THR D 107 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   LYS D 122 " --> pdb=" O   ASP D 118 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 152
      removed outlier: 3.572A  pdb=" N   GLU D 146 " --> pdb=" O   GLU D 142 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 159 through 173
    Processing helix  chain 'D' and resid 188 through 194
    Processing helix  chain 'D' and resid 204 through 209
      removed outlier: 4.009A  pdb=" N   LYS D 209 " --> pdb=" O   ARG D 206 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 268 through 291
      removed outlier: 4.332A  pdb=" N   MET D 272 " --> pdb=" O   ASP D 268 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   ASP D 273 " --> pdb=" O   TYR D 269 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ARG D 274 " --> pdb=" O   ALA D 270 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LEU D 276 " --> pdb=" O   MET D 272 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   ARG D 277 " --> pdb=" O   ASP D 273 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLU D 278 " --> pdb=" O   ARG D 274 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU D 284 " --> pdb=" O   ARG D 280 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   LEU D 286 " --> pdb=" O   TYR D 282 " (cutoff:3.500A)
      removed outlier: 5.021A  pdb=" N   VAL D 287 " --> pdb=" O   ILE D 283 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 311 through 320
    Processing helix  chain 'D' and resid 329 through 340
      removed outlier: 3.888A  pdb=" N   CYS D 337 " --> pdb=" O   ILE D 333 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 394 through 401
      removed outlier: 3.581A  pdb=" N   ILE D 398 " --> pdb=" O   ASN D 394 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 403 through 419
      removed outlier: 3.640A  pdb=" N   LEU D 415 " --> pdb=" O   VAL D 411 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   VAL D 416 " --> pdb=" O   ILE D 412 " (cutoff:3.500A)
      removed outlier: 4.880A  pdb=" N   LYS D 417 " --> pdb=" O   ARG D 413 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   LYS D 418 " --> pdb=" O   CYS D 414 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 426 through 443
    Processing helix  chain 'D' and resid 445 through 459
      removed outlier: 4.454A  pdb=" N   TYR D 449 " --> pdb=" O   GLY D 445 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   CYS D 450 " --> pdb=" O   MET D 446 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLU D 459 " --> pdb=" O   ALA D 455 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 460 through 470
      removed outlier: 3.598A  pdb=" N   THR D 464 " --> pdb=" O   VAL D 460 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 472 through 487
      removed outlier: 3.809A  pdb=" N   THR D 476 " --> pdb=" O   ASN D 472 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 512 through 532
      removed outlier: 4.101A  pdb=" N   ALA D 518 " --> pdb=" O   VAL D 514 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 67 through 78
      removed outlier: 4.581A  pdb=" N   TYR Q  74 " --> pdb=" O   ALA Q  70 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   ARG Q  75 " --> pdb=" O   ILE Q  71 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ARG Q  76 " --> pdb=" O   GLU Q  72 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 81 through 85
    Processing helix  chain 'Q' and resid 104 through 109
    Processing helix  chain 'Q' and resid 124 through 141
      removed outlier: 3.637A  pdb=" N   ALA Q 128 " --> pdb=" O   ILE Q 124 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LEU Q 129 " --> pdb=" O   PRO Q 125 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ASN Q 131 " --> pdb=" O   CYS Q 127 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLN Q 132 " --> pdb=" O   ALA Q 128 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   HIS Q 133 " --> pdb=" O   LEU Q 129 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   SER Q 135 " --> pdb=" O   ASN Q 131 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ARG Q 139 " --> pdb=" O   SER Q 135 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LYS Q 140 " --> pdb=" O   GLY Q 136 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 181 through 185
    Processing helix  chain 'Q' and resid 190 through 196
    Processing helix  chain 'Q' and resid 204 through 208
    Processing helix  chain 'Q' and resid 220 through 231
      removed outlier: 4.348A  pdb=" N   VAL Q 224 " --> pdb=" O   LEU Q 220 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ARG Q 225 " --> pdb=" O   LEU Q 221 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   SER Q 227 " --> pdb=" O   SER Q 223 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 59 through 62
      removed outlier: 3.606A  pdb=" N   LYS D  59 " --> pdb=" O   THR D  71 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 153 through 154
      removed outlier: 3.590A  pdb=" N   ARG D 153 " --> pdb=" O   LEU D 421 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 299 through 301
      removed outlier: 7.077A  pdb=" N   ILE D 300 " --> pdb=" O   ILE D 328 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'Q' and resid 95 through 96
      removed outlier: 7.682A  pdb=" N   LEU Q  95 " --> pdb=" O   LYS Q 148 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    207 hydrogen bonds defined for protein.
    597 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: 0.63

  Time building geometry restraints manager: 0.59 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1640
        1.34 -     1.46: 540
        1.46 -     1.57: 3009
        1.57 -     1.69: 0
        1.69 -     1.81: 47
  Bond restraints: 5236
  Sorted by residual:
  bond pdb=" C   ILE Q 155 "
       pdb=" N   PRO Q 156 "
    ideal  model  delta    sigma   weight residual
    1.335  1.498 -0.162 1.36e-02 5.41e+03 1.43e+02
  bond pdb=" C   TYR Q 158 "
       pdb=" N   PRO Q 159 "
    ideal  model  delta    sigma   weight residual
    1.333  1.497 -0.164 1.44e-02 4.82e+03 1.29e+02
  bond pdb=" N   ARG Q 161 "
       pdb=" CA  ARG Q 161 "
    ideal  model  delta    sigma   weight residual
    1.457  1.518 -0.061 1.33e-02 5.65e+03 2.09e+01
  bond pdb=" N   CYS Q 154 "
       pdb=" CA  CYS Q 154 "
    ideal  model  delta    sigma   weight residual
    1.454  1.495 -0.041 1.17e-02 7.31e+03 1.21e+01
  bond pdb=" N   ILE Q 155 "
       pdb=" CA  ILE Q 155 "
    ideal  model  delta    sigma   weight residual
    1.461  1.501 -0.040 1.23e-02 6.61e+03 1.04e+01
  ... (remaining 5231 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.12: 7018
        4.12 -     8.25: 38
        8.25 -    12.37: 4
       12.37 -    16.50: 2
       16.50 -    20.62: 2
  Bond angle restraints: 7064
  Sorted by residual:
  angle pdb=" C   TYR Q 158 "
        pdb=" N   PRO Q 159 "
        pdb=" CA  PRO Q 159 "
      ideal   model   delta    sigma   weight residual
     119.47  140.09  -20.62 1.16e+00 7.43e-01 3.16e+02
  angle pdb=" C   ILE Q 155 "
        pdb=" N   PRO Q 156 "
        pdb=" CA  PRO Q 156 "
      ideal   model   delta    sigma   weight residual
     119.05  137.20  -18.15 1.11e+00 8.12e-01 2.67e+02
  angle pdb=" C   PRO Q 159 "
        pdb=" CA  PRO Q 159 "
        pdb=" CB  PRO Q 159 "
      ideal   model   delta    sigma   weight residual
     112.26  102.02   10.24 1.67e+00 3.59e-01 3.76e+01
  angle pdb=" N   PRO Q 159 "
        pdb=" CD  PRO Q 159 "
        pdb=" CG  PRO Q 159 "
      ideal   model   delta    sigma   weight residual
     103.20   94.78    8.42 1.50e+00 4.44e-01 3.15e+01
  angle pdb=" N   PRO Q 156 "
        pdb=" CA  PRO Q 156 "
        pdb=" C   PRO Q 156 "
      ideal   model   delta    sigma   weight residual
     113.53  121.08   -7.55 1.39e+00 5.18e-01 2.95e+01
  ... (remaining 7059 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.46: 2925
       17.46 -    34.92: 281
       34.92 -    52.38: 52
       52.38 -    69.84: 11
       69.84 -    87.30: 6
  Dihedral angle restraints: 3275
    sinusoidal: 1328
      harmonic: 1947
  Sorted by residual:
  dihedral pdb=" CA  CYS D 221 "
           pdb=" C   CYS D 221 "
           pdb=" N   GLU D 222 "
           pdb=" CA  GLU D 222 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.79  -27.21     0      5.00e+00 4.00e-02 2.96e+01
  dihedral pdb=" CA  ILE Q 216 "
           pdb=" C   ILE Q 216 "
           pdb=" N   GLU Q 217 "
           pdb=" CA  GLU Q 217 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.70  -23.30     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" C   PRO Q 159 "
           pdb=" N   PRO Q 159 "
           pdb=" CA  PRO Q 159 "
           pdb=" CB  PRO Q 159 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -109.29  -11.41     0      2.50e+00 1.60e-01 2.08e+01
  ... (remaining 3272 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 620
       0.048 -    0.095: 173
       0.095 -    0.143: 53
       0.143 -    0.190: 9
       0.190 -    0.238: 6
  Chirality restraints: 861
  Sorted by residual:
  chirality pdb=" CA  PRO Q 156 "
            pdb=" N   PRO Q 156 "
            pdb=" C   PRO Q 156 "
            pdb=" CB  PRO Q 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.48    0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CA  ILE Q 155 "
            pdb=" N   ILE Q 155 "
            pdb=" C   ILE Q 155 "
            pdb=" CB  ILE Q 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  VAL Q  94 "
            pdb=" N   VAL Q  94 "
            pdb=" C   VAL Q  94 "
            pdb=" CB  VAL Q  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.21 2.00e-01 2.50e+01 1.15e+00
  ... (remaining 858 not shown)

  Planarity restraints: 894
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE Q 147 "    0.019 2.00e-02 2.50e+03   3.79e-02 1.43e+01
        pdb=" C   ILE Q 147 "   -0.065 2.00e-02 2.50e+03
        pdb=" O   ILE Q 147 "    0.025 2.00e-02 2.50e+03
        pdb=" N   LYS Q 148 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS Q 214 "   -0.058 5.00e-02 4.00e+02   8.92e-02 1.27e+01
        pdb=" N   PRO Q 215 "    0.154 5.00e-02 4.00e+02
        pdb=" CA  PRO Q 215 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO Q 215 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY D  64 "    0.015 2.00e-02 2.50e+03   3.06e-02 9.35e+00
        pdb=" C   GLY D  64 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   GLY D  64 "    0.020 2.00e-02 2.50e+03
        pdb=" N   LYS D  65 "    0.018 2.00e-02 2.50e+03
  ... (remaining 891 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.34: 17
        2.34 -     2.98: 2777
        2.98 -     3.62: 7797
        3.62 -     4.26: 10534
        4.26 -     4.90: 16543
  Nonbonded interactions: 37668
  Sorted by model distance:
  nonbonded pdb=" CE  LYS Q 121 "
            pdb=" O   PRO Q 159 "
     model   vdw
     1.697 3.440
  nonbonded pdb=" CG1 VAL Q  94 "
            pdb=" NZ  LYS Q 148 "
     model   vdw
     1.954 3.540
  nonbonded pdb=" CE1 TYR Q 158 "
            pdb=" OD1 ASN Q 162 "
     model   vdw
     1.969 3.340
  nonbonded pdb=" OG1 THR Q 190 "
            pdb=" OD1 ASP Q 192 "
     model   vdw
     2.153 3.040
  nonbonded pdb=" O   ASN Q 157 "
            pdb=" ND2 ASN Q 157 "
     model   vdw
     2.161 3.120
  ... (remaining 37663 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.870
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.040
  Find NCS groups from input model:        0.010
  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:0.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6784
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      :  0.007   0.164   5236  Z= 0.402
  Angle     :  0.984  20.623   7064  Z= 0.599
  Chirality :  0.052   0.238    861
  Planarity :  0.005   0.089    894
  Dihedral  : 14.664  87.297   2011
  Min Nonbonded Distance : 1.697

Molprobity Statistics.
  All-atom Clashscore : 22.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.48 %
    Favored  : 88.52 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 10.17 %
    Favored  : 88.97 %
  Cbeta Deviations :  0.16 %
  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: -3.94 (0.28), residues: 671
  helix: -1.30 (0.28), residues: 275
  sheet: -3.77 (0.58), residues: 49
  loop : -3.68 (0.27), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D 413 
 TYR   0.017   0.002   TYR D 269 
 PHE   0.011   0.001   PHE D 335 
 TRP   0.004   0.001   TRP Q 196 
 HIS   0.003   0.001   HIS D 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00668 ( 5236)
  covalent geometry    : angle       0.98396 ( 7064)
  hydrogen bonds       : bond        0.18818 (  207)
  hydrogen bonds       : angle       6.05156 (  597)

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  272 MET cc_start: 0.7996 (tmm) cc_final: 0.7286 (tmm)
REVERT: D  279 GLU cc_start: 0.7575 (pt0) cc_final: 0.6811 (mm-30)
REVERT: D  391 ARG cc_start: 0.6703 (ptm-80) cc_final: 0.6404 (ptm-80)
REVERT: Q   69 ARG cc_start: 0.9642 (mtm180) cc_final: 0.9103 (ptp90)
REVERT: Q  160 ASP cc_start: 0.6489 (OUTLIER) cc_final: 0.5991 (p0)
  outliers start: 5
  outliers final: 1
  residues processed: 74
  average time/residue: 0.1122
  time to fit residues: 9.9383
Evaluate side-chains
  57 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    8.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    8.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
D  98 GLN
D 231 GLN
D 318 ASN
D 350 GLN
D 484 HIS
** D 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.187615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.172790 restraints weight = 13837.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.170622 restraints weight = 29512.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.169790 restraints weight = 21451.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.169790 restraints weight = 20559.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.170011 restraints weight = 13936.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.4341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5892
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5236  Z= 0.134
  Angle     :  0.694   8.875   7064  Z= 0.352
  Chirality :  0.046   0.200    861
  Planarity :  0.004   0.062    894
  Dihedral  :  5.673  20.542    718
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.94 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.81 (0.31), residues: 671
  helix: -0.10 (0.31), residues: 292
  sheet: -3.13 (0.66), residues: 45
  loop : -3.47 (0.29), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Q 161 
 TYR   0.016   0.001   TYR Q 169 
 PHE   0.010   0.001   PHE D 137 
 TRP   0.006   0.001   TRP Q  82 
 HIS   0.004   0.001   HIS D 484 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 5236)
  covalent geometry    : angle       0.69394 ( 7064)
  hydrogen bonds       : bond        0.04202 (  207)
  hydrogen bonds       : angle       4.58209 (  597)

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.0825
  time to fit residues: 7.8947
Evaluate side-chains
  54 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 65 optimal weight:    0.3980
   chunk 45 optimal weight:   10.0000
   chunk 31 optimal weight:    0.0870
   chunk 4 optimal weight:   50.0000
   chunk 63 optimal weight:    0.0170
   chunk 6 optimal weight:    9.9990
   chunk 43 optimal weight:    9.9990
   chunk 58 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0970
   overall best weight:    0.2794

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

Flipped N/Q/H residues before XYZ refinement:
D  85 HIS
Q 133 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4613 r_free = 0.4613 target = 0.190624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.173394 restraints weight = 13523.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.172922 restraints weight = 26318.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.172381 restraints weight = 17697.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.172210 restraints weight = 15367.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.172170 restraints weight = 13450.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.4376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5783
moved from start:          0.3141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5236  Z= 0.113
  Angle     :  0.640   9.194   7064  Z= 0.321
  Chirality :  0.044   0.180    861
  Planarity :  0.004   0.041    894
  Dihedral  :  5.213  18.452    718
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  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: -2.13 (0.31), residues: 671
  helix:  0.38 (0.31), residues: 294
  sheet: -2.08 (0.70), residues: 46
  loop : -3.15 (0.29), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG Q 161 
 TYR   0.004   0.001   TYR D 269 
 PHE   0.016   0.001   PHE D 137 
 TRP   0.003   0.001   TRP Q 196 
 HIS   0.001   0.000   HIS D 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 5236)
  covalent geometry    : angle       0.63950 ( 7064)
  hydrogen bonds       : bond        0.03523 (  207)
  hydrogen bonds       : angle       4.02415 (  597)

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Q  117 LEU cc_start: 0.9072 (mt) cc_final: 0.8748 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.0864
  time to fit residues: 8.0353
Evaluate side-chains
  58 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 4 optimal weight:   50.0000
   chunk 42 optimal weight:   10.0000
   chunk 30 optimal weight:    4.9990
   chunk 28 optimal weight:    7.9990
   chunk 40 optimal weight:    6.9990
   chunk 11 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 12 optimal weight:    6.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
D 296 ASN
D 347 HIS
** D 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 122 GLN
** Q 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.174438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.154111 restraints weight = 14095.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.153589 restraints weight = 21476.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.152855 restraints weight = 21025.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.151978 restraints weight = 20538.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.151269 restraints weight = 21799.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.4126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6387
moved from start:          0.3115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.090   5236  Z= 0.423
  Angle     :  1.049  13.167   7064  Z= 0.532
  Chirality :  0.055   0.363    861
  Planarity :  0.007   0.082    894
  Dihedral  :  6.859  26.165    718
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 19.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.11 %
    Favored  : 86.89 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  7.76 %
    Favored  : 91.90 %
  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: -2.44 (0.32), residues: 671
  helix:  0.33 (0.32), residues: 290
  sheet: -2.83 (0.82), residues: 45
  loop : -3.39 (0.30), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG Q  69 
 TYR   0.033   0.005   TYR Q 169 
 PHE   0.027   0.004   PHE Q 167 
 TRP   0.013   0.003   TRP Q  82 
 HIS   0.007   0.002   HIS D 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00982 ( 5236)
  covalent geometry    : angle       1.04874 ( 7064)
  hydrogen bonds       : bond        0.04822 (  207)
  hydrogen bonds       : angle       5.04969 (  597)

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 56
  average time/residue: 0.0805
  time to fit residues: 5.5747
Evaluate side-chains
  40 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 21 optimal weight:    0.0070
   chunk 62 optimal weight:    0.6980
   chunk 45 optimal weight:    8.9990
   chunk 9 optimal weight:    7.9990
   chunk 41 optimal weight:    7.9990
   chunk 28 optimal weight:    0.0020
   chunk 4 optimal weight:   40.0000
   chunk 37 optimal weight:    0.0370
   chunk 5 optimal weight:   20.0000
   chunk 55 optimal weight:    0.5980
   chunk 33 optimal weight:    5.9990
   overall best weight:    0.2684

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

Flipped N/Q/H residues before XYZ refinement:
** D 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.186647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.172448 restraints weight = 13824.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.170649 restraints weight = 27865.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.169144 restraints weight = 20195.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.169064 restraints weight = 23581.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.169099 restraints weight = 14849.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.4335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5866
moved from start:          0.3647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   5236  Z= 0.121
  Angle     :  0.682   8.826   7064  Z= 0.342
  Chirality :  0.045   0.188    861
  Planarity :  0.004   0.054    894
  Dihedral  :  5.516  18.342    718
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  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: -1.93 (0.32), residues: 671
  helix:  0.50 (0.32), residues: 292
  sheet: -2.18 (0.83), residues: 43
  loop : -2.93 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG Q  69 
 TYR   0.004   0.001   TYR Q 169 
 PHE   0.027   0.002   PHE D 137 
 TRP   0.006   0.001   TRP Q 196 
 HIS   0.003   0.001   HIS D 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 5236)
  covalent geometry    : angle       0.68174 ( 7064)
  hydrogen bonds       : bond        0.03558 (  207)
  hydrogen bonds       : angle       4.13995 (  597)

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: Q  117 LEU cc_start: 0.8974 (mt) cc_final: 0.8630 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.1070
  time to fit residues: 9.1196
Evaluate side-chains
  50 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0050
   chunk 23 optimal weight:    0.3980
   chunk 6 optimal weight:   10.0000
   chunk 45 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 12 optimal weight:    7.9990
   chunk 19 optimal weight:    5.9990
   chunk 50 optimal weight:    6.9990
   overall best weight:    0.8796

-------------------------------------------------------------------------------
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 = 0.4556 r_free = 0.4556 target = 0.184957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.166760 restraints weight = 13817.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.166547 restraints weight = 20989.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.166478 restraints weight = 18182.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.165303 restraints weight = 17659.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.164254 restraints weight = 18392.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.4290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6012
moved from start:          0.3973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5236  Z= 0.125
  Angle     :  0.688   8.567   7064  Z= 0.341
  Chirality :  0.045   0.190    861
  Planarity :  0.004   0.045    894
  Dihedral  :  5.344  18.904    718
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.99 %
    Favored  : 90.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.87 (0.32), residues: 671
  helix:  0.53 (0.31), residues: 300
  sheet: -1.76 (0.84), residues: 41
  loop : -3.01 (0.31), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 391 
 TYR   0.010   0.001   TYR Q  74 
 PHE   0.024   0.002   PHE D 137 
 TRP   0.004   0.001   TRP Q 196 
 HIS   0.002   0.000   HIS D 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 5236)
  covalent geometry    : angle       0.68754 ( 7064)
  hydrogen bonds       : bond        0.03413 (  207)
  hydrogen bonds       : angle       4.04645 (  597)

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   81 MET cc_start: 0.7413 (tpt) cc_final: 0.7065 (mmm)
REVERT: D  260 MET cc_start: 0.3518 (ptt) cc_final: 0.3129 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.0904
  time to fit residues: 6.9672
Evaluate side-chains
  50 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 24 optimal weight:    0.4980
   chunk 11 optimal weight:    9.9990
   chunk 16 optimal weight:    0.0040
   chunk 6 optimal weight:    9.9990
   chunk 54 optimal weight:    0.4980
   chunk 35 optimal weight:    0.0980
   chunk 30 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.3392

-------------------------------------------------------------------------------
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 = 0.4594 r_free = 0.4594 target = 0.188979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.172675 restraints weight = 13997.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.173900 restraints weight = 25583.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.174046 restraints weight = 18098.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.173856 restraints weight = 13522.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.174072 restraints weight = 12852.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.4405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5716
moved from start:          0.4450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5236  Z= 0.109
  Angle     :  0.670  10.486   7064  Z= 0.323
  Chirality :  0.044   0.221    861
  Planarity :  0.003   0.033    894
  Dihedral  :  4.907  18.385    718
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.63 (0.33), residues: 671
  helix:  0.52 (0.31), residues: 301
  sheet: -0.92 (0.87), residues: 42
  loop : -2.79 (0.32), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 391 
 TYR   0.008   0.001   TYR Q 169 
 PHE   0.031   0.002   PHE D 137 
 TRP   0.004   0.001   TRP Q 196 
 HIS   0.003   0.001   HIS D 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 5236)
  covalent geometry    : angle       0.67043 ( 7064)
  hydrogen bonds       : bond        0.03096 (  207)
  hydrogen bonds       : angle       3.94805 (  597)

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   81 MET cc_start: 0.7513 (tpt) cc_final: 0.7228 (mmm)
REVERT: D  163 LEU cc_start: 0.6677 (mt) cc_final: 0.5451 (pp)
REVERT: Q   71 ILE cc_start: 0.8832 (mt) cc_final: 0.8494 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.0960
  time to fit residues: 8.6226
Evaluate side-chains
  54 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 47 optimal weight:   50.0000
   chunk 35 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   chunk 30 optimal weight:    0.4980
   chunk 20 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    1.2586

-------------------------------------------------------------------------------
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 = 0.4523 r_free = 0.4523 target = 0.182830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.170486 restraints weight = 14643.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.168216 restraints weight = 26955.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.166814 restraints weight = 23304.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.166887 restraints weight = 22816.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.167699 restraints weight = 13286.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.4311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5919
moved from start:          0.4435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5236  Z= 0.137
  Angle     :  0.704   9.561   7064  Z= 0.344
  Chirality :  0.044   0.200    861
  Planarity :  0.003   0.037    894
  Dihedral  :  5.220  22.114    718
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.28 %
    Favored  : 89.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.59 (0.33), residues: 671
  helix:  0.57 (0.31), residues: 303
  sheet: -0.99 (0.87), residues: 42
  loop : -2.79 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG Q 225 
 TYR   0.009   0.001   TYR D 269 
 PHE   0.025   0.002   PHE D 137 
 TRP   0.005   0.001   TRP Q  82 
 HIS   0.002   0.001   HIS D 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 5236)
  covalent geometry    : angle       0.70443 ( 7064)
  hydrogen bonds       : bond        0.03288 (  207)
  hydrogen bonds       : angle       4.02839 (  597)

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   81 MET cc_start: 0.7588 (tpt) cc_final: 0.7374 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.0856
  time to fit residues: 7.2817
Evaluate side-chains
  52 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   chunk 11 optimal weight:   20.0000
   chunk 9 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0070
   chunk 32 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.7398

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

Flipped N/Q/H residues before XYZ refinement:
** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.185320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.172632 restraints weight = 14669.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.172154 restraints weight = 26669.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.170532 restraints weight = 19970.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.170904 restraints weight = 17722.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.170667 restraints weight = 12873.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.4352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5805
moved from start:          0.4644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5236  Z= 0.115
  Angle     :  0.688   9.215   7064  Z= 0.333
  Chirality :  0.044   0.207    861
  Planarity :  0.003   0.035    894
  Dihedral  :  5.035  23.053    718
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.94 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.39 (0.33), residues: 671
  helix:  0.58 (0.31), residues: 303
  sheet: -0.75 (0.87), residues: 42
  loop : -2.52 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Q 225 
 TYR   0.008   0.001   TYR Q 169 
 PHE   0.017   0.001   PHE Q  91 
 TRP   0.004   0.001   TRP Q 196 
 HIS   0.002   0.000   HIS D 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 5236)
  covalent geometry    : angle       0.68801 ( 7064)
  hydrogen bonds       : bond        0.03055 (  207)
  hydrogen bonds       : angle       3.92667 (  597)

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   81 MET cc_start: 0.7474 (tpt) cc_final: 0.7252 (mmm)
REVERT: D  163 LEU cc_start: 0.6541 (mt) cc_final: 0.5357 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0718
  time to fit residues: 6.6367
Evaluate side-chains
  57 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0010
   chunk 48 optimal weight:    7.9990
   chunk 5 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 13 optimal weight:    9.9990
   chunk 7 optimal weight:    9.9990
   overall best weight:    0.9190

-------------------------------------------------------------------------------
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 = 0.4545 r_free = 0.4545 target = 0.184756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.171937 restraints weight = 14932.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.170101 restraints weight = 25279.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.167751 restraints weight = 20454.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.168255 restraints weight = 17575.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.168007 restraints weight = 13015.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.4313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5897
moved from start:          0.4799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5236  Z= 0.125
  Angle     :  0.705   9.066   7064  Z= 0.344
  Chirality :  0.045   0.237    861
  Planarity :  0.003   0.033    894
  Dihedral  :  5.068  22.260    718
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.54 %
    Favored  : 90.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.43 (0.33), residues: 671
  helix:  0.55 (0.31), residues: 306
  sheet: -0.62 (0.87), residues: 42
  loop : -2.60 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 413 
 TYR   0.014   0.001   TYR Q 169 
 PHE   0.032   0.002   PHE D 137 
 TRP   0.004   0.001   TRP Q 196 
 HIS   0.002   0.000   HIS D 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 5236)
  covalent geometry    : angle       0.70497 ( 7064)
  hydrogen bonds       : bond        0.03267 (  207)
  hydrogen bonds       : angle       4.03851 (  597)

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

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

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1342 Ramachandran restraints generated.
    671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   81 MET cc_start: 0.7524 (tpt) cc_final: 0.7323 (mmm)
REVERT: D  163 LEU cc_start: 0.6692 (mt) cc_final: 0.5504 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0724
  time to fit residues: 6.1438
Evaluate side-chains
  55 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 28 optimal weight:    0.0470
   chunk 7 optimal weight:   10.0000
   chunk 16 optimal weight:    0.6980
   chunk 49 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0370
   chunk 5 optimal weight:   20.0000
   overall best weight:    0.9558

-------------------------------------------------------------------------------
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 = 0.4542 r_free = 0.4542 target = 0.184497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.172201 restraints weight = 15004.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.170775 restraints weight = 27904.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.168668 restraints weight = 20930.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.169063 restraints weight = 18599.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.169040 restraints weight = 12706.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.4331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5859
moved from start:          0.4861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5236  Z= 0.122
  Angle     :  0.695   8.925   7064  Z= 0.338
  Chirality :  0.045   0.225    861
  Planarity :  0.003   0.032    894
  Dihedral  :  5.036  24.166    718
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.39 %
    Favored  : 90.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.31 (0.33), residues: 671
  helix:  0.69 (0.31), residues: 301
  sheet: -0.52 (0.88), residues: 42
  loop : -2.55 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG Q 225 
 TYR   0.013   0.001   TYR Q 169 
 PHE   0.030   0.002   PHE D 137 
 TRP   0.004   0.001   TRP Q 196 
 HIS   0.002   0.001   HIS D 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 5236)
  covalent geometry    : angle       0.69499 ( 7064)
  hydrogen bonds       : bond        0.03150 (  207)
  hydrogen bonds       : angle       4.00694 (  597)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 913.06 seconds
wall clock time: 16 minutes 28.47 seconds (988.47 seconds total)