Starting phenix.real_space_refine
on Fri Aug 22 15:53:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i6j_35199/08_2025/8i6j_35199.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i6j_35199/08_2025/8i6j_35199.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.82
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i6j_35199/08_2025/8i6j_35199.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i6j_35199/08_2025/8i6j_35199.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i6j_35199/08_2025/8i6j_35199.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i6j_35199/08_2025/8i6j_35199.cif"
  }
  resolution = 3.82
  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=   0.072
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      36      5.16       5
     C    3318      2.51       5
     N     925      2.21       5
     O    1006      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  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: 5287
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "Q"
      Number of atoms: 1371
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 170, 1371
          Classifications: {'peptide': 170}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 161}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "C"
      Number of atoms: 3889
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 500, 3889
          Classifications: {'peptide': 500}
          Link IDs: {'PTRANS': 16, 'TRANS': 483}
    Chain: "C"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.38, per 1000 atoms: 0.26
  Number of scatterers: 5287
  At special positions: 0
  Unit cell: (97.18, 74.58, 118.65, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      36     16.00
     P       2     15.00
     O    1006      8.00
     N     925      7.00
     C    3318      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 164.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1260

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 6 sheets defined
      50.7% alpha, 7.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'Q' and resid 65 through 81
    Processing helix  chain 'Q' and resid 82 through 84
      No H-bonds generated for 'chain 'Q' and resid 82 through 84'
    Processing helix  chain 'Q' and resid 128 through 141
      removed outlier: 4.112A  pdb=" N   GLN Q 132 " --> pdb=" O   ALA Q 128 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   HIS Q 133 " --> pdb=" O   LEU Q 129 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 180 through 185
      removed outlier: 4.529A  pdb=" N   PHE Q 184 " --> pdb=" O   GLY Q 180 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 190 through 200
      removed outlier: 3.666A  pdb=" N   LEU Q 194 " --> pdb=" O   THR Q 190 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 218 through 231
      removed outlier: 3.860A  pdb=" N   LYS Q 231 " --> pdb=" O   SER Q 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 37
      removed outlier: 4.281A  pdb=" N   ASN C  28 " --> pdb=" O   SER C  24 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   ALA C  29 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ILE C  37 " --> pdb=" O   ILE C  33 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 70
      removed outlier: 3.567A  pdb=" N   ILE C  66 " --> pdb=" O   ASP C  62 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE C  70 " --> pdb=" O   ILE C  66 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 91
      removed outlier: 4.008A  pdb=" N   SER C  84 " --> pdb=" O   MET C  80 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ARG C  85 " --> pdb=" O   ILE C  81 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   GLU C  90 " --> pdb=" O   THR C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 95 through 108
      removed outlier: 3.985A  pdb=" N   ILE C  99 " --> pdb=" O   THR C  95 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   VAL C 108 " --> pdb=" O   GLU C 104 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 109 through 116
      removed outlier: 4.645A  pdb=" N   LEU C 113 " --> pdb=" O   ALA C 109 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 140
      removed outlier: 3.542A  pdb=" N   LYS C 128 " --> pdb=" O   SER C 124 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ILE C 140 " --> pdb=" O   THR C 136 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 149 through 160
    Processing helix  chain 'C' and resid 168 through 184
      removed outlier: 3.847A  pdb=" N   GLN C 184 " --> pdb=" O   VAL C 180 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 212
      removed outlier: 3.731A  pdb=" N   ASP C 211 " --> pdb=" O   ILE C 208 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   SER C 212 " --> pdb=" O   ILE C 209 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 208 through 212'
    Processing helix  chain 'C' and resid 249 through 253
      removed outlier: 3.549A  pdb=" N   SER C 252 " --> pdb=" O   LYS C 249 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 260 through 284
      removed outlier: 3.932A  pdb=" N   PHE C 264 " --> pdb=" O   ARG C 260 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   GLU C 272 " --> pdb=" O   LEU C 268 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   GLU C 273 " --> pdb=" O   GLN C 269 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TYR C 274 " --> pdb=" O   MET C 270 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 297 through 307
      removed outlier: 3.745A  pdb=" N   GLN C 301 " --> pdb=" O   SER C 297 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ALA C 307 " --> pdb=" O   TYR C 303 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 316 through 324
    Processing helix  chain 'C' and resid 381 through 404
      removed outlier: 3.761A  pdb=" N   LEU C 403 " --> pdb=" O   ARG C 399 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   ASP C 404 " --> pdb=" O   ASN C 400 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 412 through 430
    Processing helix  chain 'C' and resid 433 through 442
      removed outlier: 3.931A  pdb=" N   TYR C 437 " --> pdb=" O   GLU C 433 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 445 through 456
      removed outlier: 4.126A  pdb=" N   ARG C 449 " --> pdb=" O   GLU C 445 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 458 through 473
      removed outlier: 3.686A  pdb=" N   LEU C 462 " --> pdb=" O   SER C 458 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 499 through 519
      removed outlier: 3.858A  pdb=" N   ILE C 519 " --> pdb=" O   LEU C 515 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'Q' and resid 145 through 146
      removed outlier: 3.735A  pdb=" N   PHE Q 167 " --> pdb=" O   LEU Q 117 " (cutoff:3.500A)
      removed outlier: 7.555A  pdb=" N   ILE Q 166 " --> pdb=" O   GLN Q 177 " (cutoff:3.500A)
      removed outlier: 5.627A  pdb=" N   GLN Q 177 " --> pdb=" O   ILE Q 166 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   VAL Q 168 " --> pdb=" O   LYS Q 175 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 48 through 51
    Processing sheet with id=AA3, first strand: chain 'C' and resid 142 through 143
    Processing sheet with id=AA4, first strand: chain 'C' and resid 201 through 205
      removed outlier: 3.680A  pdb=" N   ILE C 204 " --> pdb=" O   LEU C 376 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   GLY C 378 " --> pdb=" O   ILE C 204 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   THR C 373 " --> pdb=" O   LEU C 215 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU C 375 " --> pdb=" O   CYS C 213 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 218 through 220
      removed outlier: 3.504A  pdb=" N   ILE C 363 " --> pdb=" O   VAL C 218 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU C 350 " --> pdb=" O   ILE C 233 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ILE C 233 " --> pdb=" O   LEU C 350 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 240
      removed outlier: 3.615A  pdb=" N   ILE C 291 " --> pdb=" O   VAL C 239 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   VAL C 290 " --> pdb=" O   ILE C 312 " (cutoff:3.500A)

    236 hydrogen bonds defined for protein.
    681 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: 0.67

  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:
        1.23 -     1.34: 1769
        1.34 -     1.46: 950
        1.46 -     1.58: 2578
        1.58 -     1.70: 3
        1.70 -     1.81: 60
  Bond restraints: 5360
  Sorted by residual:
  bond pdb=" CG  GLU C 511 "
       pdb=" CD  GLU C 511 "
    ideal  model  delta    sigma   weight residual
    1.516  1.489  0.027 2.50e-02 1.60e+03 1.21e+00
  bond pdb=" CG  GLU Q 195 "
       pdb=" CD  GLU Q 195 "
    ideal  model  delta    sigma   weight residual
    1.516  1.490  0.026 2.50e-02 1.60e+03 1.08e+00
  bond pdb=" C4  ADP C 601 "
       pdb=" C5  ADP C 601 "
    ideal  model  delta    sigma   weight residual
    1.490  1.471  0.019 2.00e-02 2.50e+03 8.77e-01
  bond pdb=" CG  ARG Q 225 "
       pdb=" CD  ARG Q 225 "
    ideal  model  delta    sigma   weight residual
    1.520  1.544 -0.024 3.00e-02 1.11e+03 6.66e-01
  bond pdb=" N   GLN Q 122 "
       pdb=" CA  GLN Q 122 "
    ideal  model  delta    sigma   weight residual
    1.456  1.466 -0.010 1.23e-02 6.61e+03 6.28e-01
  ... (remaining 5355 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 6984
        1.62 -     3.23: 193
        3.23 -     4.85: 42
        4.85 -     6.47: 14
        6.47 -     8.08: 4
  Bond angle restraints: 7237
  Sorted by residual:
  angle pdb=" N   ILE C 195 "
        pdb=" CA  ILE C 195 "
        pdb=" C   ILE C 195 "
      ideal   model   delta    sigma   weight residual
     113.53  109.98    3.55 9.80e-01 1.04e+00 1.31e+01
  angle pdb=" N   GLU C 511 "
        pdb=" CA  GLU C 511 "
        pdb=" CB  GLU C 511 "
      ideal   model   delta    sigma   weight residual
     110.28  115.50   -5.22 1.55e+00 4.16e-01 1.13e+01
  angle pdb=" N   MET Q  73 "
        pdb=" CA  MET Q  73 "
        pdb=" CB  MET Q  73 "
      ideal   model   delta    sigma   weight residual
     110.28  115.16   -4.88 1.55e+00 4.16e-01 9.91e+00
  angle pdb=" N   GLU Q 195 "
        pdb=" CA  GLU Q 195 "
        pdb=" CB  GLU Q 195 "
      ideal   model   delta    sigma   weight residual
     110.12  114.56   -4.44 1.47e+00 4.63e-01 9.13e+00
  angle pdb=" N   TYR Q 102 "
        pdb=" CA  TYR Q 102 "
        pdb=" C   TYR Q 102 "
      ideal   model   delta    sigma   weight residual
     110.80  116.86   -6.06 2.13e+00 2.20e-01 8.11e+00
  ... (remaining 7232 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.12: 3189
       27.12 -    54.23: 131
       54.23 -    81.35: 9
       81.35 -   108.46: 5
      108.46 -   135.58: 1
  Dihedral angle restraints: 3335
    sinusoidal: 1393
      harmonic: 1942
  Sorted by residual:
  dihedral pdb=" O2A ADP C 601 "
           pdb=" O3A ADP C 601 "
           pdb=" PA  ADP C 601 "
           pdb=" PB  ADP C 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  164.42  135.58     1      2.00e+01 2.50e-03 4.11e+01
  dihedral pdb=" CA  ILE Q 150 "
           pdb=" C   ILE Q 150 "
           pdb=" N   SER Q 151 "
           pdb=" CA  SER Q 151 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.76   24.24     0      5.00e+00 4.00e-02 2.35e+01
  dihedral pdb=" CA  TYR Q 169 "
           pdb=" C   TYR Q 169 "
           pdb=" N   LEU Q 170 "
           pdb=" CA  LEU Q 170 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.17   22.83     0      5.00e+00 4.00e-02 2.09e+01
  ... (remaining 3332 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 514
       0.032 -    0.065: 209
       0.065 -    0.097: 69
       0.097 -    0.129: 47
       0.129 -    0.162: 7
  Chirality restraints: 846
  Sorted by residual:
  chirality pdb=" CB  ILE C 374 "
            pdb=" CA  ILE C 374 "
            pdb=" CG1 ILE C 374 "
            pdb=" CG2 ILE C 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.54e-01
  chirality pdb=" CA  GLU C 511 "
            pdb=" N   GLU C 511 "
            pdb=" C   GLU C 511 "
            pdb=" CB  GLU C 511 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.45e-01
  chirality pdb=" CA  TYR Q 102 "
            pdb=" N   TYR Q 102 "
            pdb=" C   TYR Q 102 "
            pdb=" CB  TYR Q 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.45e-01
  ... (remaining 843 not shown)

  Planarity restraints: 921
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 112 "    0.014 2.00e-02 2.50e+03   1.41e-02 3.47e+00
        pdb=" CG  PHE C 112 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 112 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 112 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 112 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 112 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 112 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE Q 124 "    0.026 5.00e-02 4.00e+02   4.02e-02 2.59e+00
        pdb=" N   PRO Q 125 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO Q 125 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO Q 125 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 507 "    0.007 2.00e-02 2.50e+03   1.37e-02 1.88e+00
        pdb=" C   LYS C 507 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   LYS C 507 "    0.009 2.00e-02 2.50e+03
        pdb=" N   THR C 508 "    0.008 2.00e-02 2.50e+03
  ... (remaining 918 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1164
        2.79 -     3.32: 5151
        3.32 -     3.85: 7858
        3.85 -     4.37: 8250
        4.37 -     4.90: 14508
  Nonbonded interactions: 36931
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP C 132 "
            pdb=" OH  TYR C 437 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   VAL Q 183 "
            pdb=" NZ  LYS Q 197 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" OE1 GLU C 497 "
            pdb=" NZ  LYS C 502 "
     model   vdw
     2.341 3.120
  nonbonded pdb=" O   ASN Q 157 "
            pdb=" ND2 ASN Q 157 "
     model   vdw
     2.344 3.120
  nonbonded pdb=" O   SER C 158 "
            pdb=" OG1 THR C 161 "
     model   vdw
     2.348 3.040
  ... (remaining 36926 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:             2.200
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.890
  Find NCS groups from input model:        0.020
  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:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6941
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      :  0.003   0.029   5360  Z= 0.140
  Angle     :  0.697   8.081   7237  Z= 0.359
  Chirality :  0.046   0.162    846
  Planarity :  0.004   0.040    921
  Dihedral  : 14.716 135.578   2075
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.61 %
    Favored  : 90.39 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.00 %
    Favored  : 99.83 %
  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: -0.94 (0.33), residues: 666
  helix:  1.57 (0.31), residues: 306
  sheet: -0.75 (0.66), residues: 70
  loop : -3.23 (0.29), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG Q 225 
 TYR   0.011   0.002   TYR Q 102 
 PHE   0.032   0.002   PHE C 112 
 TRP   0.019   0.002   TRP C 435 
 HIS   0.004   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 5360)
  covalent geometry    : angle       0.69743 ( 7237)
  hydrogen bonds       : bond        0.15313 (  236)
  hydrogen bonds       : angle       5.57275 (  681)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
REVERT: Q  187 MET cc_start: 0.7745 (mmt) cc_final: 0.7351 (mmm)
REVERT: C  190 ARG cc_start: 0.7336 (mmp80) cc_final: 0.7102 (mmp80)
  outliers start: 1
  outliers final: 0
  residues processed: 84
  average time/residue: 0.0769
  time to fit residues: 8.2120
Evaluate side-chains
  75 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.3980
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    7.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.4491 r_free = 0.4491 target = 0.212535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.175579 restraints weight = 7972.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.174848 restraints weight = 15177.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.176485 restraints weight = 12362.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.178550 restraints weight = 7341.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.178917 restraints weight = 6264.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.4131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6941
moved from start:          0.1147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5360  Z= 0.137
  Angle     :  0.651   6.955   7237  Z= 0.326
  Chirality :  0.045   0.155    846
  Planarity :  0.004   0.040    921
  Dihedral  :  7.136 134.912    736
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.86 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 10.82 %
    Favored  : 88.32 %
  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: -0.83 (0.33), residues: 666
  helix:  1.61 (0.31), residues: 311
  sheet: -0.47 (0.67), residues: 70
  loop : -3.26 (0.30), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG Q 225 
 TYR   0.016   0.002   TYR C 247 
 PHE   0.012   0.002   PHE C 362 
 TRP   0.010   0.001   TRP C 435 
 HIS   0.002   0.001   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 5360)
  covalent geometry    : angle       0.65124 ( 7237)
  hydrogen bonds       : bond        0.04829 (  236)
  hydrogen bonds       : angle       4.33852 (  681)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
REVERT: C  190 ARG cc_start: 0.7239 (mmp80) cc_final: 0.6940 (mmp80)
REVERT: C  275 ILE cc_start: 0.9084 (mm) cc_final: 0.8778 (mm)
  outliers start: 5
  outliers final: 5
  residues processed: 83
  average time/residue: 0.0805
  time to fit residues: 8.6557
Evaluate side-chains
  76 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Q residue   67 ASP
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  112 PHE
Chi-restraints excluded: chain C residue  188 ASN
Chi-restraints excluded: chain C residue  459 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 36 optimal weight:    0.2980
   chunk 24 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0980
   chunk 29 optimal weight:    9.9990
   chunk 30 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** C  28 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 = 0.4485 r_free = 0.4485 target = 0.212361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.174202 restraints weight = 8002.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.173980 restraints weight = 14065.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.175365 restraints weight = 12135.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.177853 restraints weight = 7918.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.177865 restraints weight = 6511.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.4123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6955
moved from start:          0.1427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5360  Z= 0.126
  Angle     :  0.628   6.528   7237  Z= 0.315
  Chirality :  0.044   0.147    846
  Planarity :  0.003   0.039    921
  Dihedral  :  7.053 134.855    736
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 14.78 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.77 (0.33), residues: 666
  helix:  1.65 (0.30), residues: 310
  sheet: -0.71 (0.74), residues: 55
  loop : -3.01 (0.30), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Q 225 
 TYR   0.011   0.001   TYR C 247 
 PHE   0.009   0.001   PHE C 185 
 TRP   0.011   0.001   TRP C 435 
 HIS   0.002   0.001   HIS C 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 5360)
  covalent geometry    : angle       0.62818 ( 7237)
  hydrogen bonds       : bond        0.04392 (  236)
  hydrogen bonds       : angle       4.07611 (  681)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Q  187 MET cc_start: 0.7738 (mmt) cc_final: 0.7389 (mmm)
REVERT: C  128 LYS cc_start: 0.8239 (pptt) cc_final: 0.7728 (pptt)
REVERT: C  275 ILE cc_start: 0.8953 (mm) cc_final: 0.8599 (mm)
  outliers start: 10
  outliers final: 6
  residues processed: 83
  average time/residue: 0.0774
  time to fit residues: 8.3222
Evaluate side-chains
  78 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Q residue   67 ASP
Chi-restraints excluded: chain Q residue  166 ILE
Chi-restraints excluded: chain Q residue  168 VAL
Chi-restraints excluded: chain Q residue  195 GLU
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  111 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 58 optimal weight:    7.9990
   chunk 37 optimal weight:    0.0070
   chunk 35 optimal weight:    0.3980
   chunk 18 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 28 optimal weight:    5.9990
   chunk 53 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
C  28 ASN
C 442 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.213014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.178710 restraints weight = 8229.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.181720 restraints weight = 14560.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.181728 restraints weight = 8777.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.183024 restraints weight = 5838.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.182999 restraints weight = 5008.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.4170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6865
moved from start:          0.1707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5360  Z= 0.117
  Angle     :  0.614   6.004   7237  Z= 0.307
  Chirality :  0.043   0.143    846
  Planarity :  0.003   0.038    921
  Dihedral  :  6.972 133.879    736
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.11 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 15.81 %
    Favored  : 81.79 %
  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: -0.68 (0.33), residues: 666
  helix:  1.75 (0.30), residues: 310
  sheet: -0.68 (0.73), residues: 55
  loop : -2.99 (0.31), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG Q 225 
 TYR   0.016   0.002   TYR C 247 
 PHE   0.011   0.001   PHE Q 167 
 TRP   0.014   0.001   TRP C 435 
 HIS   0.002   0.001   HIS C 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 5360)
  covalent geometry    : angle       0.61364 ( 7237)
  hydrogen bonds       : bond        0.04028 (  236)
  hydrogen bonds       : angle       3.97879 (  681)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: Q  187 MET cc_start: 0.7768 (mmt) cc_final: 0.7487 (mmm)
REVERT: C  190 ARG cc_start: 0.7132 (mmp80) cc_final: 0.6817 (mmp80)
REVERT: C  280 GLU cc_start: 0.7361 (tp30) cc_final: 0.7010 (mp0)
REVERT: C  376 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7907 (pt)
REVERT: C  402 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.5809 (tt)
  outliers start: 14
  outliers final: 10
  residues processed: 85
  average time/residue: 0.0688
  time to fit residues: 7.5622
Evaluate side-chains
  85 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Q residue   67 ASP
Chi-restraints excluded: chain Q residue  166 ILE
Chi-restraints excluded: chain Q residue  168 VAL
Chi-restraints excluded: chain Q residue  195 GLU
Chi-restraints excluded: chain Q residue  208 LEU
Chi-restraints excluded: chain C residue   47 MET
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  111 HIS
Chi-restraints excluded: chain C residue  376 LEU
Chi-restraints excluded: chain C residue  402 LEU
Chi-restraints excluded: chain C residue  459 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
C  28 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.211008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.173814 restraints weight = 8403.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.176055 restraints weight = 16176.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.177334 restraints weight = 10380.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.180713 restraints weight = 6369.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.180795 restraints weight = 4236.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.4130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6947
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5360  Z= 0.149
  Angle     :  0.653   7.239   7237  Z= 0.326
  Chirality :  0.045   0.149    846
  Planarity :  0.004   0.042    921
  Dihedral  :  7.049 133.379    736
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.46 %
    Favored  : 90.54 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.84 %
    Favored  : 80.41 %
  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: -0.70 (0.33), residues: 666
  helix:  1.69 (0.30), residues: 312
  sheet: -0.77 (0.73), residues: 56
  loop : -2.96 (0.31), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG Q 225 
 TYR   0.015   0.002   TYR C 274 
 PHE   0.017   0.002   PHE Q 167 
 TRP   0.014   0.002   TRP C 435 
 HIS   0.003   0.001   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 5360)
  covalent geometry    : angle       0.65279 ( 7237)
  hydrogen bonds       : bond        0.04789 (  236)
  hydrogen bonds       : angle       4.05804 (  681)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  128 LYS cc_start: 0.8266 (pptt) cc_final: 0.7636 (pptt)
REVERT: C  376 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7885 (pt)
REVERT: C  402 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.5084 (mt)
  outliers start: 16
  outliers final: 12
  residues processed: 87
  average time/residue: 0.0701
  time to fit residues: 7.9262
Evaluate side-chains
  87 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Q residue   67 ASP
Chi-restraints excluded: chain Q residue  115 VAL
Chi-restraints excluded: chain Q residue  166 ILE
Chi-restraints excluded: chain Q residue  168 VAL
Chi-restraints excluded: chain Q residue  195 GLU
Chi-restraints excluded: chain Q residue  208 LEU
Chi-restraints excluded: chain C residue   47 MET
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  111 HIS
Chi-restraints excluded: chain C residue  188 ASN
Chi-restraints excluded: chain C residue  376 LEU
Chi-restraints excluded: chain C residue  402 LEU
Chi-restraints excluded: chain C residue  459 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 39 optimal weight:    0.0670
   chunk 11 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0370
   chunk 22 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 52 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 26 optimal weight:    9.9990
   overall best weight:    0.4996

-------------------------------------------------------------------------------
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 = 0.4492 r_free = 0.4492 target = 0.213456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.175322 restraints weight = 8398.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.176016 restraints weight = 15062.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.177325 restraints weight = 11963.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.180874 restraints weight = 7373.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.181055 restraints weight = 5090.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.4189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6935
moved from start:          0.1989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5360  Z= 0.115
  Angle     :  0.629   8.899   7237  Z= 0.309
  Chirality :  0.043   0.139    846
  Planarity :  0.003   0.041    921
  Dihedral  :  6.916 132.612    736
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.70 %
    Favored  : 79.55 %
  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: -0.58 (0.33), residues: 666
  helix:  1.79 (0.30), residues: 311
  sheet: -0.52 (0.74), residues: 55
  loop : -2.94 (0.31), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG Q 225 
 TYR   0.020   0.001   TYR C 274 
 PHE   0.010   0.001   PHE Q 167 
 TRP   0.015   0.001   TRP C 435 
 HIS   0.002   0.001   HIS C 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 5360)
  covalent geometry    : angle       0.62924 ( 7237)
  hydrogen bonds       : bond        0.03804 (  236)
  hydrogen bonds       : angle       3.87353 (  681)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  128 LYS cc_start: 0.8281 (pptt) cc_final: 0.7720 (pptt)
REVERT: C  190 ARG cc_start: 0.7124 (mmp80) cc_final: 0.6795 (mmp80)
REVERT: C  280 GLU cc_start: 0.7413 (tp30) cc_final: 0.7128 (mp0)
REVERT: C  376 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7799 (pt)
REVERT: C  402 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.5948 (tt)
  outliers start: 16
  outliers final: 12
  residues processed: 87
  average time/residue: 0.0836
  time to fit residues: 9.6421
Evaluate side-chains
  83 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Q residue  115 VAL
Chi-restraints excluded: chain Q residue  166 ILE
Chi-restraints excluded: chain Q residue  168 VAL
Chi-restraints excluded: chain Q residue  195 GLU
Chi-restraints excluded: chain Q residue  208 LEU
Chi-restraints excluded: chain C residue   47 MET
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  111 HIS
Chi-restraints excluded: chain C residue  376 LEU
Chi-restraints excluded: chain C residue  402 LEU
Chi-restraints excluded: chain C residue  420 HIS
Chi-restraints excluded: chain C residue  459 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 14 optimal weight:    8.9990
   chunk 48 optimal weight:    0.9990
   chunk 15 optimal weight:    0.1980
   chunk 23 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 55 optimal weight:    0.2980
   chunk 22 optimal weight:    0.0040
   overall best weight:    0.4794

-------------------------------------------------------------------------------
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 = 0.4487 r_free = 0.4487 target = 0.213358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.177115 restraints weight = 8341.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.176875 restraints weight = 13851.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.178194 restraints weight = 11503.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.181163 restraints weight = 7516.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.181218 restraints weight = 5690.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6908
moved from start:          0.2069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5360  Z= 0.115
  Angle     :  0.637   9.191   7237  Z= 0.312
  Chirality :  0.043   0.141    846
  Planarity :  0.003   0.040    921
  Dihedral  :  6.861 131.835    736
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 19.24 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.54 (0.34), residues: 666
  helix:  1.85 (0.30), residues: 311
  sheet: -0.62 (0.73), residues: 56
  loop : -2.92 (0.31), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG Q 225 
 TYR   0.018   0.002   TYR C 437 
 PHE   0.011   0.001   PHE C 264 
 TRP   0.016   0.001   TRP C 435 
 HIS   0.002   0.001   HIS C 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 5360)
  covalent geometry    : angle       0.63698 ( 7237)
  hydrogen bonds       : bond        0.03776 (  236)
  hydrogen bonds       : angle       3.83296 (  681)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  128 LYS cc_start: 0.8346 (pptt) cc_final: 0.8117 (pptt)
REVERT: C  280 GLU cc_start: 0.7492 (tp30) cc_final: 0.7155 (mp0)
REVERT: C  376 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7909 (pt)
REVERT: C  402 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.5257 (mt)
  outliers start: 14
  outliers final: 12
  residues processed: 86
  average time/residue: 0.0747
  time to fit residues: 8.6462
Evaluate side-chains
  85 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Q residue  115 VAL
Chi-restraints excluded: chain Q residue  166 ILE
Chi-restraints excluded: chain Q residue  168 VAL
Chi-restraints excluded: chain Q residue  195 GLU
Chi-restraints excluded: chain Q residue  208 LEU
Chi-restraints excluded: chain C residue   47 MET
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  111 HIS
Chi-restraints excluded: chain C residue  376 LEU
Chi-restraints excluded: chain C residue  402 LEU
Chi-restraints excluded: chain C residue  420 HIS
Chi-restraints excluded: chain C residue  459 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 57 optimal weight:   10.0000
   chunk 39 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 42 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 29 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 56 optimal weight:    3.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4475 r_free = 0.4475 target = 0.211706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.173688 restraints weight = 8260.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.172785 restraints weight = 13349.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.173859 restraints weight = 12513.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.177048 restraints weight = 7655.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.177061 restraints weight = 5591.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.4145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7013
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5360  Z= 0.135
  Angle     :  0.673   8.963   7237  Z= 0.329
  Chirality :  0.044   0.147    846
  Planarity :  0.004   0.040    921
  Dihedral  :  6.905 130.761    736
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.16 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 19.76 %
    Favored  : 77.49 %
  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: -0.53 (0.34), residues: 666
  helix:  1.83 (0.31), residues: 312
  sheet: -0.65 (0.73), residues: 56
  loop : -2.90 (0.32), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG Q 225 
 TYR   0.018   0.002   TYR C 437 
 PHE   0.014   0.002   PHE Q 167 
 TRP   0.017   0.001   TRP C 435 
 HIS   0.003   0.001   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 5360)
  covalent geometry    : angle       0.67278 ( 7237)
  hydrogen bonds       : bond        0.04310 (  236)
  hydrogen bonds       : angle       3.92300 (  681)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  128 LYS cc_start: 0.8363 (pptt) cc_final: 0.8085 (pptt)
REVERT: C  190 ARG cc_start: 0.7124 (mmp80) cc_final: 0.6788 (mmp80)
REVERT: C  402 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.5629 (mt)
  outliers start: 16
  outliers final: 12
  residues processed: 89
  average time/residue: 0.0733
  time to fit residues: 8.6436
Evaluate side-chains
  87 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Q residue  115 VAL
Chi-restraints excluded: chain Q residue  166 ILE
Chi-restraints excluded: chain Q residue  168 VAL
Chi-restraints excluded: chain Q residue  195 GLU
Chi-restraints excluded: chain Q residue  208 LEU
Chi-restraints excluded: chain C residue   47 MET
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  111 HIS
Chi-restraints excluded: chain C residue  402 LEU
Chi-restraints excluded: chain C residue  420 HIS
Chi-restraints excluded: chain C residue  459 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 6 optimal weight:    0.0010
   chunk 44 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 0 optimal weight:    0.9990
   chunk 61 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.6590

-------------------------------------------------------------------------------
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 = 0.4474 r_free = 0.4474 target = 0.211909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.173348 restraints weight = 8366.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.174461 restraints weight = 14520.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.175568 restraints weight = 11513.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.178855 restraints weight = 7080.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.179015 restraints weight = 4894.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.4107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6972
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5360  Z= 0.129
  Angle     :  0.676  10.387   7237  Z= 0.329
  Chirality :  0.044   0.143    846
  Planarity :  0.003   0.038    921
  Dihedral  :  6.890 130.158    736
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 20.96 %
    Favored  : 76.63 %
  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: -0.55 (0.34), residues: 666
  helix:  1.86 (0.30), residues: 311
  sheet: -0.24 (0.67), residues: 71
  loop : -3.18 (0.31), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG Q 225 
 TYR   0.021   0.002   TYR C 437 
 PHE   0.012   0.001   PHE Q 167 
 TRP   0.016   0.001   TRP C 435 
 HIS   0.002   0.001   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 5360)
  covalent geometry    : angle       0.67649 ( 7237)
  hydrogen bonds       : bond        0.04080 (  236)
  hydrogen bonds       : angle       3.94141 (  681)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  128 LYS cc_start: 0.8350 (pptt) cc_final: 0.8099 (pptt)
REVERT: C  280 GLU cc_start: 0.7451 (tp30) cc_final: 0.7192 (mp0)
REVERT: C  402 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.5477 (mt)
  outliers start: 14
  outliers final: 12
  residues processed: 82
  average time/residue: 0.0694
  time to fit residues: 7.6750
Evaluate side-chains
  85 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Q residue  115 VAL
Chi-restraints excluded: chain Q residue  166 ILE
Chi-restraints excluded: chain Q residue  168 VAL
Chi-restraints excluded: chain Q residue  195 GLU
Chi-restraints excluded: chain Q residue  208 LEU
Chi-restraints excluded: chain C residue   47 MET
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  111 HIS
Chi-restraints excluded: chain C residue  402 LEU
Chi-restraints excluded: chain C residue  420 HIS
Chi-restraints excluded: chain C residue  459 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 39 optimal weight:    0.3980
   chunk 55 optimal weight:    0.9980
   chunk 40 optimal weight:    5.9990
   chunk 47 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4469 r_free = 0.4469 target = 0.211245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.173515 restraints weight = 8363.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.176912 restraints weight = 15640.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.178003 restraints weight = 9317.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.178259 restraints weight = 6219.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.179060 restraints weight = 5828.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.4119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6945
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5360  Z= 0.135
  Angle     :  0.687  10.109   7237  Z= 0.335
  Chirality :  0.044   0.146    846
  Planarity :  0.003   0.039    921
  Dihedral  :  6.914 129.598    736
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 20.96 %
    Favored  : 76.46 %
  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: -0.57 (0.34), residues: 666
  helix:  1.85 (0.31), residues: 311
  sheet: -0.13 (0.68), residues: 70
  loop : -3.23 (0.31), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG Q 225 
 TYR   0.020   0.002   TYR C 437 
 PHE   0.013   0.002   PHE Q 167 
 TRP   0.016   0.001   TRP C 435 
 HIS   0.003   0.001   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 5360)
  covalent geometry    : angle       0.68707 ( 7237)
  hydrogen bonds       : bond        0.04237 (  236)
  hydrogen bonds       : angle       3.98503 (  681)

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  128 LYS cc_start: 0.8266 (pptt) cc_final: 0.8041 (pptt)
REVERT: C  152 MET cc_start: 0.6712 (mtt) cc_final: 0.6005 (mtt)
REVERT: C  280 GLU cc_start: 0.7485 (tp30) cc_final: 0.7232 (mp0)
REVERT: C  402 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.5505 (mt)
  outliers start: 15
  outliers final: 12
  residues processed: 83
  average time/residue: 0.0515
  time to fit residues: 5.8728
Evaluate side-chains
  88 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Q residue  115 VAL
Chi-restraints excluded: chain Q residue  166 ILE
Chi-restraints excluded: chain Q residue  168 VAL
Chi-restraints excluded: chain Q residue  195 GLU
Chi-restraints excluded: chain Q residue  208 LEU
Chi-restraints excluded: chain C residue   47 MET
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  111 HIS
Chi-restraints excluded: chain C residue  402 LEU
Chi-restraints excluded: chain C residue  420 HIS
Chi-restraints excluded: chain C residue  459 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 50 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 43 optimal weight:    0.4980
   chunk 22 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 28 optimal weight:    8.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4475 r_free = 0.4475 target = 0.212006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.176258 restraints weight = 8417.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.179528 restraints weight = 16469.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.180403 restraints weight = 8754.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.180963 restraints weight = 5910.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.181580 restraints weight = 5621.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.4142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6902
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5360  Z= 0.126
  Angle     :  0.673   9.770   7237  Z= 0.328
  Chirality :  0.044   0.144    846
  Planarity :  0.003   0.038    921
  Dihedral  :  6.763 128.441    736
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 21.48 %
    Favored  : 76.29 %
  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: -0.53 (0.34), residues: 666
  helix:  1.89 (0.30), residues: 311
  sheet: -0.10 (0.68), residues: 70
  loop : -3.21 (0.31), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG Q 225 
 TYR   0.021   0.002   TYR C 437 
 PHE   0.013   0.001   PHE C 264 
 TRP   0.015   0.001   TRP C 435 
 HIS   0.003   0.001   HIS C 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 5360)
  covalent geometry    : angle       0.67271 ( 7237)
  hydrogen bonds       : bond        0.04015 (  236)
  hydrogen bonds       : angle       3.96525 (  681)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 921.68 seconds
wall clock time: 16 minutes 34.21 seconds (994.21 seconds total)