Starting phenix.real_space_refine
on Tue Aug  4 22:46:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9s0r_54418/08_2026/9s0r_54418.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9s0r_54418/08_2026/9s0r_54418.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9s0r_54418/08_2026/9s0r_54418.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9s0r_54418/08_2026/9s0r_54418.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9s0r_54418/08_2026/9s0r_54418.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9s0r_54418/08_2026/9s0r_54418.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    4696      2.51       5
     N    1134      2.21       5
     O    1190      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7062
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 445, 3531
          Classifications: {'peptide': 445}
          Link IDs: {'PTRANS': 8, 'TRANS': 436}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 445, 3531
          Classifications: {'peptide': 445}
          Link IDs: {'PTRANS': 8, 'TRANS': 436}
          Chain breaks: 2
  Time building chain proxies: 1.23, per 1000 atoms: 0.17
  Number of scatterers: 7062
  At special positions: 0
  Unit cell: (89.175, 99.325, 72.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O    1190      8.00
     N    1134      7.00
     C    4696      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: 0.55
  Conformation dependent library (CDL) restraints added in 386.5 milliseconds
  

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1644

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 0 sheets defined
      84.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 74 through 94
      removed outlier: 3.758A  pdb=" N   ILE A  78 " --> pdb=" O   LEU A  74 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   LEU A  90 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   PHE A  91 " --> pdb=" O   THR A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 120
      removed outlier: 3.772A  pdb=" N   ILE A 120 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 177
    Processing helix  chain 'A' and resid 180 through 187
      removed outlier: 3.879A  pdb=" N   PHE A 184 " --> pdb=" O   PRO A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 198
      removed outlier: 3.915A  pdb=" N   ILE A 191 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 241
      removed outlier: 3.521A  pdb=" N   ALA A 213 " --> pdb=" O   GLY A 209 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   TYR A 214 " --> pdb=" O   SER A 210 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   GLY A 218 " --> pdb=" O   TYR A 214 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   THR A 219 " --> pdb=" O   ALA A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 259
    Processing helix  chain 'A' and resid 264 through 275
    Processing helix  chain 'A' and resid 277 through 304
      removed outlier: 3.887A  pdb=" N   ALA A 293 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   ILE A 296 " --> pdb=" O   ASP A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 352
    Processing helix  chain 'A' and resid 353 through 356
    Processing helix  chain 'A' and resid 357 through 379
      removed outlier: 3.987A  pdb=" N   PHE A 373 " --> pdb=" O   SER A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 397
      removed outlier: 3.780A  pdb=" N   ALA A 386 " --> pdb=" O   THR A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 401
    Processing helix  chain 'A' and resid 403 through 436
      removed outlier: 4.011A  pdb=" N   LEU A 433 " --> pdb=" O   MET A 429 " (cutoff:3.500A)
      removed outlier: 4.857A  pdb=" N   PHE A 434 " --> pdb=" O   GLY A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 470
      Proline residue:  A 463  - end of helix
      removed outlier: 3.644A  pdb=" N   LEU A 470 " --> pdb=" O   LEU A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 487
    Processing helix  chain 'A' and resid 491 through 501
      removed outlier: 3.506A  pdb=" N   PHE A 495 " --> pdb=" O   GLY A 491 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   ASP A 501 " --> pdb=" O   LEU A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 528
      removed outlier: 3.671A  pdb=" N   TRP A 523 " --> pdb=" O   PHE A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 528 through 536
    Processing helix  chain 'A' and resid 566 through 578
    Processing helix  chain 'B' and resid 75 through 94
      removed outlier: 3.573A  pdb=" N   TRP B  89 " --> pdb=" O   ILE B  85 " (cutoff:3.500A)
      removed outlier: 4.973A  pdb=" N   LEU B  90 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   PHE B  91 " --> pdb=" O   THR B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 119
    Processing helix  chain 'B' and resid 170 through 177
      removed outlier: 3.916A  pdb=" N   ARG B 174 " --> pdb=" O   ASN B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 186
      removed outlier: 4.391A  pdb=" N   PHE B 184 " --> pdb=" O   PRO B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 198
      removed outlier: 3.869A  pdb=" N   ILE B 191 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 206
      No H-bonds generated for 'chain 'B' and resid 204 through 206'
    Processing helix  chain 'B' and resid 207 through 241
      removed outlier: 4.270A  pdb=" N   THR B 219 " --> pdb=" O   ALA B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 260
    Processing helix  chain 'B' and resid 264 through 275
    Processing helix  chain 'B' and resid 277 through 304
      removed outlier: 3.866A  pdb=" N   ALA B 293 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ILE B 296 " --> pdb=" O   ASP B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 352
      removed outlier: 3.590A  pdb=" N   LYS B 322 " --> pdb=" O   THR B 318 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   THR B 352 " --> pdb=" O   VAL B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 380
      removed outlier: 3.857A  pdb=" N   PHE B 373 " --> pdb=" O   SER B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 397
      removed outlier: 3.560A  pdb=" N   LEU B 388 " --> pdb=" O   VAL B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 398 through 401
    Processing helix  chain 'B' and resid 403 through 436
      removed outlier: 3.913A  pdb=" N   LEU B 433 " --> pdb=" O   MET B 429 " (cutoff:3.500A)
      removed outlier: 4.742A  pdb=" N   PHE B 434 " --> pdb=" O   GLY B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 469
      removed outlier: 3.761A  pdb=" N   PHE B 454 " --> pdb=" O   PHE B 450 " (cutoff:3.500A)
      Proline residue:  B 463  - end of helix
    Processing helix  chain 'B' and resid 477 through 487
    Processing helix  chain 'B' and resid 491 through 501
      removed outlier: 4.584A  pdb=" N   ASP B 501 " --> pdb=" O   LEU B 497 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 528
    Processing helix  chain 'B' and resid 528 through 536
      removed outlier: 3.870A  pdb=" N   SER B 534 " --> pdb=" O   THR B 530 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 577
    Processing helix  chain 'B' and resid 577 through 584

    538 hydrogen bonds defined for protein.
    1605 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: 0.99

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2134
        1.35 -     1.46: 2007
        1.46 -     1.58: 3033
        1.58 -     1.70: 0
        1.70 -     1.82: 74
  Bond restraints: 7248
  Sorted by residual:
  bond pdb=" C   LYS A 579 "
       pdb=" N   PRO A 580 "
    ideal  model  delta    sigma   weight residual
    1.331  1.342 -0.011 7.90e-03 1.60e+04 1.93e+00
  bond pdb=" C   PRO A 189 "
       pdb=" N   PRO A 190 "
    ideal  model  delta    sigma   weight residual
    1.336  1.344 -0.008 1.20e-02 6.94e+03 4.65e-01
  bond pdb=" C   PRO B 189 "
       pdb=" N   PRO B 190 "
    ideal  model  delta    sigma   weight residual
    1.335  1.344 -0.009 1.36e-02 5.41e+03 3.93e-01
  bond pdb=" C   LEU B 188 "
       pdb=" N   PRO B 189 "
    ideal  model  delta    sigma   weight residual
    1.329  1.336 -0.007 1.18e-02 7.18e+03 3.47e-01
  bond pdb=" C   LEU A 188 "
       pdb=" N   PRO A 189 "
    ideal  model  delta    sigma   weight residual
    1.329  1.336 -0.007 1.18e-02 7.18e+03 3.22e-01
  ... (remaining 7243 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 9714
        1.51 -     3.02: 86
        3.02 -     4.53: 19
        4.53 -     6.04: 6
        6.04 -     7.55: 7
  Bond angle restraints: 9832
  Sorted by residual:
  angle pdb=" C   ARG B 355 "
        pdb=" N   GLU B 356 "
        pdb=" CA  GLU B 356 "
      ideal   model   delta    sigma   weight residual
     121.54  127.28   -5.74 1.91e+00 2.74e-01 9.03e+00
  angle pdb=" CB  MET A 230 "
        pdb=" CG  MET A 230 "
        pdb=" SD  MET A 230 "
      ideal   model   delta    sigma   weight residual
     112.70  120.25   -7.55 3.00e+00 1.11e-01 6.34e+00
  angle pdb=" CB  MET B 569 "
        pdb=" CG  MET B 569 "
        pdb=" SD  MET B 569 "
      ideal   model   delta    sigma   weight residual
     112.70  120.12   -7.42 3.00e+00 1.11e-01 6.12e+00
  angle pdb=" CB  MET A 320 "
        pdb=" CG  MET A 320 "
        pdb=" SD  MET A 320 "
      ideal   model   delta    sigma   weight residual
     112.70  119.87   -7.17 3.00e+00 1.11e-01 5.72e+00
  angle pdb=" CB  MET A 569 "
        pdb=" CG  MET A 569 "
        pdb=" SD  MET A 569 "
      ideal   model   delta    sigma   weight residual
     112.70  119.80   -7.10 3.00e+00 1.11e-01 5.60e+00
  ... (remaining 9827 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.35: 3516
       16.35 -    32.71: 457
       32.71 -    49.06: 104
       49.06 -    65.41: 17
       65.41 -    81.76: 8
  Dihedral angle restraints: 4102
    sinusoidal: 1542
      harmonic: 2560
  Sorted by residual:
  dihedral pdb=" CA  HIS B 100 "
           pdb=" C   HIS B 100 "
           pdb=" N   GLU B 101 "
           pdb=" CA  GLU B 101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.66  -18.34     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CG  LYS A  92 "
           pdb=" CD  LYS A  92 "
           pdb=" CE  LYS A  92 "
           pdb=" NZ  LYS A  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    2.46   57.54     3      1.50e+01 4.44e-03 9.44e+00
  dihedral pdb=" CA  GLU B 101 "
           pdb=" CB  GLU B 101 "
           pdb=" CG  GLU B 101 "
           pdb=" CD  GLU B 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.80   56.80     3      1.50e+01 4.44e-03 9.42e+00
  ... (remaining 4099 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 701
       0.026 -    0.053: 297
       0.053 -    0.079: 99
       0.079 -    0.105: 35
       0.105 -    0.132: 10
  Chirality restraints: 1142
  Sorted by residual:
  chirality pdb=" CA  TYR B 462 "
            pdb=" N   TYR B 462 "
            pdb=" C   TYR B 462 "
            pdb=" CB  TYR B 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.34e-01
  chirality pdb=" CA  TYR A 462 "
            pdb=" N   TYR A 462 "
            pdb=" C   TYR A 462 "
            pdb=" CB  TYR A 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.03e-01
  chirality pdb=" CA  ILE B 476 "
            pdb=" N   ILE B 476 "
            pdb=" C   ILE B 476 "
            pdb=" CB  ILE B 476 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.71e-01
  ... (remaining 1139 not shown)

  Planarity restraints: 1200
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 188 "    0.028 5.00e-02 4.00e+02   4.14e-02 2.74e+00
        pdb=" N   PRO A 189 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 189 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 189 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 214 "   -0.008 2.00e-02 2.50e+03   1.64e-02 2.70e+00
        pdb=" C   TYR B 214 "    0.028 2.00e-02 2.50e+03
        pdb=" O   TYR B 214 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ALA B 215 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 521 "    0.006 2.00e-02 2.50e+03   1.20e-02 1.45e+00
        pdb=" C   THR B 521 "   -0.021 2.00e-02 2.50e+03
        pdb=" O   THR B 521 "    0.008 2.00e-02 2.50e+03
        pdb=" N   VAL B 522 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1197 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 842
        2.75 -     3.29: 7034
        3.29 -     3.82: 12511
        3.82 -     4.36: 13638
        4.36 -     4.90: 25114
  Nonbonded interactions: 59139
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 219 "
            pdb=" OD1 ASN A 291 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" OG1 THR B 219 "
            pdb=" OD1 ASN B 291 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OE2 GLU A 287 "
            pdb=" NH1 ARG A 457 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" OH  TYR B 214 "
            pdb=" OG  SER B 465 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   VAL A 348 "
            pdb=" OG1 THR A 352 "
     model   vdw
     2.277 3.040
  ... (remaining 59134 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=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:             3.810
  Set stop_for_unknowns flag:              0.010
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     6.630
  Find NCS groups from input model:        0.080
  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:             0.010
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
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      :  0.002   0.027   7248  Z= 0.113
  Angle     :  0.461   7.553   9832  Z= 0.238
  Chirality :  0.035   0.132   1142
  Planarity :  0.003   0.041   1200
  Dihedral  : 15.612  81.762   2458
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  : 18.98 %
    Favored  : 80.75 %
  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 are not related in a simple way.
  whole:  1.94 (0.28), residues: 878
  helix:  1.94 (0.19), residues: 698
  sheet:  None (None), residues: 0
  loop : -1.39 (0.45), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 472 
 TYR   0.009   0.001   TYR A 231 
 PHE   0.010   0.001   PHE B 373 
 TRP   0.005   0.001   TRP A 565 
 HIS   0.007   0.001   HIS B 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00240 /  0.11 ( 7248)
  covalent geometry    : angle       0.46124 /  0.24 ( 9832)
  hydrogen bonds       : bond        0.11298 /  7.39 (  538)
  hydrogen bonds       : angle       5.07557 /  3.60 ( 1605)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.256 
Fit side-chains
REVERT: A  411 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7976 (mtpt)
REVERT: B  275 GLN cc_start: 0.8073 (mt0) cc_final: 0.7806 (mt0)
REVERT: B  353 LYS cc_start: 0.8342 (mptt) cc_final: 0.7927 (mttp)
REVERT: B  532 MET cc_start: 0.8241 (tpt) cc_final: 0.7965 (tpt)
  outliers start: 2
  outliers final: 2
  residues processed: 98
  average time/residue: 0.0830
  time to fit residues: 11.0421
Evaluate side-chains
  96 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 94
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain B residue  439 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.4980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.4980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 203 HIS
** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.148236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.134772 restraints weight = 9082.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.137867 restraints weight = 4647.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.140130 restraints weight = 2997.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.141668 restraints weight = 2139.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.142493 restraints weight = 1649.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.0624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7248  Z= 0.129
  Angle     :  0.463   6.359   9832  Z= 0.249
  Chirality :  0.036   0.136   1142
  Planarity :  0.003   0.045   1200
  Dihedral  :  3.908  30.548    956
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 16.98 %
    Favored  : 80.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.28), residues: 878
  helix:  1.87 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop : -1.61 (0.46), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 202 
 TYR   0.011   0.001   TYR A 231 
 PHE   0.010   0.001   PHE B 389 
 TRP   0.004   0.001   TRP A 565 
 HIS   0.008   0.001   HIS B 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.13 ( 7248)
  covalent geometry    : angle       0.46314 /  0.25 ( 9832)
  hydrogen bonds       : bond        0.03923 /  2.56 (  538)
  hydrogen bonds       : angle       4.12050 /  2.94 ( 1605)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A  328 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8066 (mp)
REVERT: A  411 LYS cc_start: 0.8227 (mtpt) cc_final: 0.8022 (mtpt)
REVERT: B  353 LYS cc_start: 0.8307 (mptt) cc_final: 0.7947 (mttp)
  outliers start: 16
  outliers final: 13
  residues processed: 121
  average time/residue: 0.0808
  time to fit residues: 13.1913
Evaluate side-chains
  112 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 TRP
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  502 THR
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  301 SER
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  529 THR
Chi-restraints excluded: chain B residue  583 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0370
   chunk 43 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   overall best weight:    0.6258

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 100 HIS ** 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 = 0.3768 r_free = 0.3768 target = 0.153686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.138407 restraints weight = 9243.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.141780 restraints weight = 4839.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.144096 restraints weight = 3161.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.145664 restraints weight = 2322.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.146655 restraints weight = 1841.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.0814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7248  Z= 0.129
  Angle     :  0.467   7.677   9832  Z= 0.250
  Chirality :  0.036   0.137   1142
  Planarity :  0.003   0.044   1200
  Dihedral  :  3.721  16.242    952
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 15.51 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.28), residues: 878
  helix:  1.82 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop : -1.36 (0.48), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 202 
 TYR   0.011   0.001   TYR A 231 
 PHE   0.019   0.001   PHE A 373 
 TRP   0.004   0.001   TRP A 379 
 HIS   0.006   0.001   HIS B 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.13 ( 7248)
  covalent geometry    : angle       0.46722 /  0.25 ( 9832)
  hydrogen bonds       : bond        0.03820 /  2.50 (  538)
  hydrogen bonds       : angle       4.01690 /  2.87 ( 1605)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 105
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A  328 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8027 (mp)
REVERT: A  411 LYS cc_start: 0.8214 (mtpt) cc_final: 0.8005 (mtpt)
REVERT: B  115 VAL cc_start: 0.9020 (OUTLIER) cc_final: 0.8772 (p)
REVERT: B  353 LYS cc_start: 0.8377 (mptt) cc_final: 0.7980 (mttp)
  outliers start: 29
  outliers final: 19
  residues processed: 129
  average time/residue: 0.0822
  time to fit residues: 14.6303
Evaluate side-chains
  125 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   89 TRP
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  502 THR
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  301 SER
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  476 ILE
Chi-restraints excluded: chain B residue  529 THR
Chi-restraints excluded: chain B residue  583 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 87 optimal weight:    0.5980
   chunk 55 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 423 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 = 0.3761 r_free = 0.3761 target = 0.152766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.137480 restraints weight = 9321.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.140785 restraints weight = 4904.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.143180 restraints weight = 3203.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.144743 restraints weight = 2337.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.145744 restraints weight = 1851.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.0928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7248  Z= 0.138
  Angle     :  0.482   6.964   9832  Z= 0.255
  Chirality :  0.037   0.139   1142
  Planarity :  0.003   0.045   1200
  Dihedral  :  3.768  17.933    952
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 16.31 %
    Favored  : 80.35 %
  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 are not related in a simple way.
  whole:  1.72 (0.28), residues: 878
  helix:  1.71 (0.19), residues: 718
  sheet:  None (None), residues: 0
  loop : -1.47 (0.47), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 174 
 TYR   0.012   0.001   TYR A 231 
 PHE   0.018   0.001   PHE A 373 
 TRP   0.003   0.001   TRP A  89 
 HIS   0.009   0.001   HIS B 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.14 ( 7248)
  covalent geometry    : angle       0.48217 /  0.25 ( 9832)
  hydrogen bonds       : bond        0.03851 /  2.52 (  538)
  hydrogen bonds       : angle       3.99970 /  2.86 ( 1605)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  328 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8046 (mp)
REVERT: B  115 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8779 (p)
REVERT: B  263 ASP cc_start: 0.8179 (t0) cc_final: 0.7959 (t0)
REVERT: B  353 LYS cc_start: 0.8364 (mptt) cc_final: 0.7969 (mttp)
  outliers start: 25
  outliers final: 21
  residues processed: 126
  average time/residue: 0.0708
  time to fit residues: 12.4313
Evaluate side-chains
  126 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   89 TRP
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  502 THR
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  301 SER
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  418 ASN
Chi-restraints excluded: chain B residue  476 ILE
Chi-restraints excluded: chain B residue  529 THR
Chi-restraints excluded: chain B residue  583 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    1.0786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 423 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 = 0.3709 r_free = 0.3709 target = 0.148186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.133862 restraints weight = 9340.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.137118 restraints weight = 4878.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.139311 restraints weight = 3148.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.140503 restraints weight = 2301.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.141662 restraints weight = 1875.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.1127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7248  Z= 0.181
  Angle     :  0.526   6.466   9832  Z= 0.277
  Chirality :  0.039   0.154   1142
  Planarity :  0.003   0.046   1200
  Dihedral  :  3.905  18.733    952
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 16.04 %
    Favored  : 79.81 %
  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 are not related in a simple way.
  whole:  1.59 (0.28), residues: 878
  helix:  1.64 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop : -1.41 (0.48), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 202 
 TYR   0.015   0.001   TYR A 231 
 PHE   0.017   0.001   PHE A 373 
 TRP   0.004   0.001   TRP B 379 
 HIS   0.006   0.001   HIS B 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00415 /  0.18 ( 7248)
  covalent geometry    : angle       0.52585 /  0.28 ( 9832)
  hydrogen bonds       : bond        0.04165 /  2.72 (  538)
  hydrogen bonds       : angle       4.09237 /  2.93 ( 1605)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 102
  time to evaluate  : 0.233 
Fit side-chains
REVERT: A  328 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8122 (mp)
REVERT: A  571 TYR cc_start: 0.6273 (OUTLIER) cc_final: 0.4887 (t80)
REVERT: B  115 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8871 (p)
REVERT: B  263 ASP cc_start: 0.8273 (t0) cc_final: 0.7972 (t0)
REVERT: B  353 LYS cc_start: 0.8395 (mptt) cc_final: 0.7995 (mttp)
  outliers start: 31
  outliers final: 22
  residues processed: 127
  average time/residue: 0.0738
  time to fit residues: 12.9184
Evaluate side-chains
  126 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  258 ILE
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  502 THR
Chi-restraints excluded: chain A residue  571 TYR
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  301 SER
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  418 ASN
Chi-restraints excluded: chain B residue  476 ILE
Chi-restraints excluded: chain B residue  529 THR
Chi-restraints excluded: chain B residue  583 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 73 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 423 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 = 0.3730 r_free = 0.3730 target = 0.149871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.135338 restraints weight = 9321.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.138656 restraints weight = 4809.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.140977 restraints weight = 3076.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.142458 restraints weight = 2221.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.143568 restraints weight = 1742.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.1113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7248  Z= 0.140
  Angle     :  0.492   6.360   9832  Z= 0.258
  Chirality :  0.037   0.139   1142
  Planarity :  0.003   0.045   1200
  Dihedral  :  3.844  18.127    952
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 16.44 %
    Favored  : 79.95 %
  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 are not related in a simple way.
  whole:  1.64 (0.28), residues: 878
  helix:  1.69 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop : -1.42 (0.48), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 202 
 TYR   0.013   0.001   TYR A 231 
 PHE   0.015   0.001   PHE A 373 
 TRP   0.003   0.001   TRP A  89 
 HIS   0.006   0.001   HIS B 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.14 ( 7248)
  covalent geometry    : angle       0.49226 /  0.26 ( 9832)
  hydrogen bonds       : bond        0.03905 /  2.55 (  538)
  hydrogen bonds       : angle       4.02686 /  2.88 ( 1605)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A  203 HIS cc_start: 0.6821 (m-70) cc_final: 0.6530 (m170)
REVERT: A  328 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8066 (mp)
REVERT: A  571 TYR cc_start: 0.6239 (OUTLIER) cc_final: 0.4862 (t80)
REVERT: B  115 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8816 (p)
REVERT: B  263 ASP cc_start: 0.8262 (t0) cc_final: 0.7904 (t0)
REVERT: B  353 LYS cc_start: 0.8370 (mptt) cc_final: 0.7953 (mttp)
  outliers start: 27
  outliers final: 23
  residues processed: 127
  average time/residue: 0.0730
  time to fit residues: 12.8396
Evaluate side-chains
  130 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   89 TRP
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  502 THR
Chi-restraints excluded: chain A residue  571 TYR
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  301 SER
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  418 ASN
Chi-restraints excluded: chain B residue  476 ILE
Chi-restraints excluded: chain B residue  529 THR
Chi-restraints excluded: chain B residue  539 ARG
Chi-restraints excluded: chain B residue  583 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0770
   chunk 40 optimal weight:    0.9980
   chunk 77 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 75 optimal weight:    0.5980
   chunk 46 optimal weight:    0.6980
   chunk 54 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.5138

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 423 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 = 0.3747 r_free = 0.3747 target = 0.151369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.136969 restraints weight = 9212.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.140234 restraints weight = 4746.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.142501 restraints weight = 3042.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.143992 restraints weight = 2205.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.145124 restraints weight = 1731.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.1092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7248  Z= 0.119
  Angle     :  0.479   6.882   9832  Z= 0.250
  Chirality :  0.036   0.134   1142
  Planarity :  0.003   0.044   1200
  Dihedral  :  3.759  17.797    952
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 18.05 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.28), residues: 878
  helix:  1.78 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop : -1.64 (0.46), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 117 
 TYR   0.011   0.001   TYR B 118 
 PHE   0.024   0.001   PHE A 373 
 TRP   0.004   0.001   TRP A  89 
 HIS   0.006   0.001   HIS B 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.12 ( 7248)
  covalent geometry    : angle       0.47942 /  0.25 ( 9832)
  hydrogen bonds       : bond        0.03719 /  2.42 (  538)
  hydrogen bonds       : angle       3.96295 /  2.83 ( 1605)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A  203 HIS cc_start: 0.6725 (m-70) cc_final: 0.6496 (m170)
REVERT: A  571 TYR cc_start: 0.6211 (OUTLIER) cc_final: 0.4847 (t80)
REVERT: B  115 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8772 (p)
REVERT: B  263 ASP cc_start: 0.8229 (t0) cc_final: 0.7881 (t0)
REVERT: B  353 LYS cc_start: 0.8344 (mptt) cc_final: 0.7910 (mttp)
  outliers start: 21
  outliers final: 18
  residues processed: 124
  average time/residue: 0.0726
  time to fit residues: 12.6624
Evaluate side-chains
  121 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue   89 TRP
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  502 THR
Chi-restraints excluded: chain A residue  571 TYR
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  301 SER
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  418 ASN
Chi-restraints excluded: chain B residue  529 THR
Chi-restraints excluded: chain B residue  539 ARG
Chi-restraints excluded: chain B residue  583 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 86 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 481 GLN
B 313 HIS
B 423 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.149892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.135436 restraints weight = 9250.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.138669 restraints weight = 4760.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.140987 restraints weight = 3055.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.142471 restraints weight = 2206.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.143514 restraints weight = 1729.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.1152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7248  Z= 0.146
  Angle     :  0.508   6.972   9832  Z= 0.264
  Chirality :  0.037   0.144   1142
  Planarity :  0.003   0.045   1200
  Dihedral  :  3.807  18.081    952
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 18.05 %
    Favored  : 78.48 %
  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 are not related in a simple way.
  whole:  1.64 (0.28), residues: 878
  helix:  1.74 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop : -1.66 (0.46), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 202 
 TYR   0.013   0.001   TYR A 231 
 PHE   0.020   0.001   PHE A 373 
 TRP   0.004   0.001   TRP B 523 
 HIS   0.006   0.001   HIS B 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.15 ( 7248)
  covalent geometry    : angle       0.50829 /  0.26 ( 9832)
  hydrogen bonds       : bond        0.03905 /  2.55 (  538)
  hydrogen bonds       : angle       3.98718 /  2.85 ( 1605)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A  328 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8078 (mp)
REVERT: A  571 TYR cc_start: 0.6262 (OUTLIER) cc_final: 0.4888 (t80)
REVERT: B  115 VAL cc_start: 0.9061 (OUTLIER) cc_final: 0.8812 (p)
REVERT: B  353 LYS cc_start: 0.8382 (mptt) cc_final: 0.7972 (mttp)
  outliers start: 26
  outliers final: 21
  residues processed: 123
  average time/residue: 0.0790
  time to fit residues: 13.5442
Evaluate side-chains
  124 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   89 TRP
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  235 THR
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  502 THR
Chi-restraints excluded: chain A residue  571 TYR
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  301 SER
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  418 ASN
Chi-restraints excluded: chain B residue  476 ILE
Chi-restraints excluded: chain B residue  529 THR
Chi-restraints excluded: chain B residue  539 ARG
Chi-restraints excluded: chain B residue  583 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 17 optimal weight:    0.3980
   chunk 81 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 77 optimal weight:    0.5980
   chunk 52 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 75 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 203 HIS
** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 313 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.152822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.137425 restraints weight = 9351.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.140766 restraints weight = 4930.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.143137 restraints weight = 3215.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.144756 restraints weight = 2360.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.145877 restraints weight = 1855.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.1144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7248  Z= 0.134
  Angle     :  0.503   7.576   9832  Z= 0.261
  Chirality :  0.037   0.141   1142
  Planarity :  0.003   0.044   1200
  Dihedral  :  3.787  19.330    952
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 18.05 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.75 (0.28), residues: 878
  helix:  1.76 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop : -1.38 (0.48), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 202 
 TYR   0.012   0.001   TYR A 231 
 PHE   0.019   0.001   PHE A 373 
 TRP   0.004   0.001   TRP A  89 
 HIS   0.012   0.001   HIS B 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.13 ( 7248)
  covalent geometry    : angle       0.50257 /  0.26 ( 9832)
  hydrogen bonds       : bond        0.03827 /  2.50 (  538)
  hydrogen bonds       : angle       3.96133 /  2.83 ( 1605)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A  328 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8060 (mp)
REVERT: A  571 TYR cc_start: 0.6234 (OUTLIER) cc_final: 0.4846 (t80)
REVERT: B  100 HIS cc_start: 0.6375 (p-80) cc_final: 0.4747 (m170)
REVERT: B  115 VAL cc_start: 0.9059 (OUTLIER) cc_final: 0.8806 (p)
REVERT: B  353 LYS cc_start: 0.8374 (mptt) cc_final: 0.7950 (mttp)
  outliers start: 25
  outliers final: 21
  residues processed: 123
  average time/residue: 0.0796
  time to fit residues: 13.6350
Evaluate side-chains
  123 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue   89 TRP
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  502 THR
Chi-restraints excluded: chain A residue  571 TYR
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  301 SER
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  404 THR
Chi-restraints excluded: chain B residue  418 ASN
Chi-restraints excluded: chain B residue  529 THR
Chi-restraints excluded: chain B residue  539 ARG
Chi-restraints excluded: chain B residue  583 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 83 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 78 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 313 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.152741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.137271 restraints weight = 9329.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.140603 restraints weight = 4931.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.143001 restraints weight = 3223.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.144564 restraints weight = 2366.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.145668 restraints weight = 1878.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.1176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7248  Z= 0.138
  Angle     :  0.514   8.049   9832  Z= 0.264
  Chirality :  0.037   0.141   1142
  Planarity :  0.003   0.045   1200
  Dihedral  :  3.802  20.083    952
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 18.18 %
    Favored  : 78.48 %
  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 are not related in a simple way.
  whole:  1.67 (0.28), residues: 878
  helix:  1.76 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop : -1.64 (0.46), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 202 
 TYR   0.012   0.001   TYR A 231 
 PHE   0.018   0.001   PHE A 373 
 TRP   0.004   0.001   TRP A  89 
 HIS   0.011   0.001   HIS B 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.14 ( 7248)
  covalent geometry    : angle       0.51430 /  0.26 ( 9832)
  hydrogen bonds       : bond        0.03840 /  2.51 (  538)
  hydrogen bonds       : angle       3.95934 /  2.83 ( 1605)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 100
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  328 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8061 (mp)
REVERT: A  571 TYR cc_start: 0.6215 (OUTLIER) cc_final: 0.4842 (t80)
REVERT: B  115 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8807 (p)
REVERT: B  353 LYS cc_start: 0.8378 (mptt) cc_final: 0.7962 (mttp)
  outliers start: 25
  outliers final: 22
  residues processed: 121
  average time/residue: 0.0767
  time to fit residues: 12.8451
Evaluate side-chains
  125 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 100
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue   89 TRP
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  502 THR
Chi-restraints excluded: chain A residue  571 TYR
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  301 SER
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  332 SER
Chi-restraints excluded: chain B residue  404 THR
Chi-restraints excluded: chain B residue  418 ASN
Chi-restraints excluded: chain B residue  476 ILE
Chi-restraints excluded: chain B residue  529 THR
Chi-restraints excluded: chain B residue  539 ARG
Chi-restraints excluded: chain B residue  583 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 83 optimal weight:    0.7980
   chunk 27 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0770
   overall best weight:    0.6138

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 313 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.153328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.137886 restraints weight = 9313.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.141232 restraints weight = 4918.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.143615 restraints weight = 3213.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.145182 restraints weight = 2362.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.146179 restraints weight = 1868.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7248  Z= 0.129
  Angle     :  0.506   8.075   9832  Z= 0.261
  Chirality :  0.037   0.138   1142
  Planarity :  0.003   0.043   1200
  Dihedral  :  3.775  18.256    952
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 18.72 %
    Favored  : 78.07 %
  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 are not related in a simple way.
  whole:  1.70 (0.28), residues: 878
  helix:  1.77 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop : -1.59 (0.46), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 202 
 TYR   0.012   0.001   TYR A 231 
 PHE   0.027   0.001   PHE A 373 
 TRP   0.004   0.001   TRP A  89 
 HIS   0.015   0.001   HIS B 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.13 ( 7248)
  covalent geometry    : angle       0.50582 /  0.26 ( 9832)
  hydrogen bonds       : bond        0.03778 /  2.47 (  538)
  hydrogen bonds       : angle       3.95428 /  2.82 ( 1605)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1143.47 seconds
wall clock time: 20 minutes 30.52 seconds (1230.52 seconds total)