Starting phenix.real_space_refine
on Wed Jul  1 23:09:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kdf_37134/07_2026/8kdf_37134.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kdf_37134/07_2026/8kdf_37134.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kdf_37134/07_2026/8kdf_37134.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kdf_37134/07_2026/8kdf_37134.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kdf_37134/07_2026/8kdf_37134.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kdf_37134/07_2026/8kdf_37134.cif"
  }
  resolution = 3.89
  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=   0.002 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      22      5.16       5
     Cl      2      4.86       5
     C    2730      2.51       5
     N     619      2.21       5
     O     671      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4045
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 409
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 409
          Classifications: {'peptide': 52}
          Link IDs: {'PTRANS': 2, 'TRANS': 49}
    Chain: "B"
      Number of atoms: 3513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 455, 3513
          Classifications: {'peptide': 455}
          Link IDs: {'PTRANS': 23, 'TRANS': 431}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 123
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 123
          Unusual residues: {'CLR': 2, 'LBN': 1, 'VRW': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'LBN:plan-3': 1}
          Unresolved non-hydrogen planarities: 2
  Time building chain proxies: 1.12, per 1000 atoms: 0.28
  Number of scatterers: 4045
  At special positions: 0
  Unit cell: (75.1905, 87.4665, 81.3285, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      2     17.00
     S      22     16.00
     P       1     15.00
     O     671      8.00
     N     619      7.00
     C    2730      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 210 " - pdb=" SG  CYS B 164 " distance=2.13

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.40
  Conformation dependent library (CDL) restraints added in 145.5 milliseconds
  

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  932

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 0 sheets defined
      84.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 165 through 174
      removed outlier: 4.211A  pdb=" N   VAL A 172 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLY A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 206
    Processing helix  chain 'B' and resid 51 through 65
      removed outlier: 3.858A  pdb=" N   THR B  62 " --> pdb=" O   ILE B  58 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   GLY B  65 " --> pdb=" O   GLY B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 71 through 80
      removed outlier: 3.854A  pdb=" N   VAL B  75 " --> pdb=" O   THR B  71 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLU B  78 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 110
      removed outlier: 3.509A  pdb=" N   CYS B 102 " --> pdb=" O   VAL B  98 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   THR B 108 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 125
      removed outlier: 3.931A  pdb=" N   VAL B 123 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 139
      removed outlier: 3.687A  pdb=" N   ILE B 135 " --> pdb=" O   LEU B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 158
    Processing helix  chain 'B' and resid 159 through 161
      No H-bonds generated for 'chain 'B' and resid 159 through 161'
    Processing helix  chain 'B' and resid 167 through 189
      removed outlier: 4.020A  pdb=" N   LEU B 173 " --> pdb=" O   GLU B 169 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   CYS B 178 " --> pdb=" O   VAL B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 221
    Processing helix  chain 'B' and resid 239 through 252
      removed outlier: 4.047A  pdb=" N   LEU B 245 " --> pdb=" O   GLY B 241 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   PHE B 252 " --> pdb=" O   TYR B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 255
      No H-bonds generated for 'chain 'B' and resid 253 through 255'
    Processing helix  chain 'B' and resid 258 through 267
      removed outlier: 5.791A  pdb=" N   GLU B 265 " --> pdb=" O   PHE B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 280
      Proline residue:  B 275  - end of helix
      removed outlier: 3.556A  pdb=" N   ILE B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 298
    Processing helix  chain 'B' and resid 301 through 306
    Processing helix  chain 'B' and resid 310 through 321
      removed outlier: 3.667A  pdb=" N   ASP B 314 " --> pdb=" O   ALA B 310 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLY B 321 " --> pdb=" O   ASN B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 324
      No H-bonds generated for 'chain 'B' and resid 322 through 324'
    Processing helix  chain 'B' and resid 325 through 356
      removed outlier: 3.635A  pdb=" N   SER B 338 " --> pdb=" O   SER B 334 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ARG B 348 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 365
    Processing helix  chain 'B' and resid 373 through 386
    Processing helix  chain 'B' and resid 393 through 399
      removed outlier: 3.781A  pdb=" N   ILE B 397 " --> pdb=" O   ILE B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 422
      removed outlier: 4.128A  pdb=" N   ASN B 404 " --> pdb=" O   PHE B 400 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   TRP B 405 " --> pdb=" O   SER B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 454
      removed outlier: 3.566A  pdb=" N   ALA B 448 " --> pdb=" O   LEU B 444 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   THR B 454 " --> pdb=" O   SER B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 466
      removed outlier: 3.525A  pdb=" N   LEU B 466 " --> pdb=" O   PHE B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 476
      removed outlier: 3.774A  pdb=" N   VAL B 471 " --> pdb=" O   SER B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 501
      removed outlier: 4.109A  pdb=" N   GLY B 488 " --> pdb=" O   TRP B 484 " (cutoff:3.500A)

    287 hydrogen bonds defined for protein.
    828 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: 0.38

  Time building geometry restraints manager: 0.50 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 734
        1.33 -     1.46: 1346
        1.46 -     1.59: 2041
        1.59 -     1.73: 3
        1.73 -     1.86: 32
  Bond restraints: 4156
  Sorted by residual:
  bond pdb=" CG  HIS B 367 "
       pdb=" CD2 HIS B 367 "
    ideal  model  delta    sigma   weight residual
    1.354  1.312  0.042 1.10e-02 8.26e+03 1.46e+01
  bond pdb=" CG  HIS B 358 "
       pdb=" CD2 HIS B 358 "
    ideal  model  delta    sigma   weight residual
    1.354  1.317  0.037 1.10e-02 8.26e+03 1.16e+01
  bond pdb=" C   SER B 342 "
       pdb=" O   SER B 342 "
    ideal  model  delta    sigma   weight residual
    1.237  1.199  0.038 1.16e-02 7.43e+03 1.06e+01
  bond pdb=" C31 LBN B 603 "
       pdb=" C32 LBN B 603 "
    ideal  model  delta    sigma   weight residual
    1.523  1.586 -0.063 2.00e-02 2.50e+03 1.01e+01
  bond pdb=" CA  SER B 376 "
       pdb=" CB  SER B 376 "
    ideal  model  delta    sigma   weight residual
    1.528  1.481  0.047 1.59e-02 3.96e+03 8.83e+00
  ... (remaining 4151 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 4170
        1.76 -     3.52: 1250
        3.52 -     5.28: 222
        5.28 -     7.03: 32
        7.03 -     8.79: 9
  Bond angle restraints: 5683
  Sorted by residual:
  angle pdb=" CA  PHE B 262 "
        pdb=" CB  PHE B 262 "
        pdb=" CG  PHE B 262 "
      ideal   model   delta    sigma   weight residual
     113.80  119.20   -5.40 1.00e+00 1.00e+00 2.92e+01
  angle pdb=" C   PHE B 336 "
        pdb=" N   GLY B 337 "
        pdb=" CA  GLY B 337 "
      ideal   model   delta    sigma   weight residual
     120.03  126.08   -6.05 1.12e+00 7.97e-01 2.92e+01
  angle pdb=" C   CYS A 210 "
        pdb=" N   ARG A 211 "
        pdb=" CA  ARG A 211 "
      ideal   model   delta    sigma   weight residual
     121.05  128.56   -7.51 1.43e+00 4.89e-01 2.76e+01
  angle pdb=" CA  PHE B 399 "
        pdb=" CB  PHE B 399 "
        pdb=" CG  PHE B 399 "
      ideal   model   delta    sigma   weight residual
     113.80  118.57   -4.77 1.00e+00 1.00e+00 2.27e+01
  angle pdb=" CA  PHE B 200 "
        pdb=" CB  PHE B 200 "
        pdb=" CG  PHE B 200 "
      ideal   model   delta    sigma   weight residual
     113.80  109.20    4.60 1.00e+00 1.00e+00 2.11e+01
  ... (remaining 5678 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.92: 2434
       28.92 -    57.84: 56
       57.84 -    86.77: 5
       86.77 -   115.69: 1
      115.69 -   144.61: 1
  Dihedral angle restraints: 2497
    sinusoidal: 1045
      harmonic: 1452
  Sorted by residual:
  dihedral pdb=" CA  ARG A 209 "
           pdb=" C   ARG A 209 "
           pdb=" N   CYS A 210 "
           pdb=" CA  CYS A 210 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.57  -23.43     0      5.00e+00 4.00e-02 2.20e+01
  dihedral pdb=" C1  LBN B 603 "
           pdb=" O1  LBN B 603 "
           pdb=" P1  LBN B 603 "
           pdb=" O3  LBN B 603 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -84.60   60.01 -144.61     1      3.00e+01 1.11e-03 1.94e+01
  dihedral pdb=" CA  GLY B 125 "
           pdb=" C   GLY B 125 "
           pdb=" N   SER B 126 "
           pdb=" CA  SER B 126 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.38  -21.62     0      5.00e+00 4.00e-02 1.87e+01
  ... (remaining 2494 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 378
       0.062 -    0.124: 214
       0.124 -    0.186: 70
       0.186 -    0.247: 15
       0.247 -    0.309: 5
  Chirality restraints: 682
  Sorted by residual:
  chirality pdb=" CA  THR B 154 "
            pdb=" N   THR B 154 "
            pdb=" C   THR B 154 "
            pdb=" CB  THR B 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.22    0.31 2.00e-01 2.50e+01 2.39e+00
  chirality pdb=" CA  PHE B 200 "
            pdb=" N   PHE B 200 "
            pdb=" C   PHE B 200 "
            pdb=" CB  PHE B 200 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.10e+00
  chirality pdb=" CA  THR B 194 "
            pdb=" N   THR B 194 "
            pdb=" C   THR B 194 "
            pdb=" CB  THR B 194 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.24    0.29 2.00e-01 2.50e+01 2.08e+00
  ... (remaining 679 not shown)

  Planarity restraints: 665
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 248 "    0.047 2.00e-02 2.50e+03   2.41e-02 1.17e+01
        pdb=" CG  TYR B 248 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 248 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 248 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 248 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 248 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 248 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B 248 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 387 "    0.043 2.00e-02 2.50e+03   2.39e-02 1.14e+01
        pdb=" CG  TYR B 387 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 387 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 387 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 387 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 387 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 387 "    0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR B 387 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 193 "   -0.038 2.00e-02 2.50e+03   1.86e-02 8.65e+00
        pdb=" CG  TRP A 193 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 193 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 193 "    0.021 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 193 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 193 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 193 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 193 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 193 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 193 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 662 not shown)

  Histogram of nonbonded interaction distances:
        2.49 -     2.97: 1834
        2.97 -     3.45: 4355
        3.45 -     3.94: 6718
        3.94 -     4.42: 7457
        4.42 -     4.90: 12361
  Nonbonded interactions: 32725
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 103 "
            pdb=" OD1 ASP B 116 "
     model   vdw
     2.490 3.040
  nonbonded pdb=" N2  VRW B 604 "
            pdb=" O3  VRW B 604 "
     model   vdw
     2.542 2.496
  nonbonded pdb=" O   GLY B 255 "
            pdb=" N2  VRW B 604 "
     model   vdw
     2.557 3.120
  nonbonded pdb=" OD1 ASN B 317 "
            pdb=" OG  SER B 324 "
     model   vdw
     2.563 3.040
  nonbonded pdb=" OG  SER B 390 "
            pdb=" O   ASP B 392 "
     model   vdw
     2.598 3.040
  ... (remaining 32720 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.900
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7100
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      :  0.017   0.784   4158  Z= 1.412
  Angle     :  1.711  11.566   5685  Z= 1.128
  Chirality :  0.085   0.309    682
  Planarity :  0.009   0.084    665
  Dihedral  : 13.219 144.611   1562
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  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: -2.39 (0.31), residues: 501
  helix: -1.57 (0.21), residues: 373
  sheet:  None (None), residues: 0
  loop : -0.95 (0.52), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 211 
 TYR   0.049   0.007   TYR B 387 
 PHE   0.017   0.004   PHE B 350 
 TRP   0.038   0.005   TRP A 193 
 HIS   0.005   0.001   HIS B 358 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01138 /  0.71 ( 4156)
  covalent geometry    : angle       1.70400 /  1.13 ( 5683)
  SS BOND              : bond        0.09781 /  5.15 (    1)
  SS BOND              : angle       8.25482 /  3.78 (    2)
  hydrogen bonds       : bond        0.17629 / 11.80 (  287)
  hydrogen bonds       : angle       7.26109 /  5.50 (  828)
  Misc. bond           : bond        0.78429 / 41.28 (    1)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 TRP cc_start: 0.6879 (m100) cc_final: 0.6312 (m100)
REVERT: B   81 SER cc_start: 0.8396 (t) cc_final: 0.7981 (p)
REVERT: B  168 GLU cc_start: 0.7450 (mp0) cc_final: 0.7249 (tm-30)
REVERT: B  195 ARG cc_start: 0.7256 (mtp85) cc_final: 0.6527 (tpt170)
REVERT: B  267 MET cc_start: 0.8208 (mmm) cc_final: 0.7955 (mmm)
REVERT: B  280 ILE cc_start: 0.8056 (mm) cc_final: 0.7787 (tt)
REVERT: B  309 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7932 (pm20)
REVERT: B  365 MET cc_start: 0.8423 (mmt) cc_final: 0.7395 (mmt)
REVERT: B  443 CYS cc_start: 0.6841 (m) cc_final: 0.6431 (t)
REVERT: B  447 ILE cc_start: 0.7165 (mt) cc_final: 0.6659 (mt)
REVERT: B  452 TRP cc_start: 0.6442 (t60) cc_final: 0.6073 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.0711
  time to fit residues: 13.1787
Evaluate side-chains
  101 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0270
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.3980
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.6438

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  54 ASN
B 145 GLN
B 273 ASN
B 367 HIS
B 487 GLN
B 497 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.116580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.091665 restraints weight = 5937.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.094309 restraints weight = 3918.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.095671 restraints weight = 3000.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.097215 restraints weight = 2582.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.097637 restraints weight = 2275.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.2749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4158  Z= 0.136
  Angle     :  0.636   6.813   5685  Z= 0.325
  Chirality :  0.044   0.150    682
  Planarity :  0.005   0.032    665
  Dihedral  : 10.011 127.820    706
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 13.62 %
    Favored  : 82.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.37), residues: 501
  helix:  1.08 (0.25), residues: 380
  sheet:  None (None), residues: 0
  loop :  0.00 (0.62), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 427 
 TYR   0.012   0.002   TYR B 155 
 PHE   0.013   0.001   PHE B 200 
 TRP   0.018   0.001   TRP A 193 
 HIS   0.004   0.001   HIS B 319 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.14 ( 4156)
  covalent geometry    : angle       0.63512 /  0.32 ( 5683)
  SS BOND              : bond        0.00051 /  0.03 (    1)
  SS BOND              : angle       2.04599 /  0.96 (    2)
  hydrogen bonds       : bond        0.04564 /  3.04 (  287)
  hydrogen bonds       : angle       4.32050 /  3.27 (  828)
  Misc. bond           : bond        0.00010 /  0.01 (    1)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 TRP cc_start: 0.8346 (m100) cc_final: 0.8136 (m100)
REVERT: B  219 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7308 (mt)
REVERT: B  254 TYR cc_start: 0.8358 (m-80) cc_final: 0.7979 (m-80)
REVERT: B  365 MET cc_start: 0.8533 (mmt) cc_final: 0.7070 (mmt)
REVERT: B  391 LYS cc_start: 0.7784 (tptt) cc_final: 0.7203 (mptt)
REVERT: B  487 GLN cc_start: 0.8331 (tp40) cc_final: 0.7898 (tp-100)
  outliers start: 16
  outliers final: 8
  residues processed: 133
  average time/residue: 0.0593
  time to fit residues: 10.1317
Evaluate side-chains
  107 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  361 SER
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  467 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 30 optimal weight:    5.9990
   chunk 45 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 497 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.131515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.104211 restraints weight = 5568.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.107604 restraints weight = 3391.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.109741 restraints weight = 2487.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.111410 restraints weight = 2050.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.112154 restraints weight = 1796.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.3465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   4158  Z= 0.141
  Angle     :  0.607   7.471   5685  Z= 0.301
  Chirality :  0.043   0.165    682
  Planarity :  0.004   0.036    665
  Dihedral  :  9.023 109.498    706
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 17.37 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.84 (0.37), residues: 501
  helix:  1.62 (0.25), residues: 384
  sheet:  None (None), residues: 0
  loop :  0.05 (0.62), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 419 
 TYR   0.017   0.001   TYR B 124 
 PHE   0.016   0.001   PHE B 200 
 TRP   0.012   0.001   TRP A 193 
 HIS   0.003   0.001   HIS B 319 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.14 ( 4156)
  covalent geometry    : angle       0.60657 /  0.30 ( 5683)
  SS BOND              : bond        0.00265 /  0.14 (    1)
  SS BOND              : angle       1.44171 /  0.68 (    2)
  hydrogen bonds       : bond        0.04145 /  2.80 (  287)
  hydrogen bonds       : angle       4.03834 /  3.03 (  828)
  Misc. bond           : bond        0.00024 /  0.01 (    1)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 GLU cc_start: 0.7206 (tm-30) cc_final: 0.6810 (tt0)
REVERT: B  254 TYR cc_start: 0.8384 (m-80) cc_final: 0.7985 (m-80)
REVERT: B  361 SER cc_start: 0.8421 (OUTLIER) cc_final: 0.7814 (t)
REVERT: B  391 LYS cc_start: 0.7963 (tptt) cc_final: 0.7295 (mptt)
REVERT: B  487 GLN cc_start: 0.8584 (tp40) cc_final: 0.8187 (tp-100)
  outliers start: 17
  outliers final: 10
  residues processed: 99
  average time/residue: 0.0529
  time to fit residues: 7.0507
Evaluate side-chains
  96 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  305 MET
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  361 SER
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  467 SER
Chi-restraints excluded: chain B residue  499 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 39 optimal weight:    8.9990
   chunk 30 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    1.5186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 186 ASN
B 497 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.114556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.089793 restraints weight = 5786.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.092209 restraints weight = 3910.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.093880 restraints weight = 3037.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.095072 restraints weight = 2559.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.095371 restraints weight = 2281.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.3814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4158  Z= 0.140
  Angle     :  0.595   9.993   5685  Z= 0.290
  Chirality :  0.042   0.162    682
  Planarity :  0.004   0.038    665
  Dihedral  :  8.446  86.167    706
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 16.67 %
    Favored  : 78.40 %
  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:  2.12 (0.37), residues: 501
  helix:  1.82 (0.26), residues: 389
  sheet:  None (None), residues: 0
  loop :  0.05 (0.63), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 419 
 TYR   0.016   0.001   TYR B 124 
 PHE   0.013   0.001   PHE B 336 
 TRP   0.010   0.001   TRP A 193 
 HIS   0.003   0.001   HIS B 319 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.14 ( 4156)
  covalent geometry    : angle       0.59467 /  0.29 ( 5683)
  SS BOND              : bond        0.00259 /  0.14 (    1)
  SS BOND              : angle       1.41526 /  0.66 (    2)
  hydrogen bonds       : bond        0.03949 /  2.68 (  287)
  hydrogen bonds       : angle       3.92347 /  2.94 (  828)
  Misc. bond           : bond        0.00009 /  0.00 (    1)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7198 (tm-30)
REVERT: B  254 TYR cc_start: 0.8381 (m-80) cc_final: 0.8036 (m-80)
REVERT: B  361 SER cc_start: 0.8428 (OUTLIER) cc_final: 0.7729 (t)
REVERT: B  365 MET cc_start: 0.8390 (mmt) cc_final: 0.6963 (mmt)
REVERT: B  369 GLN cc_start: 0.8499 (mp10) cc_final: 0.7957 (mp10)
REVERT: B  391 LYS cc_start: 0.7699 (tptt) cc_final: 0.7020 (mptt)
REVERT: B  487 GLN cc_start: 0.8647 (tp40) cc_final: 0.8192 (tp-100)
REVERT: B  501 GLN cc_start: 0.8333 (tt0) cc_final: 0.8105 (tt0)
  outliers start: 21
  outliers final: 15
  residues processed: 103
  average time/residue: 0.0493
  time to fit residues: 6.8212
Evaluate side-chains
  100 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  187 CYS
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  361 SER
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  425 LEU
Chi-restraints excluded: chain B residue  454 THR
Chi-restraints excluded: chain B residue  467 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 40 optimal weight:    7.9990
   chunk 17 optimal weight:    8.9990
   chunk 12 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 47 optimal weight:    9.9990
   chunk 33 optimal weight:    0.8980
   chunk 31 optimal weight:    7.9990
   overall best weight:    0.8982

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.115880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.091787 restraints weight = 5824.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.094220 restraints weight = 3877.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.095964 restraints weight = 2977.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.097011 restraints weight = 2506.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.097635 restraints weight = 2237.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.4060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4158  Z= 0.115
  Angle     :  0.575   7.461   5685  Z= 0.275
  Chirality :  0.040   0.157    682
  Planarity :  0.004   0.037    665
  Dihedral  :  8.164  70.209    706
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 17.37 %
    Favored  : 77.70 %
  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:  2.46 (0.38), residues: 501
  helix:  2.12 (0.26), residues: 388
  sheet:  None (None), residues: 0
  loop : -0.02 (0.63), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 348 
 TYR   0.010   0.001   TYR B 248 
 PHE   0.020   0.001   PHE B 474 
 TRP   0.009   0.001   TRP A 193 
 HIS   0.003   0.001   HIS B 319 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.12 ( 4156)
  covalent geometry    : angle       0.57517 /  0.28 ( 5683)
  SS BOND              : bond        0.00155 /  0.08 (    1)
  SS BOND              : angle       1.19130 /  0.55 (    2)
  hydrogen bonds       : bond        0.03579 /  2.43 (  287)
  hydrogen bonds       : angle       3.75326 /  2.81 (  828)
  Misc. bond           : bond        0.00003 /  0.00 (    1)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: B  105 GLU cc_start: 0.7371 (tm-30) cc_final: 0.7093 (tm-30)
REVERT: B  254 TYR cc_start: 0.8359 (m-80) cc_final: 0.7950 (m-80)
REVERT: B  361 SER cc_start: 0.8322 (OUTLIER) cc_final: 0.7668 (t)
REVERT: B  365 MET cc_start: 0.8392 (mmt) cc_final: 0.6903 (mmt)
REVERT: B  369 GLN cc_start: 0.8448 (mp10) cc_final: 0.8168 (mp10)
REVERT: B  391 LYS cc_start: 0.7942 (tptt) cc_final: 0.7008 (mptt)
REVERT: B  487 GLN cc_start: 0.8633 (tp40) cc_final: 0.8207 (tp-100)
  outliers start: 21
  outliers final: 13
  residues processed: 116
  average time/residue: 0.0512
  time to fit residues: 8.0068
Evaluate side-chains
  108 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  361 SER
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  454 THR
Chi-restraints excluded: chain B residue  467 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 34 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 48 optimal weight:    7.9990
   chunk 31 optimal weight:    7.9990
   chunk 40 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 497 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.115623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.091385 restraints weight = 5874.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.093812 restraints weight = 3901.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.095472 restraints weight = 3000.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.096589 restraints weight = 2519.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.097475 restraints weight = 2247.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.4260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4158  Z= 0.123
  Angle     :  0.587   7.141   5685  Z= 0.281
  Chirality :  0.041   0.211    682
  Planarity :  0.004   0.038    665
  Dihedral  :  8.160  69.718    706
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 19.48 %
    Favored  : 75.82 %
  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:  2.45 (0.38), residues: 501
  helix:  2.13 (0.26), residues: 389
  sheet:  None (None), residues: 0
  loop : -0.14 (0.62), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 419 
 TYR   0.010   0.001   TYR B 248 
 PHE   0.014   0.001   PHE B 336 
 TRP   0.008   0.001   TRP A 193 
 HIS   0.003   0.001   HIS B 319 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.12 ( 4156)
  covalent geometry    : angle       0.58711 /  0.28 ( 5683)
  SS BOND              : bond        0.00224 /  0.12 (    1)
  SS BOND              : angle       1.19925 /  0.55 (    2)
  hydrogen bonds       : bond        0.03629 /  2.46 (  287)
  hydrogen bonds       : angle       3.68332 /  2.77 (  828)
  Misc. bond           : bond        0.00003 /  0.00 (    1)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  254 TYR cc_start: 0.8356 (m-80) cc_final: 0.7972 (m-80)
REVERT: B  361 SER cc_start: 0.8307 (OUTLIER) cc_final: 0.7402 (t)
REVERT: B  365 MET cc_start: 0.8418 (mmt) cc_final: 0.6947 (mmt)
REVERT: B  391 LYS cc_start: 0.7944 (tptt) cc_final: 0.7006 (mptt)
REVERT: B  487 GLN cc_start: 0.8661 (tp40) cc_final: 0.8258 (tp-100)
REVERT: B  498 LYS cc_start: 0.8246 (tppp) cc_final: 0.7892 (mttm)
  outliers start: 20
  outliers final: 14
  residues processed: 108
  average time/residue: 0.0547
  time to fit residues: 7.8637
Evaluate side-chains
  103 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  361 SER
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  425 LEU
Chi-restraints excluded: chain B residue  454 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 47 optimal weight:    6.9990
   chunk 45 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 35 optimal weight:    7.9990
   overall best weight:    1.2786

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.115491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.091160 restraints weight = 5912.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.093560 restraints weight = 3854.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.095295 restraints weight = 2947.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.096470 restraints weight = 2466.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.097094 restraints weight = 2206.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.4312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4158  Z= 0.130
  Angle     :  0.605   8.138   5685  Z= 0.289
  Chirality :  0.041   0.187    682
  Planarity :  0.004   0.042    665
  Dihedral  :  8.166  69.968    706
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 18.31 %
    Favored  : 75.59 %
  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:  2.42 (0.38), residues: 501
  helix:  2.09 (0.26), residues: 390
  sheet:  None (None), residues: 0
  loop : -0.10 (0.61), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 421 
 TYR   0.007   0.001   TYR B 155 
 PHE   0.022   0.001   PHE B 474 
 TRP   0.007   0.001   TRP A 193 
 HIS   0.002   0.001   HIS B 319 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.13 ( 4156)
  covalent geometry    : angle       0.60422 /  0.29 ( 5683)
  SS BOND              : bond        0.00242 /  0.13 (    1)
  SS BOND              : angle       1.24041 /  0.57 (    2)
  hydrogen bonds       : bond        0.03637 /  2.47 (  287)
  hydrogen bonds       : angle       3.64843 /  2.74 (  828)
  Misc. bond           : bond        0.00018 /  0.01 (    1)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 GLU cc_start: 0.7360 (tm-30) cc_final: 0.7059 (tm-30)
REVERT: B  254 TYR cc_start: 0.8410 (m-80) cc_final: 0.8068 (m-80)
REVERT: B  361 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.7558 (t)
REVERT: B  365 MET cc_start: 0.8433 (mmt) cc_final: 0.6979 (mmt)
REVERT: B  369 GLN cc_start: 0.8499 (mp10) cc_final: 0.7700 (mp10)
REVERT: B  391 LYS cc_start: 0.7964 (tptt) cc_final: 0.7015 (mptt)
REVERT: B  487 GLN cc_start: 0.8673 (tp40) cc_final: 0.8296 (tp-100)
REVERT: B  498 LYS cc_start: 0.8280 (tppp) cc_final: 0.8042 (mtpp)
  outliers start: 26
  outliers final: 22
  residues processed: 112
  average time/residue: 0.0540
  time to fit residues: 8.0571
Evaluate side-chains
  116 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  301 SER
Chi-restraints excluded: chain B residue  305 MET
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  361 SER
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  397 ILE
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  425 LEU
Chi-restraints excluded: chain B residue  454 THR
Chi-restraints excluded: chain B residue  499 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 45 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 30 optimal weight:    9.9990
   chunk 13 optimal weight:    0.0570
   chunk 40 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.7298

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.117804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.093341 restraints weight = 5688.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.095733 restraints weight = 3846.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.097309 restraints weight = 2983.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.098560 restraints weight = 2536.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.098845 restraints weight = 2267.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.4496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4158  Z= 0.113
  Angle     :  0.591   7.017   5685  Z= 0.280
  Chirality :  0.040   0.177    682
  Planarity :  0.004   0.041    665
  Dihedral  :  8.168  73.929    706
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 20.66 %
    Favored  : 75.35 %
  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:  2.60 (0.38), residues: 501
  helix:  2.19 (0.26), residues: 391
  sheet:  None (None), residues: 0
  loop :  0.06 (0.61), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 421 
 TYR   0.010   0.001   TYR B 248 
 PHE   0.014   0.001   PHE B 336 
 TRP   0.007   0.001   TRP A 193 
 HIS   0.003   0.001   HIS B 319 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.11 ( 4156)
  covalent geometry    : angle       0.59086 /  0.28 ( 5683)
  SS BOND              : bond        0.00214 /  0.11 (    1)
  SS BOND              : angle       1.04777 /  0.48 (    2)
  hydrogen bonds       : bond        0.03391 /  2.30 (  287)
  hydrogen bonds       : angle       3.60064 /  2.69 (  828)
  Misc. bond           : bond        0.00002 /  0.00 (    1)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 GLU cc_start: 0.7309 (tm-30) cc_final: 0.7000 (tm-30)
REVERT: B  117 TYR cc_start: 0.8783 (t80) cc_final: 0.8258 (t80)
REVERT: B  254 TYR cc_start: 0.8364 (m-80) cc_final: 0.7922 (m-80)
REVERT: B  369 GLN cc_start: 0.8532 (mp10) cc_final: 0.7777 (mp10)
REVERT: B  391 LYS cc_start: 0.7931 (tptt) cc_final: 0.7046 (mptt)
REVERT: B  487 GLN cc_start: 0.8612 (tp40) cc_final: 0.8264 (tp-100)
REVERT: B  498 LYS cc_start: 0.8443 (tppp) cc_final: 0.8156 (mttm)
  outliers start: 17
  outliers final: 15
  residues processed: 114
  average time/residue: 0.0435
  time to fit residues: 6.6243
Evaluate side-chains
  116 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  301 SER
Chi-restraints excluded: chain B residue  305 MET
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  454 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.3386

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.116008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.091176 restraints weight = 5959.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.093477 restraints weight = 3967.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.095282 restraints weight = 3060.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.096187 restraints weight = 2580.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.097074 restraints weight = 2329.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.4501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4158  Z= 0.130
  Angle     :  0.610   7.089   5685  Z= 0.288
  Chirality :  0.041   0.168    682
  Planarity :  0.004   0.042    665
  Dihedral  :  8.243  72.432    706
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 19.48 %
    Favored  : 75.35 %
  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:  2.60 (0.38), residues: 501
  helix:  2.21 (0.26), residues: 390
  sheet:  None (None), residues: 0
  loop : -0.00 (0.61), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 211 
 TYR   0.012   0.001   TYR B 318 
 PHE   0.022   0.001   PHE B 474 
 TRP   0.006   0.001   TRP B 405 
 HIS   0.002   0.001   HIS B 319 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.13 ( 4156)
  covalent geometry    : angle       0.60962 /  0.29 ( 5683)
  SS BOND              : bond        0.00234 /  0.12 (    1)
  SS BOND              : angle       1.30608 /  0.59 (    2)
  hydrogen bonds       : bond        0.03588 /  2.44 (  287)
  hydrogen bonds       : angle       3.63059 /  2.71 (  828)
  Misc. bond           : bond        0.00004 /  0.00 (    1)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7100 (tm-30)
REVERT: B  117 TYR cc_start: 0.8792 (t80) cc_final: 0.8264 (t80)
REVERT: B  254 TYR cc_start: 0.8395 (m-80) cc_final: 0.8026 (m-80)
REVERT: B  369 GLN cc_start: 0.8523 (mp10) cc_final: 0.7935 (mp10)
REVERT: B  391 LYS cc_start: 0.7985 (tptt) cc_final: 0.7111 (mptt)
REVERT: B  487 GLN cc_start: 0.8571 (tp40) cc_final: 0.8220 (tp-100)
REVERT: B  498 LYS cc_start: 0.8372 (tppp) cc_final: 0.8017 (mttm)
  outliers start: 22
  outliers final: 19
  residues processed: 114
  average time/residue: 0.0524
  time to fit residues: 7.9311
Evaluate side-chains
  118 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  217 VAL
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  305 MET
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  425 LEU
Chi-restraints excluded: chain B residue  454 THR
Chi-restraints excluded: chain B residue  499 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 48 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 15 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    1.0786

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.116887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.092474 restraints weight = 5789.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.094979 restraints weight = 3838.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.096607 restraints weight = 2933.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.097862 restraints weight = 2470.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.098805 restraints weight = 2180.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.4596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4158  Z= 0.123
  Angle     :  0.607   9.221   5685  Z= 0.284
  Chirality :  0.041   0.166    682
  Planarity :  0.004   0.042    665
  Dihedral  :  8.213  74.767    706
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 19.48 %
    Favored  : 75.82 %
  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:  2.65 (0.38), residues: 501
  helix:  2.24 (0.26), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.04 (0.62), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  48 
 TYR   0.013   0.001   TYR B 318 
 PHE   0.013   0.001   PHE B 336 
 TRP   0.005   0.001   TRP B 257 
 HIS   0.003   0.001   HIS B 319 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.12 ( 4156)
  covalent geometry    : angle       0.60694 /  0.28 ( 5683)
  SS BOND              : bond        0.00241 /  0.13 (    1)
  SS BOND              : angle       1.16680 /  0.53 (    2)
  hydrogen bonds       : bond        0.03485 /  2.36 (  287)
  hydrogen bonds       : angle       3.64228 /  2.71 (  828)
  Misc. bond           : bond        0.00006 /  0.00 (    1)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 GLU cc_start: 0.7359 (tm-30) cc_final: 0.7151 (tm-30)
REVERT: B  117 TYR cc_start: 0.8772 (t80) cc_final: 0.8248 (t80)
REVERT: B  254 TYR cc_start: 0.8373 (m-80) cc_final: 0.8008 (m-80)
REVERT: B  296 TYR cc_start: 0.8761 (m-10) cc_final: 0.8188 (m-80)
REVERT: B  369 GLN cc_start: 0.8512 (mp10) cc_final: 0.7894 (mp10)
REVERT: B  391 LYS cc_start: 0.7978 (tptt) cc_final: 0.7110 (mptt)
REVERT: B  487 GLN cc_start: 0.8550 (tp40) cc_final: 0.8222 (tp-100)
REVERT: B  498 LYS cc_start: 0.8369 (tppp) cc_final: 0.8039 (mtpp)
  outliers start: 20
  outliers final: 20
  residues processed: 112
  average time/residue: 0.0538
  time to fit residues: 8.0447
Evaluate side-chains
  116 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue  178 CYS
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  279 ILE
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  301 SER
Chi-restraints excluded: chain B residue  305 MET
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  326 ILE
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  396 VAL
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  454 THR
Chi-restraints excluded: chain B residue  499 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 41 optimal weight:   10.0000
   chunk 4 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 20 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0170
   chunk 27 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   overall best weight:    1.3822

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.116374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.091260 restraints weight = 5838.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.093855 restraints weight = 3789.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.095576 restraints weight = 2866.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.096909 restraints weight = 2404.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.097857 restraints weight = 2113.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.4571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4158  Z= 0.134
  Angle     :  0.631  12.231   5685  Z= 0.294
  Chirality :  0.041   0.162    682
  Planarity :  0.004   0.042    665
  Dihedral  :  8.286  82.143    706
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 18.78 %
    Favored  : 75.59 %
  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:  2.62 (0.38), residues: 501
  helix:  2.22 (0.26), residues: 390
  sheet:  None (None), residues: 0
  loop :  0.01 (0.61), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 419 
 TYR   0.010   0.001   TYR B 248 
 PHE   0.023   0.001   PHE B 474 
 TRP   0.005   0.001   TRP B 484 
 HIS   0.002   0.001   HIS B 319 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.13 ( 4156)
  covalent geometry    : angle       0.63061 /  0.29 ( 5683)
  SS BOND              : bond        0.00284 /  0.15 (    1)
  SS BOND              : angle       1.30869 /  0.60 (    2)
  hydrogen bonds       : bond        0.03638 /  2.46 (  287)
  hydrogen bonds       : angle       3.68949 /  2.73 (  828)
  Misc. bond           : bond        0.00002 /  0.00 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 784.85 seconds
wall clock time: 14 minutes 18.72 seconds (858.72 seconds total)