Starting phenix.real_space_refine
on Sun Aug 24 16:22:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fli_29279/08_2025/8fli_29279.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fli_29279/08_2025/8fli_29279.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fli_29279/08_2025/8fli_29279.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fli_29279/08_2025/8fli_29279.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fli_29279/08_2025/8fli_29279.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fli_29279/08_2025/8fli_29279.cif"
  }
  resolution = 3.8
  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=   0.001 sd=   0.046
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     828      5.49       5
     Mg      3      5.21       5
     S       8      5.16       5
     C   10319      2.51       5
     N    3961      2.21       5
     O    6392      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 21511
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 17751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 828, 17751
          Classifications: {'RNA': 828}
          Modifications used: {'rna2p_pur': 65, 'rna2p_pyr': 43, 'rna3p_pur': 400, 'rna3p_pyr': 320}
          Link IDs: {'rna2p': 108, 'rna3p': 719}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 458, 3757
          Classifications: {'peptide': 458}
          Link IDs: {'PTRANS': 17, 'TRANS': 440}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 4.30, per 1000 atoms: 0.20
  Number of scatterers: 21511
  At special positions: 0
  Unit cell: (117.3, 158.7, 238.05, 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)
     S       8     16.00
     P     828     15.00
     Mg      3     11.99
     O    6392      8.00
     N    3961      7.00
     C   10319      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.59
  Conformation dependent library (CDL) restraints added in 548.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  858

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 4 sheets defined
      38.9% alpha, 7.2% beta
      211 base pairs and 351 stacking pairs defined.
    Time for finding SS restraints: 3.46
  Creating SS restraints...
    Processing helix  chain 'B' and resid 22 through 26
      removed outlier: 3.706A  pdb=" N   ILE B  26 " --> pdb=" O   TRP B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 27 through 48
      removed outlier: 3.612A  pdb=" N   ALA B  31 " --> pdb=" O   ASP B  27 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   ASN B  32 " --> pdb=" O   TRP B  28 " (cutoff:3.500A)
      removed outlier: 4.912A  pdb=" N   ARG B  33 " --> pdb=" O   ALA B  29 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLU B  48 " --> pdb=" O   LYS B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 62
      removed outlier: 5.088A  pdb=" N   TRP B  59 " --> pdb=" O   LYS B  55 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   THR B  62 " --> pdb=" O   GLN B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 77
      removed outlier: 3.608A  pdb=" N   ALA B  71 " --> pdb=" O   GLY B  67 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ASP B  77 " --> pdb=" O   LYS B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 103
      removed outlier: 3.966A  pdb=" N   LYS B 102 " --> pdb=" O   ALA B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 143
      removed outlier: 3.652A  pdb=" N   MET B 139 " --> pdb=" O   LYS B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 154
    Processing helix  chain 'B' and resid 168 through 174
      removed outlier: 4.171A  pdb=" N   ALA B 172 " --> pdb=" O   THR B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 200
      removed outlier: 3.568A  pdb=" N   ILE B 200 " --> pdb=" O   PHE B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 207
    Processing helix  chain 'B' and resid 214 through 220
    Processing helix  chain 'B' and resid 243 through 252
      removed outlier: 3.634A  pdb=" N   ALA B 248 " --> pdb=" O   SER B 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 263
      removed outlier: 3.597A  pdb=" N   HIS B 262 " --> pdb=" O   LEU B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 297
      removed outlier: 3.751A  pdb=" N   GLN B 295 " --> pdb=" O   THR B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 349
      removed outlier: 5.282A  pdb=" N   ALA B 344 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ILE B 349 " --> pdb=" O   PHE B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 363 through 378
      Proline residue:  B 370  - end of helix
      removed outlier: 3.571A  pdb=" N   LYS B 373 " --> pdb=" O   ASN B 369 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLY B 374 " --> pdb=" O   PRO B 370 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   TRP B 375 " --> pdb=" O   ILE B 371 " (cutoff:3.500A)
      removed outlier: 5.765A  pdb=" N   ALA B 376 " --> pdb=" O   ILE B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 389
      removed outlier: 3.586A  pdb=" N   ASN B 389 " --> pdb=" O   LYS B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 404
      removed outlier: 4.565A  pdb=" N   LYS B 398 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ARG B 401 " --> pdb=" O   HIS B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 419
    Processing sheet with id=AA1, first strand: chain 'B' and resid 115 through 119
      removed outlier: 3.847A  pdb=" N   ARG B 115 " --> pdb=" O   ILE B 131 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ILE B 131 " --> pdb=" O   ARG B 115 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   VAL B 117 " --> pdb=" O   LEU B 129 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU B 129 " --> pdb=" O   VAL B 117 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ILE B 119 " --> pdb=" O   ARG B 127 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ARG B 127 " --> pdb=" O   ILE B 119 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 269 through 272
      removed outlier: 3.804A  pdb=" N   TYR B 187 " --> pdb=" O   GLY B 281 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 319 through 321
      removed outlier: 3.562A  pdb=" N   PHE B 319 " --> pdb=" O   ILE B 326 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE B 326 " --> pdb=" O   PHE B 319 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ARG B 327 " --> pdb=" O   LEU B 334 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU B 334 " --> pdb=" O   ARG B 327 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 420 through 421
      removed outlier: 3.503A  pdb=" N   THR B 432 " --> pdb=" O   ARG B 444 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ARG B 444 " --> pdb=" O   THR B 432 " (cutoff:3.500A)

    92 hydrogen bonds defined for protein.
    255 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      544 hydrogen bonds
      932 hydrogen bond angles
      0 basepair planarities
      211 basepair parallelities
      351 stacking parallelities
  Total time for adding SS restraints: 5.61

  Time building geometry restraints manager: 2.55 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2711
        1.33 -     1.45: 10877
        1.45 -     1.57: 8463
        1.57 -     1.69: 1653
        1.69 -     1.81: 12
  Bond restraints: 23716
  Sorted by residual:
  bond pdb=" N   TYR B 419 "
       pdb=" CA  TYR B 419 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 1.16e-02 7.43e+03 1.12e+01
  bond pdb=" CA  HIS B 397 "
       pdb=" C   HIS B 397 "
    ideal  model  delta    sigma   weight residual
    1.522  1.470  0.052 1.72e-02 3.38e+03 9.16e+00
  bond pdb=" C   THR B 415 "
       pdb=" O   THR B 415 "
    ideal  model  delta    sigma   weight residual
    1.235  1.271 -0.035 1.26e-02 6.30e+03 7.90e+00
  bond pdb=" C   LYS B 410 "
       pdb=" N   PRO B 411 "
    ideal  model  delta    sigma   weight residual
    1.328  1.357 -0.029 1.25e-02 6.40e+03 5.40e+00
  bond pdb=" N   TRP B 414 "
       pdb=" CA  TRP B 414 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.029 1.29e-02 6.01e+03 5.13e+00
  ... (remaining 23711 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.62: 36125
        4.62 -     9.24: 42
        9.24 -    13.86: 2
       13.86 -    18.48: 0
       18.48 -    23.10: 1
  Bond angle restraints: 36170
  Sorted by residual:
  angle pdb=" O3'   U A 859 "
        pdb=" C3'   U A 859 "
        pdb=" C2'   U A 859 "
      ideal   model   delta    sigma   weight residual
     113.70   90.60   23.10 1.50e+00 4.44e-01 2.37e+02
  angle pdb=" C4'   U A 859 "
        pdb=" C3'   U A 859 "
        pdb=" O3'   U A 859 "
      ideal   model   delta    sigma   weight residual
     113.00  126.61  -13.61 1.50e+00 4.44e-01 8.23e+01
  angle pdb=" C   LYS B 418 "
        pdb=" N   TYR B 419 "
        pdb=" CA  TYR B 419 "
      ideal   model   delta    sigma   weight residual
     122.67  114.94    7.73 1.59e+00 3.96e-01 2.36e+01
  angle pdb=" C3'   G A 840 "
        pdb=" O3'   G A 840 "
        pdb=" P     G A 841 "
      ideal   model   delta    sigma   weight residual
     120.20  126.84   -6.64 1.50e+00 4.44e-01 1.96e+01
  angle pdb=" C4'   U A 825 "
        pdb=" C3'   U A 825 "
        pdb=" O3'   U A 825 "
      ideal   model   delta    sigma   weight residual
     113.00  106.42    6.58 1.50e+00 4.44e-01 1.92e+01
  ... (remaining 36165 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.51: 12765
       35.51 -    71.03: 2187
       71.03 -   106.54: 298
      106.54 -   142.06: 8
      142.06 -   177.57: 8
  Dihedral angle restraints: 15266
    sinusoidal: 13939
      harmonic: 1327
  Sorted by residual:
  dihedral pdb=" O4'   U A 595 "
           pdb=" C1'   U A 595 "
           pdb=" N1    U A 595 "
           pdb=" C2    U A 595 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   41.16  158.84     1      1.50e+01 4.44e-03 8.25e+01
  dihedral pdb=" O4'   C A  -6 "
           pdb=" C1'   C A  -6 "
           pdb=" N1    C A  -6 "
           pdb=" C2    C A  -6 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   50.66  149.34     1      1.50e+01 4.44e-03 7.94e+01
  dihedral pdb=" O4'   U A 498 "
           pdb=" C1'   U A 498 "
           pdb=" N1    U A 498 "
           pdb=" C2    U A 498 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   56.66  175.34     1      1.70e+01 3.46e-03 6.63e+01
  ... (remaining 15263 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 4201
       0.054 -    0.107: 409
       0.107 -    0.161: 53
       0.161 -    0.215: 16
       0.215 -    0.268: 8
  Chirality restraints: 4687
  Sorted by residual:
  chirality pdb=" P     G A 828 "
            pdb=" OP1   G A 828 "
            pdb=" OP2   G A 828 "
            pdb=" O5'   G A 828 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.68   -0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" C1'   G A 531 "
            pdb=" O4'   G A 531 "
            pdb=" C2'   G A 531 "
            pdb=" N9    G A 531 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.22    0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" C1'   A A 630 "
            pdb=" O4'   A A 630 "
            pdb=" C2'   A A 630 "
            pdb=" N9    A A 630 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.23    0.23 2.00e-01 2.50e+01 1.33e+00
  ... (remaining 4684 not shown)

  Planarity restraints: 1481
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A 305 "    0.025 2.00e-02 2.50e+03   2.79e-02 1.75e+01
        pdb=" N1    C A 305 "   -0.033 2.00e-02 2.50e+03
        pdb=" C2    C A 305 "    0.054 2.00e-02 2.50e+03
        pdb=" O2    C A 305 "   -0.032 2.00e-02 2.50e+03
        pdb=" N3    C A 305 "   -0.016 2.00e-02 2.50e+03
        pdb=" C4    C A 305 "    0.026 2.00e-02 2.50e+03
        pdb=" N4    C A 305 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    C A 305 "   -0.006 2.00e-02 2.50e+03
        pdb=" C6    C A 305 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 112 "   -0.058 5.00e-02 4.00e+02   8.78e-02 1.23e+01
        pdb=" N   PRO B 113 "    0.152 5.00e-02 4.00e+02
        pdb=" CA  PRO B 113 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO B 113 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 410 "    0.016 2.00e-02 2.50e+03   3.24e-02 1.05e+01
        pdb=" C   LYS B 410 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   LYS B 410 "    0.021 2.00e-02 2.50e+03
        pdb=" N   PRO B 411 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1478 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.19: 16
        2.19 -     2.86: 7122
        2.86 -     3.54: 33277
        3.54 -     4.22: 64014
        4.22 -     4.90: 81169
  Nonbonded interactions: 185598
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B 470 "
            pdb=" CD1 TRP B 471 "
     model   vdw
     1.508 3.260
  nonbonded pdb=" O3'   G A   0 "
            pdb="MG    MG A 903 "
     model   vdw
     1.862 2.170
  nonbonded pdb=" OP2   U A   1 "
            pdb="MG    MG A 903 "
     model   vdw
     1.895 2.170
  nonbonded pdb=" OP1   A A   6 "
            pdb="MG    MG A 901 "
     model   vdw
     1.901 2.170
  nonbonded pdb=" O   LYS B 348 "
            pdb=" OD1 ASP B 351 "
     model   vdw
     1.923 3.040
  ... (remaining 185593 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:             3.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     22.360
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:   27.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
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      :  0.005   0.055  23716  Z= 0.250
  Angle     :  0.680  23.097  36170  Z= 0.356
  Chirality :  0.036   0.268   4687
  Planarity :  0.005   0.088   1481
  Dihedral  : 26.204 177.569  14408
  Min Nonbonded Distance : 1.508

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 16.45 %
    Favored  : 82.89 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 41.33 %
    Favored  : 58.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.70 (0.36), residues: 456
  helix: -2.28 (0.36), residues: 188
  sheet: -1.99 (0.88), residues: 38
  loop : -2.69 (0.36), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 401 
 TYR   0.016   0.002   TYR B  66 
 PHE   0.013   0.002   PHE B 430 
 TRP   0.016   0.002   TRP B 471 
 HIS   0.004   0.001   HIS B 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (23716)
  covalent geometry    : angle       0.68039 (36170)
  hydrogen bonds       : bond        0.14094 (  636)
  hydrogen bonds       : angle       5.71795 ( 1187)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 35
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 35
  average time/residue: 0.1720
  time to fit residues: 9.1762
Evaluate side-chains
  35 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 34
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  209 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.7980
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    5.9990
   chunk 123 optimal weight:    4.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    8.9990
   overall best weight:    3.9588

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  63 HIS
B 174 GLN
** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.094025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.066172 restraints weight = 84970.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.068107 restraints weight = 36247.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.069276 restraints weight = 24257.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 68)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.069908 restraints weight = 19993.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.070210 restraints weight = 18149.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.1305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057  23716  Z= 0.295
  Angle     :  0.747  12.882  36170  Z= 0.367
  Chirality :  0.037   0.251   4687
  Planarity :  0.006   0.087   1481
  Dihedral  : 26.163 174.933  13453
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 17.32 %
    Favored  : 82.02 %
  Rotamer:
    Outliers :  6.38 %
    Allowed  : 37.76 %
    Favored  : 55.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.59 (0.35), residues: 456
  helix: -2.14 (0.36), residues: 182
  sheet: -2.23 (1.11), residues: 24
  loop : -2.64 (0.35), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 105 
 TYR   0.015   0.002   TYR B  66 
 PHE   0.015   0.002   PHE B 430 
 TRP   0.013   0.002   TRP B 471 
 HIS   0.004   0.001   HIS B 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00574 (23716)
  covalent geometry    : angle       0.74739 (36170)
  hydrogen bonds       : bond        0.08486 (  636)
  hydrogen bonds       : angle       3.27097 ( 1187)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 37
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  228 GLN cc_start: 0.8035 (pm20) cc_final: 0.7597 (pm20)
REVERT: B  417 ASN cc_start: 0.9081 (t0) cc_final: 0.8858 (t0)
REVERT: B  471 TRP cc_start: 0.7017 (m-10) cc_final: 0.6755 (m-10)
  outliers start: 25
  outliers final: 15
  residues processed: 58
  average time/residue: 0.1719
  time to fit residues: 15.2195
Evaluate side-chains
  49 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 34
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue  116 ARG
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  196 CYS
Chi-restraints excluded: chain B residue  249 ASN
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  316 GLU
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  458 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 66 optimal weight:   20.0000
   chunk 65 optimal weight:    7.9990
   chunk 59 optimal weight:    7.9990
   chunk 29 optimal weight:   10.0000
   chunk 68 optimal weight:   20.0000
   chunk 67 optimal weight:   40.0000
   chunk 81 optimal weight:   20.0000
   chunk 102 optimal weight:    0.7980
   chunk 112 optimal weight:    0.8980
   chunk 117 optimal weight:    0.8980
   chunk 104 optimal weight:    0.6980
   overall best weight:    2.2582

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  63 HIS
** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.095910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.068313 restraints weight = 83900.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.070328 restraints weight = 34770.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.071503 restraints weight = 23111.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 70)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.072178 restraints weight = 18837.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.072469 restraints weight = 16969.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.1653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  23716  Z= 0.179
  Angle     :  0.617  13.185  36170  Z= 0.309
  Chirality :  0.032   0.272   4687
  Planarity :  0.005   0.086   1481
  Dihedral  : 25.886 173.097  13451
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 14.91 %
    Favored  : 84.43 %
  Rotamer:
    Outliers :  7.40 %
    Allowed  : 36.48 %
    Favored  : 56.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.27 (0.36), residues: 456
  helix: -1.81 (0.36), residues: 190
  sheet: -2.03 (0.84), residues: 36
  loop : -2.51 (0.37), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 478 
 TYR   0.019   0.001   TYR B  66 
 PHE   0.008   0.002   PHE B 321 
 TRP   0.015   0.002   TRP B 226 
 HIS   0.003   0.001   HIS B 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (23716)
  covalent geometry    : angle       0.61683 (36170)
  hydrogen bonds       : bond        0.06863 (  636)
  hydrogen bonds       : angle       2.84452 ( 1187)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 42
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   74 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8245 (mtm-85)
REVERT: B  226 TRP cc_start: 0.7334 (t60) cc_final: 0.7003 (t60)
REVERT: B  228 GLN cc_start: 0.7943 (pm20) cc_final: 0.7652 (pm20)
REVERT: B  390 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.7710 (tmm-80)
REVERT: B  438 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7697 (pp20)
  outliers start: 29
  outliers final: 18
  residues processed: 67
  average time/residue: 0.1440
  time to fit residues: 14.6149
Evaluate side-chains
  60 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 39
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 ARG
Chi-restraints excluded: chain B residue   82 LYS
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  196 CYS
Chi-restraints excluded: chain B residue  224 PHE
Chi-restraints excluded: chain B residue  227 LYS
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  316 GLU
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  351 ASP
Chi-restraints excluded: chain B residue  387 ILE
Chi-restraints excluded: chain B residue  390 ARG
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  438 GLU
Chi-restraints excluded: chain B residue  458 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 25 optimal weight:    7.9990
   chunk 28 optimal weight:   10.0000
   chunk 74 optimal weight:   10.0000
   chunk 80 optimal weight:    9.9990
   chunk 46 optimal weight:   30.0000
   chunk 78 optimal weight:    6.9990
   chunk 8 optimal weight:    8.9990
   chunk 111 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 61 optimal weight:   20.0000
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  63 HIS
** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.090915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.062974 restraints weight = 88294.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.064829 restraints weight = 38465.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.065992 restraints weight = 26213.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 64)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.066606 restraints weight = 21738.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.066872 restraints weight = 19824.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.2535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.073  23716  Z= 0.452
  Angle     :  0.926  12.974  36170  Z= 0.448
  Chirality :  0.045   0.294   4687
  Planarity :  0.007   0.092   1481
  Dihedral  : 26.307 175.904  13451
  Min Nonbonded Distance : 1.805

Molprobity Statistics.
  All-atom Clashscore : 18.74
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 19.08 %
    Favored  : 80.26 %
  Rotamer:
    Outliers : 10.46 %
    Allowed  : 33.93 %
    Favored  : 55.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.82 (0.35), residues: 456
  helix: -2.18 (0.35), residues: 182
  sheet: -2.31 (0.82), residues: 38
  loop : -2.90 (0.35), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 478 
 TYR   0.016   0.002   TYR B  66 
 PHE   0.031   0.004   PHE B 321 
 TRP   0.023   0.003   TRP B 402 
 HIS   0.014   0.002   HIS B 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00884 (23716)
  covalent geometry    : angle       0.92638 (36170)
  hydrogen bonds       : bond        0.10203 (  636)
  hydrogen bonds       : angle       3.58246 ( 1187)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 34
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  109 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7642 (t80)
REVERT: B  125 LYS cc_start: 0.6695 (OUTLIER) cc_final: 0.6385 (tttm)
REVERT: B  228 GLN cc_start: 0.8370 (pm20) cc_final: 0.8045 (pm20)
REVERT: B  390 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8180 (tmm-80)
REVERT: B  438 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8002 (pp20)
REVERT: B  448 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8524 (tmtt)
  outliers start: 41
  outliers final: 27
  residues processed: 70
  average time/residue: 0.1876
  time to fit residues: 19.4827
Evaluate side-chains
  64 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 32
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue   74 ARG
Chi-restraints excluded: chain B residue   82 LYS
Chi-restraints excluded: chain B residue  109 TYR
Chi-restraints excluded: chain B residue  125 LYS
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  196 CYS
Chi-restraints excluded: chain B residue  224 PHE
Chi-restraints excluded: chain B residue  249 ASN
Chi-restraints excluded: chain B residue  260 LYS
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  283 SER
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  316 GLU
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  350 ARG
Chi-restraints excluded: chain B residue  351 ASP
Chi-restraints excluded: chain B residue  355 GLU
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  387 ILE
Chi-restraints excluded: chain B residue  390 ARG
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  438 GLU
Chi-restraints excluded: chain B residue  448 LYS
Chi-restraints excluded: chain B residue  458 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 125 optimal weight:    7.9990
   chunk 61 optimal weight:   20.0000
   chunk 56 optimal weight:    6.9990
   chunk 92 optimal weight:    0.9990
   chunk 103 optimal weight:    5.9990
   chunk 118 optimal weight:    0.6980
   chunk 97 optimal weight:    3.9990
   chunk 98 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9980
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.095814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.068781 restraints weight = 84380.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.070552 restraints weight = 36330.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.071700 restraints weight = 24111.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.072343 restraints weight = 19720.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.072688 restraints weight = 17858.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  23716  Z= 0.146
  Angle     :  0.614  14.370  36170  Z= 0.307
  Chirality :  0.032   0.347   4687
  Planarity :  0.005   0.089   1481
  Dihedral  : 25.890 171.365  13451
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 14.25 %
    Favored  : 85.09 %
  Rotamer:
    Outliers :  6.89 %
    Allowed  : 37.50 %
    Favored  : 55.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.14 (0.37), residues: 456
  helix: -1.70 (0.37), residues: 189
  sheet: -1.62 (1.09), residues: 22
  loop : -2.48 (0.37), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 301 
 TYR   0.018   0.001   TYR B  66 
 PHE   0.017   0.001   PHE B 321 
 TRP   0.020   0.002   TRP B 226 
 HIS   0.004   0.001   HIS B 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (23716)
  covalent geometry    : angle       0.61447 (36170)
  hydrogen bonds       : bond        0.06794 (  636)
  hydrogen bonds       : angle       2.77729 ( 1187)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 39
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  226 TRP cc_start: 0.7392 (t60) cc_final: 0.6954 (t60)
REVERT: B  228 GLN cc_start: 0.8034 (pm20) cc_final: 0.7662 (pm20)
REVERT: B  328 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7906 (mtmm)
  outliers start: 27
  outliers final: 17
  residues processed: 61
  average time/residue: 0.1691
  time to fit residues: 15.8841
Evaluate side-chains
  57 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 39
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  224 PHE
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  316 GLU
Chi-restraints excluded: chain B residue  328 LYS
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  355 GLU
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  387 ILE
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  458 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 63 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   chunk 18 optimal weight:    8.9990
   chunk 119 optimal weight:    2.9990
   chunk 81 optimal weight:   20.0000
   chunk 108 optimal weight:    0.6980
   chunk 97 optimal weight:    0.0000
   chunk 59 optimal weight:    7.9990
   chunk 117 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   overall best weight:    2.9390

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  63 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.094474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.067036 restraints weight = 84494.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.068988 restraints weight = 34533.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.070167 restraints weight = 22718.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 67)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.070851 restraints weight = 18510.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 63)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.071177 restraints weight = 16681.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  23716  Z= 0.228
  Angle     :  0.667  13.240  36170  Z= 0.330
  Chirality :  0.033   0.349   4687
  Planarity :  0.006   0.090   1481
  Dihedral  : 25.870 171.053  13451
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 16.89 %
    Favored  : 82.46 %
  Rotamer:
    Outliers :  7.65 %
    Allowed  : 36.99 %
    Favored  : 55.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.07 (0.37), residues: 456
  helix: -1.61 (0.37), residues: 188
  sheet: -1.39 (1.11), residues: 22
  loop : -2.50 (0.36), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 401 
 TYR   0.016   0.001   TYR B  66 
 PHE   0.010   0.002   PHE B 321 
 TRP   0.012   0.001   TRP B 226 
 HIS   0.007   0.001   HIS B 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (23716)
  covalent geometry    : angle       0.66741 (36170)
  hydrogen bonds       : bond        0.07129 (  636)
  hydrogen bonds       : angle       2.89923 ( 1187)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 36
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   74 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8254 (mtm-85)
REVERT: B  226 TRP cc_start: 0.7389 (t60) cc_final: 0.6932 (t60)
REVERT: B  228 GLN cc_start: 0.8137 (pm20) cc_final: 0.7791 (pm20)
REVERT: B  328 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.7990 (mtmm)
REVERT: B  390 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.7542 (tmm-80)
  outliers start: 30
  outliers final: 20
  residues processed: 62
  average time/residue: 0.1680
  time to fit residues: 15.4672
Evaluate side-chains
  60 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 37
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue   74 ARG
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  196 CYS
Chi-restraints excluded: chain B residue  224 PHE
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  316 GLU
Chi-restraints excluded: chain B residue  328 LYS
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  355 GLU
Chi-restraints excluded: chain B residue  387 ILE
Chi-restraints excluded: chain B residue  390 ARG
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  458 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 113 optimal weight:    1.9990
   chunk 110 optimal weight:    4.9990
   chunk 96 optimal weight:    0.2980
   chunk 63 optimal weight:   10.0000
   chunk 68 optimal weight:   20.0000
   chunk 89 optimal weight:    0.7980
   chunk 115 optimal weight:    5.9990
   chunk 67 optimal weight:   40.0000
   chunk 31 optimal weight:   10.0000
   chunk 118 optimal weight:    0.9990
   chunk 23 optimal weight:    7.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  63 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.096112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.068961 restraints weight = 85128.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.070791 restraints weight = 37022.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.071959 restraints weight = 24784.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 68)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.072619 restraints weight = 20357.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.072888 restraints weight = 18421.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  23716  Z= 0.155
  Angle     :  0.605  13.755  36170  Z= 0.302
  Chirality :  0.031   0.349   4687
  Planarity :  0.005   0.090   1481
  Dihedral  : 25.823 171.860  13451
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 14.91 %
    Favored  : 84.43 %
  Rotamer:
    Outliers :  7.65 %
    Allowed  : 36.22 %
    Favored  : 56.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.82 (0.37), residues: 456
  helix: -1.39 (0.38), residues: 188
  sheet: -1.33 (1.08), residues: 22
  loop : -2.37 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 401 
 TYR   0.017   0.001   TYR B  66 
 PHE   0.009   0.001   PHE B 321 
 TRP   0.016   0.002   TRP B 226 
 HIS   0.003   0.001   HIS B 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (23716)
  covalent geometry    : angle       0.60466 (36170)
  hydrogen bonds       : bond        0.06592 (  636)
  hydrogen bonds       : angle       2.72222 ( 1187)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 38
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   74 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8227 (mtm-85)
REVERT: B  228 GLN cc_start: 0.8022 (pm20) cc_final: 0.7673 (pm20)
REVERT: B  328 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8005 (mtmm)
REVERT: B  390 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.7515 (tmm-80)
REVERT: B  453 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7942 (mmt180)
  outliers start: 30
  outliers final: 20
  residues processed: 65
  average time/residue: 0.1834
  time to fit residues: 17.2927
Evaluate side-chains
  61 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 37
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 ARG
Chi-restraints excluded: chain B residue   82 LYS
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  167 CYS
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  316 GLU
Chi-restraints excluded: chain B residue  328 LYS
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  355 GLU
Chi-restraints excluded: chain B residue  387 ILE
Chi-restraints excluded: chain B residue  390 ARG
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  453 ARG
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  460 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 121 optimal weight:    0.6980
   chunk 28 optimal weight:   10.0000
   chunk 77 optimal weight:    6.9990
   chunk 57 optimal weight:    6.9990
   chunk 53 optimal weight:   20.0000
   chunk 94 optimal weight:    0.8980
   chunk 36 optimal weight:    8.9990
   chunk 126 optimal weight:    5.9990
   chunk 124 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   overall best weight:    3.7186

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.094693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.067243 restraints weight = 86010.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.069093 restraints weight = 38166.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.070244 restraints weight = 25640.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 75)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.070880 restraints weight = 21156.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.071178 restraints weight = 19202.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  23716  Z= 0.268
  Angle     :  0.694  14.368  36170  Z= 0.339
  Chirality :  0.034   0.352   4687
  Planarity :  0.006   0.093   1481
  Dihedral  : 25.839 171.150  13451
  Min Nonbonded Distance : 1.844

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 17.54 %
    Favored  : 81.80 %
  Rotamer:
    Outliers :  7.65 %
    Allowed  : 36.73 %
    Favored  : 55.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.00 (0.37), residues: 456
  helix: -1.54 (0.37), residues: 188
  sheet: -1.50 (1.11), residues: 23
  loop : -2.45 (0.37), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 401 
 TYR   0.015   0.002   TYR B  66 
 PHE   0.013   0.002   PHE B 430 
 TRP   0.014   0.002   TRP B 402 
 HIS   0.007   0.001   HIS B 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00525 (23716)
  covalent geometry    : angle       0.69368 (36170)
  hydrogen bonds       : bond        0.07330 (  636)
  hydrogen bonds       : angle       2.96385 ( 1187)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 36
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   74 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8232 (mtm-85)
REVERT: B  228 GLN cc_start: 0.8181 (pm20) cc_final: 0.7794 (pm20)
REVERT: B  328 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8040 (mtmm)
REVERT: B  390 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.7551 (tmm-80)
REVERT: B  448 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8508 (tmtt)
REVERT: B  453 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7963 (mmt180)
  outliers start: 30
  outliers final: 20
  residues processed: 63
  average time/residue: 0.1707
  time to fit residues: 15.9825
Evaluate side-chains
  61 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 36
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue   74 ARG
Chi-restraints excluded: chain B residue   82 LYS
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  167 CYS
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  316 GLU
Chi-restraints excluded: chain B residue  328 LYS
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  355 GLU
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  387 ILE
Chi-restraints excluded: chain B residue  390 ARG
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  448 LYS
Chi-restraints excluded: chain B residue  453 ARG
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  460 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 90 optimal weight:    4.9990
   chunk 13 optimal weight:    8.9990
   chunk 120 optimal weight:    2.9990
   chunk 43 optimal weight:   20.0000
   chunk 95 optimal weight:    0.8980
   chunk 79 optimal weight:    9.9990
   chunk 20 optimal weight:   10.9990
   chunk 38 optimal weight:    6.9990
   chunk 70 optimal weight:   10.0000
   chunk 88 optimal weight:    0.0670
   overall best weight:    3.1924

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.094877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 89)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.067395 restraints weight = 85311.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.069303 restraints weight = 37582.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.070506 restraints weight = 25426.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.071127 restraints weight = 20985.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.071370 restraints weight = 19060.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  23716  Z= 0.231
  Angle     :  0.660  14.692  36170  Z= 0.327
  Chirality :  0.034   0.359   4687
  Planarity :  0.005   0.093   1481
  Dihedral  : 25.871 171.101  13451
  Min Nonbonded Distance : 1.883

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 16.89 %
    Favored  : 82.46 %
  Rotamer:
    Outliers :  7.65 %
    Allowed  : 36.22 %
    Favored  : 56.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.02 (0.37), residues: 456
  helix: -1.57 (0.37), residues: 188
  sheet: -1.66 (1.07), residues: 23
  loop : -2.43 (0.37), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 401 
 TYR   0.016   0.002   TYR B  66 
 PHE   0.009   0.002   PHE B 321 
 TRP   0.024   0.002   TRP B 226 
 HIS   0.005   0.001   HIS B 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 (23716)
  covalent geometry    : angle       0.65968 (36170)
  hydrogen bonds       : bond        0.07126 (  636)
  hydrogen bonds       : angle       2.89015 ( 1187)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 37
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   74 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8243 (mtm-85)
REVERT: B  228 GLN cc_start: 0.8198 (pm20) cc_final: 0.7802 (pm20)
REVERT: B  328 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8080 (mtmm)
REVERT: B  390 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.7703 (tmm-80)
REVERT: B  448 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8507 (tmtt)
REVERT: B  453 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7949 (mmt180)
  outliers start: 30
  outliers final: 22
  residues processed: 63
  average time/residue: 0.1476
  time to fit residues: 13.9492
Evaluate side-chains
  62 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 35
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue   74 ARG
Chi-restraints excluded: chain B residue   82 LYS
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  167 CYS
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  283 SER
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  316 GLU
Chi-restraints excluded: chain B residue  328 LYS
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  355 GLU
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  387 ILE
Chi-restraints excluded: chain B residue  390 ARG
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  448 LYS
Chi-restraints excluded: chain B residue  453 ARG
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  460 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 87 optimal weight:    5.9990
   chunk 105 optimal weight:    0.8980
   chunk 57 optimal weight:    6.9990
   chunk 51 optimal weight:   10.0000
   chunk 42 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   chunk 90 optimal weight:    4.9990
   chunk 99 optimal weight:    3.9990
   chunk 123 optimal weight:    3.9990
   chunk 121 optimal weight:    0.9990
   chunk 109 optimal weight:    0.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.095720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.068352 restraints weight = 85234.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.070300 restraints weight = 36978.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 68)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.071535 restraints weight = 24873.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.072130 restraints weight = 20412.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 60)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.072512 restraints weight = 18549.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.2520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  23716  Z= 0.178
  Angle     :  0.621  15.061  36170  Z= 0.308
  Chirality :  0.031   0.365   4687
  Planarity :  0.005   0.094   1481
  Dihedral  : 25.831 171.358  13451
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 16.23 %
    Favored  : 83.11 %
  Rotamer:
    Outliers :  6.38 %
    Allowed  : 37.76 %
    Favored  : 55.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.86 (0.37), residues: 456
  helix: -1.42 (0.37), residues: 188
  sheet: -1.41 (1.08), residues: 22
  loop : -2.39 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 401 
 TYR   0.016   0.001   TYR B  66 
 PHE   0.008   0.001   PHE B 321 
 TRP   0.020   0.002   TRP B 226 
 HIS   0.004   0.001   HIS B 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (23716)
  covalent geometry    : angle       0.62082 (36170)
  hydrogen bonds       : bond        0.06719 (  636)
  hydrogen bonds       : angle       2.76887 ( 1187)

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

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

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  912 Ramachandran restraints generated.
    456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 36
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   74 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8236 (mtm-85)
REVERT: B  328 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8058 (mtmm)
REVERT: B  390 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.7542 (tmm-80)
  outliers start: 25
  outliers final: 22
  residues processed: 58
  average time/residue: 0.1452
  time to fit residues: 13.2558
Evaluate side-chains
  60 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 35
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 ARG
Chi-restraints excluded: chain B residue   82 LYS
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  167 CYS
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  283 SER
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  316 GLU
Chi-restraints excluded: chain B residue  328 LYS
Chi-restraints excluded: chain B residue  335 ILE
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  355 GLU
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  387 ILE
Chi-restraints excluded: chain B residue  390 ARG
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  460 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 12 optimal weight:   10.0000
   chunk 41 optimal weight:    7.9990
   chunk 43 optimal weight:   20.0000
   chunk 69 optimal weight:   10.0000
   chunk 107 optimal weight:    0.0770
   chunk 78 optimal weight:    6.9990
   chunk 99 optimal weight:    1.9990
   chunk 54 optimal weight:    9.9990
   chunk 6 optimal weight:   10.0000
   chunk 125 optimal weight:    4.9990
   overall best weight:    4.4146

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

Flipped N/Q/H residues before XYZ refinement:
** B  24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.092999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.065532 restraints weight = 86298.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.067372 restraints weight = 38834.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.068502 restraints weight = 26580.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 64)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.069137 restraints weight = 22128.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.069390 restraints weight = 20105.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055  23716  Z= 0.330
  Angle     :  0.777  14.146  36170  Z= 0.380
  Chirality :  0.039   0.390   4687
  Planarity :  0.006   0.096   1481
  Dihedral  : 26.056 173.645  13451
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 18.64 %
    Favored  : 80.70 %
  Rotamer:
    Outliers :  7.65 %
    Allowed  : 36.73 %
    Favored  : 55.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.27 (0.36), residues: 456
  helix: -1.76 (0.36), residues: 182
  sheet: -2.31 (0.83), residues: 38
  loop : -2.49 (0.37), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 401 
 TYR   0.018   0.002   TYR B  66 
 PHE   0.014   0.002   PHE B 430 
 TRP   0.016   0.002   TRP B 402 
 HIS   0.009   0.001   HIS B 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00645 (23716)
  covalent geometry    : angle       0.77737 (36170)
  hydrogen bonds       : bond        0.08379 (  636)
  hydrogen bonds       : angle       3.16686 ( 1187)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3980.82 seconds
wall clock time: 69 minutes 17.17 seconds (4157.17 seconds total)