Starting phenix.real_space_refine
on Wed Jun 18 12:55:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fli_29279/06_2025/8fli_29279.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fli_29279/06_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_29279/06_2025/8fli_29279.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fli_29279/06_2025/8fli_29279.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fli_29279/06_2025/8fli_29279.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fli_29279/06_2025/8fli_29279.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.78, per 1000 atoms: 0.73
  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: 5.23
  Conformation dependent library (CDL) restraints added in 993.3 milliseconds
  

  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: 10.30
  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: 11.88

  Time building geometry restraints manager: 6.42 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:               0.010
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.350
  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:             0.030
  Extract box with map and model:          0.770
  Check model and map are aligned:         0.140
  Set scattering table:                    0.170
  Process input model:                     62.420
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   71.140
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.016   0.002   TRP B 471 
 HIS   0.004   0.001   HIS B 379 
 PHE   0.013   0.002   PHE B 430 
 TYR   0.016   0.002   TYR B  66 
 ARG   0.006   0.001   ARG B 401 

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

*********************** 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  : 0.919 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 35
  average time/residue: 0.3681
  time to fit residues: 20.1029
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  : 0.852 
-------------------------------------------------------------------------------
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 107 optimal weight:    0.8980
   chunk 96 optimal weight:    0.7980
   chunk 53 optimal weight:   10.0000
   chunk 32 optimal weight:    8.9990
   chunk 64 optimal weight:   20.0000
   chunk 51 optimal weight:    8.9990
   chunk 99 optimal weight:    1.9990
   chunk 38 optimal weight:    6.9990
   chunk 60 optimal weight:    9.9990
   chunk 74 optimal weight:   10.0000
   chunk 115 optimal weight:    0.9980
   overall best weight:    2.3384

-------------------------------------------------------------------------------
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 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 = 0.3760 r_free = 0.3760 target = 0.096004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.068313 restraints weight = 83941.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.070326 restraints weight = 34223.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.071576 restraints weight = 22540.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.1026

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= 0.190
  Angle     :  0.644  13.122  36170  Z= 0.320
  Chirality :  0.032   0.246   4687
  Planarity :  0.005   0.086   1481
  Dihedral  : 26.020 174.181  13453
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 15.13 %
    Favored  : 84.21 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 36.48 %
    Favored  : 58.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.37 (0.36), residues: 456
  helix: -1.96 (0.37), residues: 183
  sheet: -2.14 (0.86), residues: 38
  loop : -2.48 (0.36), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 471 
 HIS   0.003   0.001   HIS B 407 
 PHE   0.010   0.002   PHE B 430 
 TYR   0.016   0.001   TYR B  66 
 ARG   0.005   0.001   ARG B 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07456 (  636)
  hydrogen bonds       : angle       3.00942 ( 1187)
  covalent geometry    : bond        0.00369 (23716)
  covalent geometry    : angle       0.64359 (36170)

*********************** 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: 21
    poor density    : 41
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  226 TRP cc_start: 0.7427 (t60) cc_final: 0.7115 (t60)
REVERT: B  228 GLN cc_start: 0.7838 (pm20) cc_final: 0.7554 (pm20)
REVERT: B  417 ASN cc_start: 0.9074 (t0) cc_final: 0.8867 (t0)
REVERT: B  471 TRP cc_start: 0.6674 (m-10) cc_final: 0.6466 (m-10)
  outliers start: 21
  outliers final: 12
  residues processed: 58
  average time/residue: 0.3613
  time to fit residues: 32.3656
Evaluate side-chains
  50 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 38
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
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  270 LEU
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 49 optimal weight:    5.9990
   chunk 61 optimal weight:   20.0000
   chunk 86 optimal weight:    3.9990
   chunk 6 optimal weight:   10.0000
   chunk 112 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 77 optimal weight:    5.9990
   chunk 18 optimal weight:    8.9990
   chunk 56 optimal weight:    8.9990
   chunk 82 optimal weight:    5.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    5.3990

-------------------------------------------------------------------------------
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 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 = 0.3677 r_free = 0.3677 target = 0.091676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.063700 restraints weight = 86878.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.065619 restraints weight = 37837.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.066769 restraints weight = 25766.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.2206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.067  23716  Z= 0.397
  Angle     :  0.875  12.492  36170  Z= 0.426
  Chirality :  0.043   0.270   4687
  Planarity :  0.006   0.089   1481
  Dihedral  : 26.288 176.537  13451
  Min Nonbonded Distance : 1.810

Molprobity Statistics.
  All-atom Clashscore : 16.99
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 17.32 %
    Favored  : 82.02 %
  Rotamer:
    Outliers :  8.93 %
    Allowed  : 34.95 %
    Favored  : 56.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.65 (0.35), residues: 456
  helix: -2.16 (0.36), residues: 182
  sheet: -2.15 (1.10), residues: 24
  loop : -2.72 (0.34), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 402 
 HIS   0.015   0.002   HIS B 407 
 PHE   0.018   0.003   PHE B 430 
 TYR   0.018   0.002   TYR B  66 
 ARG   0.006   0.001   ARG B 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09656 (  636)
  hydrogen bonds       : angle       3.49602 ( 1187)
  covalent geometry    : bond        0.00776 (23716)
  covalent geometry    : angle       0.87517 (36170)

*********************** 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: 35
    poor density    : 36
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  228 GLN cc_start: 0.8348 (pm20) cc_final: 0.7869 (pm20)
REVERT: B  260 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8164 (ptmt)
REVERT: B  390 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8196 (tmm-80)
REVERT: B  417 ASN cc_start: 0.9142 (t0) cc_final: 0.8924 (t0)
REVERT: B  438 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8041 (pp20)
REVERT: B  471 TRP cc_start: 0.7772 (m-10) cc_final: 0.7519 (m-10)
  outliers start: 35
  outliers final: 22
  residues processed: 67
  average time/residue: 0.3933
  time to fit residues: 39.1276
Evaluate side-chains
  58 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 33
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
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  116 ARG
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  178 VAL
Chi-restraints excluded: chain B residue  196 CYS
Chi-restraints excluded: chain B residue  224 PHE
Chi-restraints excluded: chain B residue  260 LYS
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  342 ILE
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  351 ASP
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  458 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 5 optimal weight:   20.0000
   chunk 57 optimal weight:    5.9990
   chunk 49 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 91 optimal weight:    3.9990
   chunk 11 optimal weight:   10.0000
   chunk 124 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 73 optimal weight:    8.9990
   chunk 113 optimal weight:    2.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.3700 r_free = 0.3700 target = 0.092787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.065122 restraints weight = 85772.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 69)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.067056 restraints weight = 36477.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.068232 restraints weight = 24419.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  23716  Z= 0.301
  Angle     :  0.752  12.675  36170  Z= 0.370
  Chirality :  0.038   0.307   4687
  Planarity :  0.006   0.090   1481
  Dihedral  : 26.134 172.271  13451
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 16.23 %
    Favored  : 83.11 %
  Rotamer:
    Outliers :  8.67 %
    Allowed  : 35.46 %
    Favored  : 55.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.48 (0.35), residues: 456
  helix: -1.99 (0.36), residues: 182
  sheet: -1.98 (1.09), residues: 24
  loop : -2.66 (0.35), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 402 
 HIS   0.008   0.001   HIS B 407 
 PHE   0.015   0.002   PHE B 297 
 TYR   0.017   0.002   TYR B  66 
 ARG   0.005   0.001   ARG B 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08041 (  636)
  hydrogen bonds       : angle       3.19203 ( 1187)
  covalent geometry    : bond        0.00586 (23716)
  covalent geometry    : angle       0.75249 (36170)

*********************** 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
  70 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 36
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   28 TRP cc_start: 0.8232 (OUTLIER) cc_final: 0.7451 (m-90)
REVERT: B   66 TYR cc_start: 0.8108 (t80) cc_final: 0.7521 (t80)
REVERT: B  109 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.7556 (t80)
REVERT: B  228 GLN cc_start: 0.8289 (pm20) cc_final: 0.7769 (pm20)
REVERT: B  390 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.7720 (tmm-80)
REVERT: B  416 LYS cc_start: 0.8932 (tptt) cc_final: 0.8690 (tppt)
REVERT: B  432 THR cc_start: 0.9673 (OUTLIER) cc_final: 0.9375 (p)
REVERT: B  438 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7996 (pp20)
REVERT: B  448 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8509 (tmtt)
  outliers start: 34
  outliers final: 22
  residues processed: 65
  average time/residue: 0.3789
  time to fit residues: 37.6032
Evaluate side-chains
  64 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 36
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 TRP
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue   82 LYS
Chi-restraints excluded: chain B residue  109 TYR
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  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  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  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  432 THR
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 56 optimal weight:    8.9990
   chunk 80 optimal weight:   10.0000
   chunk 115 optimal weight:    2.9990
   chunk 113 optimal weight:    0.4980
   chunk 31 optimal weight:   10.0000
   chunk 43 optimal weight:   20.0000
   chunk 119 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 94 optimal weight:    0.7980
   chunk 57 optimal weight:    6.9990
   overall best weight:    1.6384

-------------------------------------------------------------------------------
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 = 0.3765 r_free = 0.3765 target = 0.096246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.069162 restraints weight = 84079.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.071140 restraints weight = 34574.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.072341 restraints weight = 22532.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.2321

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= 0.143
  Angle     :  0.593  13.729  36170  Z= 0.297
  Chirality :  0.031   0.348   4687
  Planarity :  0.005   0.088   1481
  Dihedral  : 25.834 172.222  13451
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 14.91 %
    Favored  : 84.43 %
  Rotamer:
    Outliers :  6.89 %
    Allowed  : 37.24 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.37), residues: 456
  helix: -1.60 (0.37), residues: 189
  sheet: -1.58 (1.11), residues: 22
  loop : -2.40 (0.37), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 226 
 HIS   0.004   0.001   HIS B 407 
 PHE   0.010   0.001   PHE B 321 
 TYR   0.017   0.001   TYR B  66 
 ARG   0.002   0.001   ARG B 301 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06583 (  636)
  hydrogen bonds       : angle       2.73582 ( 1187)
  covalent geometry    : bond        0.00277 (23716)
  covalent geometry    : angle       0.59253 (36170)

*********************** 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
  70 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 43
  time to evaluate  : 0.853 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   66 TYR cc_start: 0.7902 (t80) cc_final: 0.7382 (t80)
REVERT: B   74 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8199 (mtm-85)
REVERT: B  228 GLN cc_start: 0.7960 (pm20) cc_final: 0.7684 (pm20)
REVERT: B  250 MET cc_start: 0.9254 (tpp) cc_final: 0.9041 (tpp)
REVERT: B  328 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8167 (mmmm)
REVERT: B  416 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8550 (tppt)
REVERT: B  432 THR cc_start: 0.9604 (OUTLIER) cc_final: 0.9309 (p)
REVERT: B  438 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7870 (pp20)
  outliers start: 27
  outliers final: 14
  residues processed: 66
  average time/residue: 0.3821
  time to fit residues: 37.3712
Evaluate side-chains
  57 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 38
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   74 ARG
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  196 CYS
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  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  416 LYS
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  432 THR
Chi-restraints excluded: chain B residue  438 GLU
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 46 optimal weight:   30.0000
   chunk 72 optimal weight:   10.0000
   chunk 102 optimal weight:    0.7980
   chunk 43 optimal weight:    9.9990
   chunk 49 optimal weight:    6.9990
   chunk 16 optimal weight:   10.0000
   chunk 23 optimal weight:    7.9990
   chunk 36 optimal weight:    8.9990
   chunk 61 optimal weight:   20.0000
   chunk 81 optimal weight:   20.0000
   chunk 99 optimal weight:    3.9990
   overall best weight:    5.7588

-------------------------------------------------------------------------------
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 = 0.3682 r_free = 0.3682 target = 0.091669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.064232 restraints weight = 89158.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.066083 restraints weight = 40164.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.067225 restraints weight = 27513.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.067  23716  Z= 0.408
  Angle     :  0.874  12.394  36170  Z= 0.424
  Chirality :  0.043   0.344   4687
  Planarity :  0.006   0.092   1481
  Dihedral  : 26.219 179.713  13451
  Min Nonbonded Distance : 1.823

Molprobity Statistics.
  All-atom Clashscore : 17.51
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 18.20 %
    Favored  : 81.14 %
  Rotamer:
    Outliers :  9.69 %
    Allowed  : 35.71 %
    Favored  : 54.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.59 (0.35), residues: 456
  helix: -2.04 (0.35), residues: 182
  sheet: -2.31 (0.82), residues: 38
  loop : -2.70 (0.36), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 402 
 HIS   0.012   0.002   HIS B 407 
 PHE   0.024   0.003   PHE B 321 
 TYR   0.015   0.002   TYR B  66 
 ARG   0.006   0.001   ARG B 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09482 (  636)
  hydrogen bonds       : angle       3.42796 ( 1187)
  covalent geometry    : bond        0.00795 (23716)
  covalent geometry    : angle       0.87438 (36170)

*********************** 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
  71 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 33
  time to evaluate  : 0.981 
Fit side-chains
   revert: symmetry clash
REVERT: B   28 TRP cc_start: 0.8250 (OUTLIER) cc_final: 0.7655 (m-10)
REVERT: B  328 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8187 (mtmm)
REVERT: B  390 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7794 (tmm-80)
REVERT: B  438 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8154 (pp20)
REVERT: B  448 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8545 (tmtt)
REVERT: B  471 TRP cc_start: 0.8512 (m-10) cc_final: 0.8297 (m-10)
  outliers start: 38
  outliers final: 23
  residues processed: 67
  average time/residue: 0.4249
  time to fit residues: 42.9988
Evaluate side-chains
  60 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 32
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 TRP
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  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  225 VAL
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 92 optimal weight:    7.9990
   chunk 95 optimal weight:    0.8980
   chunk 79 optimal weight:    8.9990
   chunk 43 optimal weight:   20.0000
   chunk 65 optimal weight:    6.9990
   chunk 31 optimal weight:   10.0000
   chunk 4 optimal weight:    6.9990
   chunk 24 optimal weight:    6.9990
   chunk 69 optimal weight:   10.0000
   chunk 115 optimal weight:    0.7980
   chunk 100 optimal weight:    0.2980
   overall best weight:    3.1984

-------------------------------------------------------------------------------
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 = 0.3721 r_free = 0.3721 target = 0.093644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.066445 restraints weight = 87408.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.068307 restraints weight = 38329.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.069456 restraints weight = 25998.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.2726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  23716  Z= 0.245
  Angle     :  0.703  12.714  36170  Z= 0.348
  Chirality :  0.036   0.383   4687
  Planarity :  0.005   0.091   1481
  Dihedral  : 26.074 174.792  13451
  Min Nonbonded Distance : 1.874

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 16.45 %
    Favored  : 82.89 %
  Rotamer:
    Outliers :  9.44 %
    Allowed  : 34.69 %
    Favored  : 55.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.36 (0.36), residues: 456
  helix: -1.75 (0.36), residues: 188
  sheet: -2.20 (0.83), residues: 38
  loop : -2.67 (0.36), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 226 
 HIS   0.007   0.001   HIS B 407 
 PHE   0.024   0.002   PHE B 321 
 TYR   0.017   0.002   TYR B  66 
 ARG   0.004   0.001   ARG B 301 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07516 (  636)
  hydrogen bonds       : angle       3.03618 ( 1187)
  covalent geometry    : bond        0.00478 (23716)
  covalent geometry    : angle       0.70311 (36170)

*********************** 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
  76 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 39
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
REVERT: B   28 TRP cc_start: 0.8157 (OUTLIER) cc_final: 0.7422 (m-90)
REVERT: B   66 TYR cc_start: 0.7950 (t80) cc_final: 0.7352 (t80)
REVERT: B  328 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8057 (mtmm)
REVERT: B  390 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.7740 (tmm-80)
REVERT: B  416 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8663 (tppt)
REVERT: B  438 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8189 (pp20)
REVERT: B  448 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8525 (tmtt)
REVERT: B  471 TRP cc_start: 0.8399 (m-10) cc_final: 0.8193 (m-10)
  outliers start: 37
  outliers final: 26
  residues processed: 70
  average time/residue: 0.4819
  time to fit residues: 49.9342
Evaluate side-chains
  70 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 38
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 TRP
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  168 THR
Chi-restraints excluded: chain B residue  196 CYS
Chi-restraints excluded: chain B residue  225 VAL
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  328 LYS
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  355 GLU
Chi-restraints excluded: chain B residue  387 ILE
Chi-restraints excluded: chain B residue  390 ARG
Chi-restraints excluded: chain B residue  416 LYS
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  437 LYS
Chi-restraints excluded: chain B residue  438 GLU
Chi-restraints excluded: chain B residue  448 LYS
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 49 optimal weight:    5.9990
   chunk 44 optimal weight:   30.0000
   chunk 119 optimal weight:    0.0870
   chunk 19 optimal weight:   10.0000
   chunk 46 optimal weight:   20.0000
   chunk 76 optimal weight:    5.9990
   chunk 91 optimal weight:    0.4980
   chunk 35 optimal weight:    5.9990
   chunk 92 optimal weight:    8.9990
   chunk 77 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    3.7164

-------------------------------------------------------------------------------
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 = 0.3717 r_free = 0.3717 target = 0.093408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.066138 restraints weight = 88055.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.068030 restraints weight = 38445.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.069200 restraints weight = 26110.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  23716  Z= 0.276
  Angle     :  0.723  15.193  36170  Z= 0.356
  Chirality :  0.037   0.386   4687
  Planarity :  0.006   0.091   1481
  Dihedral  : 26.081 175.311  13451
  Min Nonbonded Distance : 1.875

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 17.98 %
    Favored  : 81.36 %
  Rotamer:
    Outliers :  9.18 %
    Allowed  : 34.95 %
    Favored  : 55.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.36 (0.36), residues: 456
  helix: -1.75 (0.36), residues: 188
  sheet: -2.30 (0.84), residues: 39
  loop : -2.65 (0.37), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 226 
 HIS   0.007   0.001   HIS B 407 
 PHE   0.017   0.002   PHE B 321 
 TYR   0.017   0.002   TYR B  66 
 ARG   0.008   0.001   ARG B 440 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07624 (  636)
  hydrogen bonds       : angle       3.06953 ( 1187)
  covalent geometry    : bond        0.00541 (23716)
  covalent geometry    : angle       0.72331 (36170)

*********************** 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
  73 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 37
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   28 TRP cc_start: 0.8158 (OUTLIER) cc_final: 0.7442 (m-90)
REVERT: B  228 GLN cc_start: 0.8055 (pm20) cc_final: 0.7681 (pm20)
REVERT: B  328 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8070 (mtmm)
REVERT: B  390 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.7761 (tmm-80)
REVERT: B  416 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8688 (tppt)
REVERT: B  438 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8202 (pp20)
REVERT: B  448 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8523 (tmtt)
REVERT: B  471 TRP cc_start: 0.8409 (m-10) cc_final: 0.8172 (m-10)
  outliers start: 36
  outliers final: 27
  residues processed: 67
  average time/residue: 0.3987
  time to fit residues: 39.8895
Evaluate side-chains
  69 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 36
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 TRP
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  168 THR
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  196 CYS
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  328 LYS
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  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  416 LYS
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  437 LYS
Chi-restraints excluded: chain B residue  438 GLU
Chi-restraints excluded: chain B residue  448 LYS
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 108 optimal weight:    6.9990
   chunk 55 optimal weight:   10.0000
   chunk 84 optimal weight:    0.9990
   chunk 117 optimal weight:    0.9980
   chunk 23 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 30 optimal weight:   10.0000
   chunk 13 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 62 optimal weight:   10.0000
   chunk 4 optimal weight:    8.9990
   overall best weight:    4.1988

-------------------------------------------------------------------------------
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 = 0.3714 r_free = 0.3714 target = 0.093216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.065921 restraints weight = 87508.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.067814 restraints weight = 38611.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.068983 restraints weight = 26160.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.2758

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= 0.308
  Angle     :  0.745  14.222  36170  Z= 0.365
  Chirality :  0.037   0.388   4687
  Planarity :  0.007   0.149   1481
  Dihedral  : 26.084 175.588  13451
  Min Nonbonded Distance : 1.867

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 17.54 %
    Favored  : 81.80 %
  Rotamer:
    Outliers :  9.18 %
    Allowed  : 34.69 %
    Favored  : 56.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.41 (0.36), residues: 456
  helix: -1.79 (0.36), residues: 188
  sheet: -2.32 (0.83), residues: 39
  loop : -2.68 (0.37), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 226 
 HIS   0.007   0.001   HIS B 407 
 PHE   0.015   0.002   PHE B 321 
 TYR   0.017   0.002   TYR B  66 
 ARG   0.015   0.001   ARG B 401 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07764 (  636)
  hydrogen bonds       : angle       3.10254 ( 1187)
  covalent geometry    : bond        0.00603 (23716)
  covalent geometry    : angle       0.74455 (36170)

*********************** 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
  71 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 35
  time to evaluate  : 0.878 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   28 TRP cc_start: 0.8154 (OUTLIER) cc_final: 0.7609 (m-90)
REVERT: B  328 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8085 (mtmm)
REVERT: B  390 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.7749 (tmm-80)
REVERT: B  416 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8699 (tppt)
REVERT: B  438 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8248 (pp20)
REVERT: B  448 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8524 (tmtt)
REVERT: B  453 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7787 (mmt180)
  outliers start: 36
  outliers final: 28
  residues processed: 65
  average time/residue: 0.4007
  time to fit residues: 38.6560
Evaluate side-chains
  71 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 36
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 TRP
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  196 CYS
Chi-restraints excluded: chain B residue  225 VAL
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  328 LYS
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  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  416 LYS
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  437 LYS
Chi-restraints excluded: chain B residue  438 GLU
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 22 optimal weight:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 76 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 83 optimal weight:    1.9990
   chunk 10 optimal weight:    8.9990
   chunk 52 optimal weight:   10.0000
   chunk 45 optimal weight:   30.0000
   chunk 89 optimal weight:    3.9990
   chunk 53 optimal weight:   20.0000
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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 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 = 0.3710 r_free = 0.3710 target = 0.093048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.065736 restraints weight = 88113.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.067604 restraints weight = 38860.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.068785 restraints weight = 26501.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.2769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  23716  Z= 0.315
  Angle     :  0.752  14.551  36170  Z= 0.369
  Chirality :  0.038   0.389   4687
  Planarity :  0.006   0.094   1481
  Dihedral  : 26.093 175.949  13451
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 18.20 %
    Favored  : 81.14 %
  Rotamer:
    Outliers :  9.95 %
    Allowed  : 34.44 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.44 (0.36), residues: 456
  helix: -1.79 (0.36), residues: 188
  sheet: -2.38 (0.83), residues: 39
  loop : -2.70 (0.37), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.003   TRP B 471 
 HIS   0.008   0.001   HIS B 407 
 PHE   0.014   0.002   PHE B 321 
 TYR   0.016   0.002   TYR B  66 
 ARG   0.009   0.001   ARG B 401 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07869 (  636)
  hydrogen bonds       : angle       3.12921 ( 1187)
  covalent geometry    : bond        0.00616 (23716)
  covalent geometry    : angle       0.75192 (36170)

********************** 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
  75 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 36
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   28 TRP cc_start: 0.8151 (OUTLIER) cc_final: 0.7611 (m-90)
REVERT: B  328 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8088 (mtmm)
REVERT: B  390 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.7759 (tmm-80)
REVERT: B  416 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8709 (tppt)
REVERT: B  438 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8280 (pp20)
REVERT: B  448 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8525 (tmtt)
REVERT: B  453 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7792 (mmt180)
  outliers start: 39
  outliers final: 30
  residues processed: 69
  average time/residue: 0.3664
  time to fit residues: 37.8204
Evaluate side-chains
  73 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 36
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 TRP
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  148 GLU
Chi-restraints excluded: chain B residue  167 CYS
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  225 VAL
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  328 LYS
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  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  416 LYS
Chi-restraints excluded: chain B residue  427 HIS
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  437 LYS
Chi-restraints excluded: chain B residue  438 GLU
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 60 optimal weight:    8.9990
   chunk 93 optimal weight:    3.9990
   chunk 80 optimal weight:   10.0000
   chunk 90 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 11 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 109 optimal weight:    0.5980
   chunk 15 optimal weight:    7.9990
   chunk 112 optimal weight:    2.9990
   chunk 118 optimal weight:    0.8980
   overall best weight:    2.4986

-------------------------------------------------------------------------------
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 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 = 0.3744 r_free = 0.3744 target = 0.094819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.067622 restraints weight = 85641.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.069531 restraints weight = 37864.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.070716 restraints weight = 25591.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.2794

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= 0.202
  Angle     :  0.655  14.935  36170  Z= 0.326
  Chirality :  0.033   0.403   4687
  Planarity :  0.005   0.094   1481
  Dihedral  : 25.986 175.653  13451
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  : 16.45 %
    Favored  : 82.89 %
  Rotamer:
    Outliers :  9.18 %
    Allowed  : 34.44 %
    Favored  : 56.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.12 (0.37), residues: 456
  helix: -1.57 (0.37), residues: 188
  sheet: -1.95 (0.86), residues: 36
  loop : -2.55 (0.38), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP B 471 
 HIS   0.006   0.001   HIS B 407 
 PHE   0.015   0.001   PHE B 321 
 TYR   0.018   0.001   TYR B  66 
 ARG   0.004   0.001   ARG B  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06944 (  636)
  hydrogen bonds       : angle       2.88271 ( 1187)
  covalent geometry    : bond        0.00392 (23716)
  covalent geometry    : angle       0.65469 (36170)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7140.80 seconds
wall clock time: 126 minutes 0.56 seconds (7560.56 seconds total)