Starting phenix.real_space_refine
on Wed Feb  4 13:53:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rsi_24672/02_2026/7rsi_24672_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rsi_24672/02_2026/7rsi_24672.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rsi_24672/02_2026/7rsi_24672_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rsi_24672/02_2026/7rsi_24672_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rsi_24672/02_2026/7rsi_24672.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rsi_24672/02_2026/7rsi_24672.map"
  }
  resolution = 4.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
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: 7
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     Mg      1      5.21       5
     S      31      5.16       5
     C    3472      2.51       5
     N     953      2.21       5
     O    1027      1.98       5
     H    5400      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10886
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 6416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 392, 6416
          Classifications: {'peptide': 392}
          Link IDs: {'PTRANS': 8, 'TRANS': 383}
          Chain breaks: 5
    Chain: "C"
      Number of atoms: 4442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 294, 4442
          Classifications: {'peptide': 294}
          Link IDs: {'PTRANS': 6, 'TRANS': 287}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 74
          Unresolved non-hydrogen angles: 94
          Unresolved non-hydrogen dihedrals: 56
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 40
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.86, per 1000 atoms: 0.17
  Number of scatterers: 10886
  At special positions: 0
  Unit cell: (64.61, 97.37, 111.02, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      31     16.00
     P       2     15.00
     Mg      1     11.99
     O    1027      8.00
     N     953      7.00
     C    3472      6.00
     H    5400      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.87
  Conformation dependent library (CDL) restraints added in 361.8 milliseconds
  

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1318

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 3 sheets defined
      63.4% alpha, 9.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'B' and resid 5 through 22
    Processing helix  chain 'B' and resid 38 through 51
    Processing helix  chain 'B' and resid 87 through 105
    Processing helix  chain 'B' and resid 112 through 126
      removed outlier: 3.672A  pdb=" N   GLU B 116 " --> pdb=" O   SER B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 152
      removed outlier: 3.644A  pdb=" N   GLN B 140 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 173
    Processing helix  chain 'B' and resid 201 through 221
      removed outlier: 4.504A  pdb=" N   THR B 208 " --> pdb=" O   GLU B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 241
    Processing helix  chain 'B' and resid 245 through 263
    Processing helix  chain 'B' and resid 265 through 280
      removed outlier: 4.925A  pdb=" N   HIS B 271 " --> pdb=" O   MET B 267 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   CYS B 272 " --> pdb=" O   GLU B 268 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   LEU B 273 " --> pdb=" O   ALA B 269 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   SER B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 306
    Processing helix  chain 'B' and resid 306 through 326
    Processing helix  chain 'B' and resid 327 through 329
      No H-bonds generated for 'chain 'B' and resid 327 through 329'
    Processing helix  chain 'B' and resid 346 through 364
      removed outlier: 4.284A  pdb=" N   ARG B 359 " --> pdb=" O   GLU B 355 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ALA B 362 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 382
      removed outlier: 4.205A  pdb=" N   LYS B 380 " --> pdb=" O   ALA B 376 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 411
      removed outlier: 3.638A  pdb=" N   VAL B 403 " --> pdb=" O   GLY B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 434
      removed outlier: 3.524A  pdb=" N   ASP B 418 " --> pdb=" O   GLY B 414 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL B 422 " --> pdb=" O   ASP B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 440 through 453
    Processing helix  chain 'B' and resid 455 through 460
    Processing helix  chain 'B' and resid 464 through 486
      removed outlier: 3.545A  pdb=" N   TYR B 482 " --> pdb=" O   ALA B 478 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 22 through 28
    Processing helix  chain 'C' and resid 85 through 92
    Processing helix  chain 'C' and resid 93 through 102
      removed outlier: 3.598A  pdb=" N   ARG C  99 " --> pdb=" O   LYS C  95 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   SER C 100 " --> pdb=" O   PRO C  96 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 124
    Processing helix  chain 'C' and resid 131 through 147
    Processing helix  chain 'C' and resid 199 through 213
    Processing helix  chain 'C' and resid 280 through 293
    Processing helix  chain 'C' and resid 311 through 316
    Processing helix  chain 'C' and resid 317 through 320
      removed outlier: 3.877A  pdb=" N   LEU C 320 " --> pdb=" O   LYS C 317 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 317 through 320'
    Processing helix  chain 'C' and resid 335 through 337
      No H-bonds generated for 'chain 'C' and resid 335 through 337'
    Processing helix  chain 'C' and resid 338 through 353
    Processing sheet with id=AA1, first strand: chain 'C' and resid 78 through 80
      removed outlier: 6.980A  pdb=" N   VAL C  14 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 8.687A  pdb=" N   PHE C  80 " --> pdb=" O   VAL C  14 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   VAL C  16 " --> pdb=" O   PHE C  80 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   LYS C  13 " --> pdb=" O   MET C 328 " (cutoff:3.500A)
      removed outlier: 7.848A  pdb=" N   ALA C 330 " --> pdb=" O   LYS C  13 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   VAL C  15 " --> pdb=" O   ALA C 330 " (cutoff:3.500A)
      removed outlier: 7.638A  pdb=" N   VAL C 332 " --> pdb=" O   VAL C  15 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   ARG C  17 " --> pdb=" O   VAL C 332 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   CYS C 107 " --> pdb=" O   SER C 255 " (cutoff:3.500A)
      removed outlier: 7.635A  pdb=" N   ILE C 257 " --> pdb=" O   CYS C 107 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   VAL C 109 " --> pdb=" O   ILE C 257 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 36
    Processing sheet with id=AA3, first strand: chain 'C' and resid 178 through 181

    336 hydrogen bonds defined for protein.
    993 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.36

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        0.96 -     1.13: 5386
        1.13 -     1.30: 918
        1.30 -     1.47: 2206
        1.47 -     1.64: 2426
        1.64 -     1.81: 48
  Bond restraints: 10984
  Sorted by residual:
  bond pdb=" CZ3 TRP B 314 "
       pdb=" HZ3 TRP B 314 "
    ideal  model  delta    sigma   weight residual
    0.930  1.093 -0.163 2.00e-02 2.50e+03 6.61e+01
  bond pdb=" CD2 PHE B 409 "
       pdb=" HD2 PHE B 409 "
    ideal  model  delta    sigma   weight residual
    0.930  1.092 -0.162 2.00e-02 2.50e+03 6.58e+01
  bond pdb=" CE1 TYR B 230 "
       pdb=" HE1 TYR B 230 "
    ideal  model  delta    sigma   weight residual
    0.930  1.092 -0.162 2.00e-02 2.50e+03 6.58e+01
  bond pdb=" N   VAL C 187 "
       pdb=" H   VAL C 187 "
    ideal  model  delta    sigma   weight residual
    0.860  1.022 -0.162 2.00e-02 2.50e+03 6.54e+01
  bond pdb=" CD2 PHE B 203 "
       pdb=" HD2 PHE B 203 "
    ideal  model  delta    sigma   weight residual
    0.930  1.092 -0.162 2.00e-02 2.50e+03 6.54e+01
  ... (remaining 10979 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.28: 18048
        3.28 -     6.55: 1595
        6.55 -     9.83: 100
        9.83 -    13.10: 14
       13.10 -    16.38: 6
  Bond angle restraints: 19763
  Sorted by residual:
  angle pdb=" N   ASP B 339 "
        pdb=" CA  ASP B 339 "
        pdb=" C   ASP B 339 "
      ideal   model   delta    sigma   weight residual
     111.69   99.23   12.46 1.23e+00 6.61e-01 1.03e+02
  angle pdb=" C   GLN C 196 "
        pdb=" N   PRO C 197 "
        pdb=" CA  PRO C 197 "
      ideal   model   delta    sigma   weight residual
     120.52  129.44   -8.92 9.90e-01 1.02e+00 8.12e+01
  angle pdb=" C   SER C 333 "
        pdb=" N   PRO C 334 "
        pdb=" CA  PRO C 334 "
      ideal   model   delta    sigma   weight residual
     119.64  128.12   -8.48 1.01e+00 9.80e-01 7.05e+01
  angle pdb=" C   GLY B  51 "
        pdb=" N   PRO B  52 "
        pdb=" CA  PRO B  52 "
      ideal   model   delta    sigma   weight residual
     119.47  129.14   -9.67 1.16e+00 7.43e-01 6.95e+01
  angle pdb=" C   GLY C 175 "
        pdb=" N   PRO C 176 "
        pdb=" CA  PRO C 176 "
      ideal   model   delta    sigma   weight residual
     119.93  128.84   -8.91 1.07e+00 8.73e-01 6.94e+01
  ... (remaining 19758 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.00: 5039
       33.00 -    66.00: 87
       66.00 -    98.99: 5
       98.99 -   131.99: 1
      131.99 -   164.99: 2
  Dihedral angle restraints: 5134
    sinusoidal: 2746
      harmonic: 2388
  Sorted by residual:
  dihedral pdb=" O1B ADP C 502 "
           pdb=" O3A ADP C 502 "
           pdb=" PB  ADP C 502 "
           pdb=" PA  ADP C 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  104.98 -164.99     1      2.00e+01 2.50e-03 4.72e+01
  dihedral pdb=" C5' ADP C 502 "
           pdb=" O5' ADP C 502 "
           pdb=" PA  ADP C 502 "
           pdb=" O2A ADP C 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  101.71 -161.70     1      2.00e+01 2.50e-03 4.68e+01
  dihedral pdb=" O2A ADP C 502 "
           pdb=" O3A ADP C 502 "
           pdb=" PA  ADP C 502 "
           pdb=" PB  ADP C 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   56.76 -116.76     1      2.00e+01 2.50e-03 3.48e+01
  ... (remaining 5131 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 485
       0.055 -    0.109: 252
       0.109 -    0.163: 85
       0.163 -    0.218: 19
       0.218 -    0.272: 4
  Chirality restraints: 845
  Sorted by residual:
  chirality pdb=" CA  ARG B 126 "
            pdb=" N   ARG B 126 "
            pdb=" C   ARG B 126 "
            pdb=" CB  ARG B 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" CA  TYR B 218 "
            pdb=" N   TYR B 218 "
            pdb=" C   TYR B 218 "
            pdb=" CB  TYR B 218 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CA  ASN B 242 "
            pdb=" N   ASN B 242 "
            pdb=" C   ASN B 242 "
            pdb=" CB  ASN B 242 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.34e+00
  ... (remaining 842 not shown)

  Planarity restraints: 1619
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' ADP C 502 "   -0.468 2.00e-02 2.50e+03   1.84e-01 9.35e+02
        pdb=" C2  ADP C 502 "    0.056 2.00e-02 2.50e+03
        pdb=" C4  ADP C 502 "    0.128 2.00e-02 2.50e+03
        pdb=" C5  ADP C 502 "    0.025 2.00e-02 2.50e+03
        pdb=" C6  ADP C 502 "   -0.071 2.00e-02 2.50e+03
        pdb=" C8  ADP C 502 "    0.175 2.00e-02 2.50e+03
        pdb=" N1  ADP C 502 "   -0.046 2.00e-02 2.50e+03
        pdb=" N3  ADP C 502 "    0.139 2.00e-02 2.50e+03
        pdb=" N6  ADP C 502 "   -0.193 2.00e-02 2.50e+03
        pdb=" N7  ADP C 502 "    0.066 2.00e-02 2.50e+03
        pdb=" N9  ADP C 502 "    0.188 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 271 "    0.078 2.00e-02 2.50e+03   7.91e-02 1.41e+02
        pdb=" CG  HIS B 271 "    0.038 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 271 "    0.073 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 271 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 271 "    0.039 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 271 "   -0.019 2.00e-02 2.50e+03
        pdb=" HD1 HIS B 271 "   -0.183 2.00e-02 2.50e+03
        pdb=" HD2 HIS B 271 "   -0.063 2.00e-02 2.50e+03
        pdb=" HE1 HIS B 271 "    0.059 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS C  31 "    0.066 2.00e-02 2.50e+03   7.67e-02 1.32e+02
        pdb=" CG  HIS C  31 "    0.044 2.00e-02 2.50e+03
        pdb=" ND1 HIS C  31 "    0.078 2.00e-02 2.50e+03
        pdb=" CD2 HIS C  31 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE1 HIS C  31 "    0.038 2.00e-02 2.50e+03
        pdb=" NE2 HIS C  31 "   -0.021 2.00e-02 2.50e+03
        pdb=" HD1 HIS C  31 "   -0.178 2.00e-02 2.50e+03
        pdb=" HD2 HIS C  31 "   -0.063 2.00e-02 2.50e+03
        pdb=" HE1 HIS C  31 "    0.053 2.00e-02 2.50e+03
  ... (remaining 1616 not shown)

  Histogram of nonbonded interaction distances:
        1.15 -     1.84: 138
        1.84 -     2.53: 9851
        2.53 -     3.22: 35371
        3.22 -     3.91: 43301
        3.91 -     4.60: 67281
  Nonbonded interactions: 155942
  Sorted by model distance:
  nonbonded pdb=" O   ARG B  21 "
            pdb="HH11 ARG B  21 "
     model   vdw
     1.154 2.450
  nonbonded pdb=" OE1 GLU B 156 "
            pdb=" H   GLU B 156 "
     model   vdw
     1.384 2.450
  nonbonded pdb=" OE1 GLU B 225 "
            pdb=" H   GLU B 225 "
     model   vdw
     1.415 2.450
  nonbonded pdb=" OE1 GLU B 437 "
            pdb=" H   GLU B 437 "
     model   vdw
     1.504 2.450
  nonbonded pdb=" OG1 THR C  93 "
            pdb=" H   THR C  94 "
     model   vdw
     1.513 2.450
  ... (remaining 155937 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.070
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.450
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7093
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      :  0.015   0.102   5584  Z= 0.948
  Angle     :  1.512  16.376   7533  Z= 1.030
  Chirality :  0.073   0.272    845
  Planarity :  0.009   0.184    956
  Dihedral  : 12.443 164.987   2054
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.90 %
    Allowed  :  4.52 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.31), residues: 664
  helix:  0.01 (0.23), residues: 398
  sheet: -1.10 (0.64), residues: 49
  loop : -0.06 (0.47), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  19 
 TYR   0.068   0.008   TYR B 482 
 PHE   0.030   0.006   PHE B 280 
 TRP   0.022   0.007   TRP B 314 
 HIS   0.007   0.002   HIS C 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.01489 ( 5584)
  covalent geometry    : angle       1.51234 ( 7533)
  hydrogen bonds       : bond        0.17460 (  336)
  hydrogen bonds       : angle       7.56430 (  993)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  276 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue ILE  281 is missing expected H atoms. Skipping.
Residue SER  284 is missing expected H atoms. Skipping.
Residue LEU  285 is missing expected H atoms. Skipping.
Residue LEU  286 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue VAL  291 is missing expected H atoms. Skipping.
Residue ILE  292 is missing expected H atoms. Skipping.
Residue LEU  295 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue LYS  299 is missing expected H atoms. Skipping.
Evaluate side-chains
  133 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  223 MET cc_start: 0.9538 (mmp) cc_final: 0.9319 (mmm)
REVERT: C  166 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7877 (tm-30)
REVERT: C  173 ASN cc_start: 0.7473 (t0) cc_final: 0.7210 (t0)
REVERT: C  176 PRO cc_start: 0.8545 (Cg_exo) cc_final: 0.8288 (Cg_endo)
REVERT: C  236 LEU cc_start: 0.7363 (tp) cc_final: 0.7093 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1717
  time to fit residues: 28.8020
Evaluate side-chains
  106 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 100 HIS
B 209 HIS
B 324 ASN
B 330 GLN
B 464 GLN
** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.081363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.058903 restraints weight = 101951.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.062419 restraints weight = 59180.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.065142 restraints weight = 38359.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.067242 restraints weight = 26716.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.068870 restraints weight = 19616.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5098
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5584  Z= 0.236
  Angle     :  0.710   7.389   7533  Z= 0.405
  Chirality :  0.041   0.155    845
  Planarity :  0.005   0.037    956
  Dihedral  : 11.067 170.651    752
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.82 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  1.56 %
    Favored  : 98.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.32), residues: 664
  helix:  0.23 (0.25), residues: 413
  sheet: -0.82 (0.62), residues: 62
  loop : -0.52 (0.47), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  40 
 TYR   0.022   0.003   TYR B 169 
 PHE   0.019   0.002   PHE B 430 
 TRP   0.008   0.002   TRP B 314 
 HIS   0.006   0.002   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 5584)
  covalent geometry    : angle       0.70973 ( 7533)
  hydrogen bonds       : bond        0.07015 (  336)
  hydrogen bonds       : angle       6.30360 (  993)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  276 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue ILE  281 is missing expected H atoms. Skipping.
Residue SER  284 is missing expected H atoms. Skipping.
Residue LEU  285 is missing expected H atoms. Skipping.
Residue LEU  286 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue VAL  291 is missing expected H atoms. Skipping.
Residue ILE  292 is missing expected H atoms. Skipping.
Residue LEU  295 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue LYS  299 is missing expected H atoms. Skipping.
Evaluate side-chains
  126 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  125 LEU cc_start: 0.7601 (mt) cc_final: 0.7399 (mt)
REVERT: C  166 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7657 (tm-30)
REVERT: C  236 LEU cc_start: 0.7859 (tp) cc_final: 0.7074 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1648
  time to fit residues: 25.9156
Evaluate side-chains
  96 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 35 optimal weight:   10.0000
   chunk 53 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 63 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 54 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
** C 247 GLN ** 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 = 0.3736 r_free = 0.3736 target = 0.079447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.057507 restraints weight = 103649.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.060811 restraints weight = 61913.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.063313 restraints weight = 41335.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.065252 restraints weight = 29736.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.066707 restraints weight = 22509.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6807
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5584  Z= 0.165
  Angle     :  0.587   6.442   7533  Z= 0.333
  Chirality :  0.039   0.153    845
  Planarity :  0.004   0.050    956
  Dihedral  : 10.491 168.247    752
  Min Nonbonded Distance : 1.741

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.32), residues: 664
  helix:  0.49 (0.25), residues: 413
  sheet: -0.50 (0.67), residues: 62
  loop : -0.84 (0.46), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 450 
 TYR   0.016   0.002   TYR B 482 
 PHE   0.020   0.002   PHE C  76 
 TRP   0.008   0.001   TRP B 314 
 HIS   0.011   0.001   HIS C 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 5584)
  covalent geometry    : angle       0.58709 ( 7533)
  hydrogen bonds       : bond        0.06053 (  336)
  hydrogen bonds       : angle       5.88047 (  993)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  276 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue ILE  281 is missing expected H atoms. Skipping.
Residue SER  284 is missing expected H atoms. Skipping.
Residue LEU  285 is missing expected H atoms. Skipping.
Residue LEU  286 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue VAL  291 is missing expected H atoms. Skipping.
Residue ILE  292 is missing expected H atoms. Skipping.
Residue LEU  295 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue LYS  299 is missing expected H atoms. Skipping.
Evaluate side-chains
  116 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  125 LEU cc_start: 0.8485 (mt) cc_final: 0.8284 (mt)
REVERT: B  223 MET cc_start: 0.9601 (mmp) cc_final: 0.9366 (mmm)
REVERT: C  232 PHE cc_start: 0.9015 (m-80) cc_final: 0.8416 (m-80)
REVERT: C  236 LEU cc_start: 0.6486 (tp) cc_final: 0.6065 (tp)
REVERT: C  338 PHE cc_start: 0.7847 (m-80) cc_final: 0.7586 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1577
  time to fit residues: 23.6594
Evaluate side-chains
  99 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 10 optimal weight:    0.8980
   chunk 35 optimal weight:    9.9990
   chunk 16 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 7 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
B 170 ASN
B 209 HIS
B 474 GLN
C 211 ASN
** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.079437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.058012 restraints weight = 110809.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.061262 restraints weight = 67188.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.063679 restraints weight = 45266.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.065550 restraints weight = 32656.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.066989 restraints weight = 24782.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6867
moved from start:          0.3725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5584  Z= 0.148
  Angle     :  0.540   5.904   7533  Z= 0.306
  Chirality :  0.038   0.151    845
  Planarity :  0.004   0.049    956
  Dihedral  :  9.948 160.469    752
  Min Nonbonded Distance : 1.853

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.33), residues: 664
  helix:  0.71 (0.25), residues: 417
  sheet: -0.59 (0.67), residues: 62
  loop : -0.90 (0.46), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  40 
 TYR   0.016   0.001   TYR B 169 
 PHE   0.013   0.002   PHE B 430 
 TRP   0.004   0.001   TRP B   6 
 HIS   0.008   0.002   HIS B 419 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 5584)
  covalent geometry    : angle       0.53985 ( 7533)
  hydrogen bonds       : bond        0.05242 (  336)
  hydrogen bonds       : angle       5.65960 (  993)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  276 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue ILE  281 is missing expected H atoms. Skipping.
Residue SER  284 is missing expected H atoms. Skipping.
Residue LEU  285 is missing expected H atoms. Skipping.
Residue LEU  286 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue VAL  291 is missing expected H atoms. Skipping.
Residue ILE  292 is missing expected H atoms. Skipping.
Residue LEU  295 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue LYS  299 is missing expected H atoms. Skipping.
Evaluate side-chains
  113 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  139 ILE cc_start: 0.9776 (pt) cc_final: 0.9518 (pt)
REVERT: B  142 GLN cc_start: 0.9450 (mt0) cc_final: 0.9150 (mt0)
REVERT: B  223 MET cc_start: 0.9602 (mmp) cc_final: 0.9344 (mmm)
REVERT: B  481 TYR cc_start: 0.6437 (m-10) cc_final: 0.6008 (m-10)
REVERT: C  232 PHE cc_start: 0.8974 (m-80) cc_final: 0.8344 (m-80)
REVERT: C  338 PHE cc_start: 0.7813 (m-80) cc_final: 0.7556 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1801
  time to fit residues: 25.9859
Evaluate side-chains
  96 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 56 optimal weight:    6.9990
   chunk 36 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 170 ASN
B 470 ASN
** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 247 GLN ** 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 = 0.3706 r_free = 0.3706 target = 0.078149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.059409 restraints weight = 114519.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.061999 restraints weight = 74481.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.064005 restraints weight = 52781.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.065557 restraints weight = 39572.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.066727 restraints weight = 30911.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6987
moved from start:          0.4006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5584  Z= 0.193
  Angle     :  0.586   6.856   7533  Z= 0.333
  Chirality :  0.038   0.137    845
  Planarity :  0.004   0.049    956
  Dihedral  :  9.240 136.597    752
  Min Nonbonded Distance : 1.830

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.32), residues: 664
  helix:  0.57 (0.25), residues: 417
  sheet: -0.77 (0.67), residues: 62
  loop : -1.16 (0.44), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 450 
 TYR   0.018   0.002   TYR B 169 
 PHE   0.018   0.002   PHE B 430 
 TRP   0.004   0.001   TRP B   6 
 HIS   0.007   0.002   HIS B 419 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 5584)
  covalent geometry    : angle       0.58576 ( 7533)
  hydrogen bonds       : bond        0.05344 (  336)
  hydrogen bonds       : angle       5.71325 (  993)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  276 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue ILE  281 is missing expected H atoms. Skipping.
Residue SER  284 is missing expected H atoms. Skipping.
Residue LEU  285 is missing expected H atoms. Skipping.
Residue LEU  286 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue VAL  291 is missing expected H atoms. Skipping.
Residue ILE  292 is missing expected H atoms. Skipping.
Residue LEU  295 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue LYS  299 is missing expected H atoms. Skipping.
Evaluate side-chains
  108 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  223 MET cc_start: 0.9583 (mmp) cc_final: 0.9321 (mmm)
REVERT: C  107 CYS cc_start: 0.7997 (t) cc_final: 0.7670 (t)
REVERT: C  236 LEU cc_start: 0.6728 (tp) cc_final: 0.6242 (tp)
REVERT: C  338 PHE cc_start: 0.7757 (m-80) cc_final: 0.7549 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1901
  time to fit residues: 26.2730
Evaluate side-chains
  91 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 60 optimal weight:    0.6980
   chunk 16 optimal weight:    4.9990
   chunk 42 optimal weight:    7.9990
   chunk 4 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 66 optimal weight:    0.3980
   chunk 38 optimal weight:    7.9990
   chunk 28 optimal weight:    0.6980
   chunk 40 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B 143 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 = 0.3774 r_free = 0.3774 target = 0.080671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.059766 restraints weight = 112303.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.062746 restraints weight = 71690.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.065038 restraints weight = 49919.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.066828 restraints weight = 36787.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.068201 restraints weight = 28332.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6793
moved from start:          0.4220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   5584  Z= 0.122
  Angle     :  0.522   6.094   7533  Z= 0.289
  Chirality :  0.038   0.144    845
  Planarity :  0.004   0.048    956
  Dihedral  :  8.805 125.766    752
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.32), residues: 664
  helix:  0.78 (0.25), residues: 419
  sheet: -0.82 (0.70), residues: 57
  loop : -1.16 (0.43), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 442 
 TYR   0.016   0.001   TYR C 159 
 PHE   0.056   0.002   PHE C 232 
 TRP   0.005   0.001   TRP B   6 
 HIS   0.009   0.001   HIS B 426 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 5584)
  covalent geometry    : angle       0.52240 ( 7533)
  hydrogen bonds       : bond        0.04831 (  336)
  hydrogen bonds       : angle       5.40325 (  993)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  276 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue ILE  281 is missing expected H atoms. Skipping.
Residue SER  284 is missing expected H atoms. Skipping.
Residue LEU  285 is missing expected H atoms. Skipping.
Residue LEU  286 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue VAL  291 is missing expected H atoms. Skipping.
Residue ILE  292 is missing expected H atoms. Skipping.
Residue LEU  295 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue LYS  299 is missing expected H atoms. Skipping.
Evaluate side-chains
  114 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  139 ILE cc_start: 0.9813 (pt) cc_final: 0.9593 (pt)
REVERT: B  142 GLN cc_start: 0.9423 (mt0) cc_final: 0.9123 (mt0)
REVERT: B  223 MET cc_start: 0.9617 (mmp) cc_final: 0.9399 (mmm)
REVERT: B  315 ILE cc_start: 0.9485 (mm) cc_final: 0.9284 (mm)
REVERT: B  318 CYS cc_start: 0.9379 (m) cc_final: 0.9091 (p)
REVERT: B  426 HIS cc_start: 0.9254 (t-170) cc_final: 0.8947 (t-90)
REVERT: C  236 LEU cc_start: 0.7024 (tp) cc_final: 0.6576 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1906
  time to fit residues: 27.8424
Evaluate side-chains
  99 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 65 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 43 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 61 optimal weight:   30.0000
   chunk 40 optimal weight:    0.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** B 143 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 = 0.3696 r_free = 0.3696 target = 0.077638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.059077 restraints weight = 109425.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.061660 restraints weight = 71209.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.063645 restraints weight = 50294.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.065178 restraints weight = 37533.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.066354 restraints weight = 29309.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7000
moved from start:          0.4534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5584  Z= 0.188
  Angle     :  0.580   6.052   7533  Z= 0.329
  Chirality :  0.037   0.136    845
  Planarity :  0.004   0.047    956
  Dihedral  :  8.367 114.799    752
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.33), residues: 664
  helix:  0.67 (0.25), residues: 417
  sheet: -1.23 (0.65), residues: 62
  loop : -1.26 (0.44), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 393 
 TYR   0.019   0.002   TYR B 169 
 PHE   0.015   0.002   PHE B 430 
 TRP   0.004   0.001   TRP B   6 
 HIS   0.008   0.002   HIS B 419 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 5584)
  covalent geometry    : angle       0.58025 ( 7533)
  hydrogen bonds       : bond        0.04967 (  336)
  hydrogen bonds       : angle       5.53395 (  993)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  276 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue ILE  281 is missing expected H atoms. Skipping.
Residue SER  284 is missing expected H atoms. Skipping.
Residue LEU  285 is missing expected H atoms. Skipping.
Residue LEU  286 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue VAL  291 is missing expected H atoms. Skipping.
Residue ILE  292 is missing expected H atoms. Skipping.
Residue LEU  295 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue LYS  299 is missing expected H atoms. Skipping.
Evaluate side-chains
  105 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  139 ILE cc_start: 0.9812 (pt) cc_final: 0.9591 (pt)
REVERT: B  142 GLN cc_start: 0.9443 (mt0) cc_final: 0.9138 (mt0)
REVERT: B  223 MET cc_start: 0.9593 (mmp) cc_final: 0.9344 (mmm)
REVERT: C  236 LEU cc_start: 0.6856 (tp) cc_final: 0.6365 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1903
  time to fit residues: 25.5067
Evaluate side-chains
  90 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 56 optimal weight:    8.9990
   chunk 5 optimal weight:    6.9990
   chunk 36 optimal weight:    0.3980
   chunk 8 optimal weight:    2.9990
   chunk 18 optimal weight:    0.3980
   chunk 9 optimal weight:    0.8980
   chunk 61 optimal weight:   30.0000
   chunk 29 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.080075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.060582 restraints weight = 110592.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.063394 restraints weight = 71616.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.065537 restraints weight = 50353.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.067164 restraints weight = 37318.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.068373 restraints weight = 28967.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6944
moved from start:          0.4684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5584  Z= 0.119
  Angle     :  0.520   6.242   7533  Z= 0.286
  Chirality :  0.038   0.175    845
  Planarity :  0.004   0.049    956
  Dihedral  :  7.952 102.506    752
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.33), residues: 664
  helix:  0.96 (0.26), residues: 418
  sheet: -1.18 (0.65), residues: 62
  loop : -1.17 (0.44), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 442 
 TYR   0.021   0.002   TYR B 383 
 PHE   0.048   0.002   PHE C 232 
 TRP   0.014   0.001   TRP B   6 
 HIS   0.006   0.001   HIS B 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 5584)
  covalent geometry    : angle       0.52028 ( 7533)
  hydrogen bonds       : bond        0.04618 (  336)
  hydrogen bonds       : angle       5.30030 (  993)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  276 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue ILE  281 is missing expected H atoms. Skipping.
Residue SER  284 is missing expected H atoms. Skipping.
Residue LEU  285 is missing expected H atoms. Skipping.
Residue LEU  286 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue VAL  291 is missing expected H atoms. Skipping.
Residue ILE  292 is missing expected H atoms. Skipping.
Residue LEU  295 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue LYS  299 is missing expected H atoms. Skipping.
Evaluate side-chains
  107 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  139 ILE cc_start: 0.9809 (pt) cc_final: 0.9572 (pt)
REVERT: B  142 GLN cc_start: 0.9418 (mt0) cc_final: 0.9100 (mt0)
REVERT: B  223 MET cc_start: 0.9575 (mmp) cc_final: 0.9306 (mmm)
REVERT: B  263 LYS cc_start: 0.9004 (mmtt) cc_final: 0.8668 (mmtt)
REVERT: B  315 ILE cc_start: 0.9433 (mm) cc_final: 0.9221 (mm)
REVERT: B  318 CYS cc_start: 0.9525 (m) cc_final: 0.9198 (p)
REVERT: B  426 HIS cc_start: 0.9371 (t-90) cc_final: 0.8987 (t-90)
REVERT: C  232 PHE cc_start: 0.8083 (m-80) cc_final: 0.7506 (m-80)
REVERT: C  236 LEU cc_start: 0.6903 (tp) cc_final: 0.6467 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1587
  time to fit residues: 21.9281
Evaluate side-chains
  97 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 60 optimal weight:    0.4980
   chunk 3 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 61 optimal weight:    9.9990
   chunk 50 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 64 optimal weight:    6.9990
   chunk 34 optimal weight:    8.9990
   overall best weight:    2.4786

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

Flipped N/Q/H residues before XYZ refinement:
C 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.075939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.057883 restraints weight = 113456.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.060281 restraints weight = 75255.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.062077 restraints weight = 54012.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.063451 restraints weight = 41035.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.064487 restraints weight = 32584.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7013
moved from start:          0.4835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5584  Z= 0.197
  Angle     :  0.598   6.226   7533  Z= 0.340
  Chirality :  0.038   0.137    845
  Planarity :  0.004   0.047    956
  Dihedral  :  7.192  94.172    752
  Min Nonbonded Distance : 1.838

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.33), residues: 664
  helix:  0.67 (0.26), residues: 419
  sheet: -1.25 (0.65), residues: 62
  loop : -1.39 (0.45), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 126 
 TYR   0.020   0.002   TYR B 169 
 PHE   0.023   0.002   PHE C 232 
 TRP   0.010   0.002   TRP B 249 
 HIS   0.008   0.002   HIS B 419 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 5584)
  covalent geometry    : angle       0.59835 ( 7533)
  hydrogen bonds       : bond        0.04903 (  336)
  hydrogen bonds       : angle       5.50138 (  993)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  276 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue ILE  281 is missing expected H atoms. Skipping.
Residue SER  284 is missing expected H atoms. Skipping.
Residue LEU  285 is missing expected H atoms. Skipping.
Residue LEU  286 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue VAL  291 is missing expected H atoms. Skipping.
Residue ILE  292 is missing expected H atoms. Skipping.
Residue LEU  295 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue LYS  299 is missing expected H atoms. Skipping.
Evaluate side-chains
  101 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  315 ILE cc_start: 0.9464 (mm) cc_final: 0.9250 (mm)
REVERT: B  318 CYS cc_start: 0.9499 (m) cc_final: 0.9220 (p)
REVERT: B  426 HIS cc_start: 0.9381 (t-90) cc_final: 0.9039 (t-90)
REVERT: C  236 LEU cc_start: 0.6913 (tp) cc_final: 0.6355 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1689
  time to fit residues: 21.7588
Evaluate side-chains
  88 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 51 optimal weight:    8.9990
   chunk 38 optimal weight:    6.9990
   chunk 55 optimal weight:    1.9990
   chunk 41 optimal weight:   10.0000
   chunk 12 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 53 optimal weight:    5.9990
   chunk 60 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
** B 143 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 = 0.3666 r_free = 0.3666 target = 0.077360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.059103 restraints weight = 106581.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.061655 restraints weight = 68603.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.063616 restraints weight = 48311.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.065083 restraints weight = 35999.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.066192 restraints weight = 28105.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6866
moved from start:          0.4935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5584  Z= 0.130
  Angle     :  0.524   5.802   7533  Z= 0.288
  Chirality :  0.038   0.134    845
  Planarity :  0.004   0.048    956
  Dihedral  :  6.771  88.425    752
  Min Nonbonded Distance : 1.842

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.33), residues: 664
  helix:  0.90 (0.26), residues: 419
  sheet: -1.14 (0.67), residues: 62
  loop : -1.46 (0.42), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 442 
 TYR   0.017   0.002   TYR B 317 
 PHE   0.029   0.002   PHE C 232 
 TRP   0.009   0.001   TRP B   6 
 HIS   0.006   0.001   HIS B 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 5584)
  covalent geometry    : angle       0.52389 ( 7533)
  hydrogen bonds       : bond        0.04559 (  336)
  hydrogen bonds       : angle       5.29292 (  993)

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

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

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1328 Ramachandran restraints generated.
    664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  276 is missing expected H atoms. Skipping.
Residue THR  279 is missing expected H atoms. Skipping.
Residue ILE  281 is missing expected H atoms. Skipping.
Residue SER  284 is missing expected H atoms. Skipping.
Residue LEU  285 is missing expected H atoms. Skipping.
Residue LEU  286 is missing expected H atoms. Skipping.
Residue LEU  288 is missing expected H atoms. Skipping.
Residue VAL  291 is missing expected H atoms. Skipping.
Residue ILE  292 is missing expected H atoms. Skipping.
Residue LEU  295 is missing expected H atoms. Skipping.
Residue SER  298 is missing expected H atoms. Skipping.
Residue LYS  299 is missing expected H atoms. Skipping.
Evaluate side-chains
  106 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  142 GLN cc_start: 0.9422 (mt0) cc_final: 0.9119 (mt0)
REVERT: B  223 MET cc_start: 0.9634 (mmp) cc_final: 0.9426 (mmm)
REVERT: B  315 ILE cc_start: 0.9472 (mm) cc_final: 0.9261 (mm)
REVERT: B  318 CYS cc_start: 0.9491 (m) cc_final: 0.9195 (p)
REVERT: B  426 HIS cc_start: 0.9394 (t-90) cc_final: 0.9061 (t-90)
REVERT: C  232 PHE cc_start: 0.8200 (m-80) cc_final: 0.7627 (m-80)
REVERT: C  236 LEU cc_start: 0.6904 (tp) cc_final: 0.6475 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1637
  time to fit residues: 22.1168
Evaluate side-chains
  96 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 47 optimal weight:    9.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** B 143 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 = 0.3755 r_free = 0.3755 target = 0.079929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.059882 restraints weight = 112751.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.062722 restraints weight = 73067.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.064924 restraints weight = 51472.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.066599 restraints weight = 38264.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.067843 restraints weight = 29706.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6932
moved from start:          0.5117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5584  Z= 0.118
  Angle     :  0.498   6.208   7533  Z= 0.274
  Chirality :  0.037   0.133    845
  Planarity :  0.004   0.050    956
  Dihedral  :  6.472  81.476    752
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.33), residues: 664
  helix:  1.30 (0.26), residues: 412
  sheet: -1.02 (0.68), residues: 62
  loop : -1.41 (0.41), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 442 
 TYR   0.016   0.002   TYR B 383 
 PHE   0.024   0.002   PHE B 430 
 TRP   0.010   0.001   TRP B   6 
 HIS   0.006   0.001   HIS B 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 5584)
  covalent geometry    : angle       0.49769 ( 7533)
  hydrogen bonds       : bond        0.04240 (  336)
  hydrogen bonds       : angle       5.09156 (  993)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2383.93 seconds
wall clock time: 41 minutes 14.39 seconds (2474.39 seconds total)