Starting phenix.real_space_refine
on Mon Apr 28 02:42:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ij5_35465/04_2025/8ij5_35465.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ij5_35465/04_2025/8ij5_35465.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ij5_35465/04_2025/8ij5_35465.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ij5_35465/04_2025/8ij5_35465.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ij5_35465/04_2025/8ij5_35465.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ij5_35465/04_2025/8ij5_35465.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    4314      2.51       5
     N    1144      2.21       5
     O    1321      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 6815
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 2804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 358, 2804
          Classifications: {'peptide': 358}
          Link IDs: {'PTRANS': 17, 'TRANS': 340}
          Chain breaks: 3
    Chain: "E"
      Number of atoms: 4011
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 520, 4011
          Classifications: {'peptide': 520}
          Link IDs: {'PTRANS': 24, 'TRANS': 495}
          Chain breaks: 4
  Time building chain proxies: 4.75, per 1000 atoms: 0.70
  Number of scatterers: 6815
  At special positions: 0
  Unit cell: (68.64, 104.28, 118.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1321      8.00
     N    1144      7.00
     C    4314      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 203 " - pdb=" SG  CYS B 210 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 258 " - pdb=" SG  CYS B 299 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 400 " - pdb=" SG  CYS B 412 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  89 " - pdb=" SG  CYS E  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 138 " - pdb=" SG  CYS E 158 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 172 " - pdb=" SG  CYS E 185 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 508 " - pdb=" SG  CYS E 565 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.72
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1604

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 18 sheets defined
      11.2% alpha, 27.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'B' and resid 150 through 157
      removed outlier: 3.596A  pdb=" N   TRP B 155 " --> pdb=" O   LYS B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 169
    Processing helix  chain 'B' and resid 187 through 191
      removed outlier: 3.505A  pdb=" N   TYR B 190 " --> pdb=" O   VAL B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 234
      removed outlier: 4.097A  pdb=" N   PHE B 229 " --> pdb=" O   GLN B 225 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ASN B 230 " --> pdb=" O   VAL B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 258
    Processing helix  chain 'B' and resid 319 through 328
      removed outlier: 3.526A  pdb=" N   GLN B 327 " --> pdb=" O   GLU B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 349
    Processing helix  chain 'B' and resid 365 through 378
    Processing helix  chain 'E' and resid 205 through 210
    Processing helix  chain 'E' and resid 217 through 224
    Processing helix  chain 'E' and resid 244 through 248
    Processing sheet with id=AA1, first strand: chain 'B' and resid 117 through 118
    Processing sheet with id=AA2, first strand: chain 'B' and resid 123 through 125
      removed outlier: 3.876A  pdb=" N   LYS B 124 " --> pdb=" O   ALA B 427 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 123 through 125
      removed outlier: 3.876A  pdb=" N   LYS B 124 " --> pdb=" O   ALA B 427 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLU B 426 " --> pdb=" O   SER B 395 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 216 through 223
      removed outlier: 6.405A  pdb=" N   PHE B 179 " --> pdb=" O   VAL B 219 " (cutoff:3.500A)
      removed outlier: 5.580A  pdb=" N   THR B 221 " --> pdb=" O   ILE B 177 " (cutoff:3.500A)
      removed outlier: 5.665A  pdb=" N   ILE B 177 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   THR B 223 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   LEU B 175 " --> pdb=" O   THR B 223 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   ASP B 139 " --> pdb=" O   LEU B 271 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   VAL B 273 " --> pdb=" O   ASP B 139 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   TYR B 141 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   THR B 275 " --> pdb=" O   TYR B 141 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   LEU B 143 " --> pdb=" O   THR B 275 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR B 276 " --> pdb=" O   ALA B 335 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   LEU B 332 " --> pdb=" O   THR B 355 " (cutoff:3.500A)
      removed outlier: 7.978A  pdb=" N   GLY B 357 " --> pdb=" O   LEU B 332 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   PHE B 334 " --> pdb=" O   GLY B 357 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 411 through 413
      removed outlier: 3.617A  pdb=" N   VAL B 381 " --> pdb=" O   CYS B 412 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 39 through 41
      removed outlier: 6.419A  pdb=" N   ASP E 451 " --> pdb=" O   ALA E 441 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ALA E 441 " --> pdb=" O   ASP E 451 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   SER E 437 " --> pdb=" O   GLY E 455 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 53 through 56
    Processing sheet with id=AA8, first strand: chain 'E' and resid 117 through 118
      removed outlier: 3.703A  pdb=" N   HIS E 143 " --> pdb=" O   PHE E 118 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 127 through 131
      removed outlier: 4.107A  pdb=" N   SER E 127 " --> pdb=" O   CYS E 138 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 190 through 192
    Processing sheet with id=AB2, first strand: chain 'E' and resid 256 through 259
    Processing sheet with id=AB3, first strand: chain 'E' and resid 310 through 313
    Processing sheet with id=AB4, first strand: chain 'E' and resid 331 through 333
    Processing sheet with id=AB5, first strand: chain 'E' and resid 374 through 378
      removed outlier: 6.299A  pdb=" N   ILE E 374 " --> pdb=" O   ALA E 391 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   ALA E 391 " --> pdb=" O   ILE E 374 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   ALA E 389 " --> pdb=" O   PRO E 376 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLY E 378 " --> pdb=" O   ASP E 387 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 374 through 378
      removed outlier: 6.299A  pdb=" N   ILE E 374 " --> pdb=" O   ALA E 391 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   ALA E 391 " --> pdb=" O   ILE E 374 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   ALA E 389 " --> pdb=" O   PRO E 376 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLY E 378 " --> pdb=" O   ASP E 387 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLN E 419 " --> pdb=" O   ILE E 405 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 564 through 568
      removed outlier: 3.608A  pdb=" N   GLN E 564 " --> pdb=" O   LEU E 509 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   GLU E 566 " --> pdb=" O   PHE E 507 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 520 through 521
    Processing sheet with id=AB9, first strand: chain 'E' and resid 525 through 528
      removed outlier: 3.697A  pdb=" N   GLU E 526 " --> pdb=" O   GLU E 590 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLU E 590 " --> pdb=" O   GLU E 526 " (cutoff:3.500A)

    200 hydrogen bonds defined for protein.
    507 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: 2.05

  Time building geometry restraints manager: 2.01 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2257
        1.34 -     1.46: 1601
        1.46 -     1.59: 3037
        1.59 -     1.71: 0
        1.71 -     1.83: 57
  Bond restraints: 6952
  Sorted by residual:
  bond pdb=" N   MET E 148 "
       pdb=" CA  MET E 148 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.030 1.29e-02 6.01e+03 5.52e+00
  bond pdb=" N   GLU E 117 "
       pdb=" CA  GLU E 117 "
    ideal  model  delta    sigma   weight residual
    1.455  1.482 -0.027 1.25e-02 6.40e+03 4.69e+00
  bond pdb=" N   GLU E 147 "
       pdb=" CA  GLU E 147 "
    ideal  model  delta    sigma   weight residual
    1.462  1.489 -0.027 1.27e-02 6.20e+03 4.66e+00
  bond pdb=" N   TYR E 142 "
       pdb=" CA  TYR E 142 "
    ideal  model  delta    sigma   weight residual
    1.456  1.482 -0.026 1.23e-02 6.61e+03 4.46e+00
  bond pdb=" C   VAL E 416 "
       pdb=" N   PRO E 417 "
    ideal  model  delta    sigma   weight residual
    1.331  1.355 -0.025 1.31e-02 5.83e+03 3.64e+00
  ... (remaining 6947 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 9254
        2.08 -     4.16: 133
        4.16 -     6.24: 17
        6.24 -     8.32: 4
        8.32 -    10.40: 1
  Bond angle restraints: 9409
  Sorted by residual:
  angle pdb=" C   VAL E 459 "
        pdb=" N   ASP E 460 "
        pdb=" CA  ASP E 460 "
      ideal   model   delta    sigma   weight residual
     121.54  127.85   -6.31 1.91e+00 2.74e-01 1.09e+01
  angle pdb=" N   VAL E 342 "
        pdb=" CA  VAL E 342 "
        pdb=" C   VAL E 342 "
      ideal   model   delta    sigma   weight residual
     113.71  110.61    3.10 9.50e-01 1.11e+00 1.06e+01
  angle pdb=" N   MET E 148 "
        pdb=" CA  MET E 148 "
        pdb=" C   MET E 148 "
      ideal   model   delta    sigma   weight residual
     110.80  103.87    6.93 2.13e+00 2.20e-01 1.06e+01
  angle pdb=" CA  GLU E 147 "
        pdb=" C   GLU E 147 "
        pdb=" O   GLU E 147 "
      ideal   model   delta    sigma   weight residual
     120.98  117.73    3.25 1.08e+00 8.57e-01 9.08e+00
  angle pdb=" CA  LEU B  90 "
        pdb=" CB  LEU B  90 "
        pdb=" CG  LEU B  90 "
      ideal   model   delta    sigma   weight residual
     116.30  126.70  -10.40 3.50e+00 8.16e-02 8.82e+00
  ... (remaining 9404 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.70: 3400
       17.70 -    35.41: 518
       35.41 -    53.11: 199
       53.11 -    70.81: 45
       70.81 -    88.51: 8
  Dihedral angle restraints: 4170
    sinusoidal: 1661
      harmonic: 2509
  Sorted by residual:
  dihedral pdb=" CB  CYS E 172 "
           pdb=" SG  CYS E 172 "
           pdb=" SG  CYS E 185 "
           pdb=" CB  CYS E 185 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.84   37.16     1      1.00e+01 1.00e-02 1.95e+01
  dihedral pdb=" CA  CYS B 258 "
           pdb=" CB  CYS B 258 "
           pdb=" SG  CYS B 258 "
           pdb=" SG  CYS B 299 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00   -5.09  -67.91     1      2.00e+01 2.50e-03 1.50e+01
  dihedral pdb=" CA  LEU B 118 "
           pdb=" C   LEU B 118 "
           pdb=" N   ARG B 119 "
           pdb=" CA  ARG B 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.17   18.83     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 4167 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 769
       0.048 -    0.095: 201
       0.095 -    0.143: 62
       0.143 -    0.191: 0
       0.191 -    0.239: 1
  Chirality restraints: 1033
  Sorted by residual:
  chirality pdb=" CA  MET E 148 "
            pdb=" N   MET E 148 "
            pdb=" C   MET E 148 "
            pdb=" CB  MET E 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CA  ASP E 460 "
            pdb=" N   ASP E 460 "
            pdb=" C   ASP E 460 "
            pdb=" CB  ASP E 460 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.00e-01
  chirality pdb=" CA  ILE B 425 "
            pdb=" N   ILE B 425 "
            pdb=" C   ILE B 425 "
            pdb=" CB  ILE B 425 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.63e-01
  ... (remaining 1030 not shown)

  Planarity restraints: 1237
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL E  57 "   -0.040 5.00e-02 4.00e+02   6.01e-02 5.78e+00
        pdb=" N   PRO E  58 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO E  58 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO E  58 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E  57 "   -0.009 2.00e-02 2.50e+03   1.83e-02 3.37e+00
        pdb=" C   VAL E  57 "    0.032 2.00e-02 2.50e+03
        pdb=" O   VAL E  57 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   PRO E  58 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET E 430 "   -0.028 5.00e-02 4.00e+02   4.28e-02 2.93e+00
        pdb=" N   PRO E 431 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO E 431 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO E 431 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1234 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1185
        2.77 -     3.30: 6128
        3.30 -     3.83: 11319
        3.83 -     4.37: 13529
        4.37 -     4.90: 23444
  Nonbonded interactions: 55605
  Sorted by model distance:
  nonbonded pdb=" N   GLY E 334 "
            pdb=" O   LYS E 338 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" O   MET B 191 "
            pdb=" NH2 ARG B 242 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" O   LEU B 211 "
            pdb=" OG  SER B 239 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" N   ASP B 139 "
            pdb=" OD1 ASP B 139 "
     model   vdw
     2.298 3.120
  nonbonded pdb=" O   LEU E 116 "
            pdb=" N   ARG E 145 "
     model   vdw
     2.324 3.120
  ... (remaining 55600 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 individual isotropic
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:             1.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.630
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:12.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
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      :  0.003   0.040   6959  Z= 0.147
  Angle     :  0.616  10.395   9423  Z= 0.330
  Chirality :  0.045   0.239   1033
  Planarity :  0.004   0.060   1237
  Dihedral  : 19.835  88.512   2545
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.07 %
    Favored  : 90.81 %
  Rotamer:
    Outliers : 11.22 %
    Allowed  : 34.19 %
    Favored  : 54.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.39 (0.27), residues: 860
  helix: -1.39 (0.54), residues: 80
  sheet: -0.58 (0.33), residues: 275
  loop : -2.31 (0.25), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 264 
 HIS   0.003   0.001   HIS B 218 
 PHE   0.014   0.001   PHE B 440 
 TYR   0.016   0.001   TYR B 136 
 ARG   0.007   0.000   ARG E  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25941 (  192)
  hydrogen bonds       : angle      10.18415 (  507)
  SS BOND              : bond        0.00345 (    7)
  SS BOND              : angle       1.24379 (   14)
  covalent geometry    : bond        0.00315 ( 6952)
  covalent geometry    : angle       0.61499 ( 9409)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 171
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
REVERT: B  146 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6762 (mt)
REVERT: B  386 ARG cc_start: 0.6486 (mtt90) cc_final: 0.6052 (mtt90)
  outliers start: 83
  outliers final: 75
  residues processed: 243
  average time/residue: 0.9635
  time to fit residues: 248.5560
Evaluate side-chains
  243 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 167
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   88 ARG
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  121 ASP
Chi-restraints excluded: chain B residue  127 SER
Chi-restraints excluded: chain B residue  129 GLN
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  152 ASP
Chi-restraints excluded: chain B residue  170 LYS
Chi-restraints excluded: chain B residue  185 LYS
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  239 SER
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  261 LYS
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  303 SER
Chi-restraints excluded: chain B residue  310 SER
Chi-restraints excluded: chain B residue  317 SER
Chi-restraints excluded: chain B residue  330 ILE
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  348 SER
Chi-restraints excluded: chain B residue  360 SER
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain B residue  430 ARG
Chi-restraints excluded: chain B residue  440 PHE
Chi-restraints excluded: chain B residue  458 ASP
Chi-restraints excluded: chain E residue   37 SER
Chi-restraints excluded: chain E residue   53 VAL
Chi-restraints excluded: chain E residue   75 THR
Chi-restraints excluded: chain E residue  120 SER
Chi-restraints excluded: chain E residue  127 SER
Chi-restraints excluded: chain E residue  145 ARG
Chi-restraints excluded: chain E residue  177 ILE
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  200 LEU
Chi-restraints excluded: chain E residue  214 ILE
Chi-restraints excluded: chain E residue  220 GLU
Chi-restraints excluded: chain E residue  255 SER
Chi-restraints excluded: chain E residue  279 THR
Chi-restraints excluded: chain E residue  301 GLN
Chi-restraints excluded: chain E residue  313 THR
Chi-restraints excluded: chain E residue  323 VAL
Chi-restraints excluded: chain E residue  345 VAL
Chi-restraints excluded: chain E residue  348 SER
Chi-restraints excluded: chain E residue  358 THR
Chi-restraints excluded: chain E residue  366 VAL
Chi-restraints excluded: chain E residue  369 ARG
Chi-restraints excluded: chain E residue  388 ILE
Chi-restraints excluded: chain E residue  402 ILE
Chi-restraints excluded: chain E residue  407 ASN
Chi-restraints excluded: chain E residue  445 ASP
Chi-restraints excluded: chain E residue  473 VAL
Chi-restraints excluded: chain E residue  502 CYS
Chi-restraints excluded: chain E residue  517 LEU
Chi-restraints excluded: chain E residue  526 GLU
Chi-restraints excluded: chain E residue  528 LEU
Chi-restraints excluded: chain E residue  558 SER
Chi-restraints excluded: chain E residue  562 LEU
Chi-restraints excluded: chain E residue  564 GLN
Chi-restraints excluded: chain E residue  565 CYS
Chi-restraints excluded: chain E residue  590 GLU
Chi-restraints excluded: chain E residue  601 THR
Chi-restraints excluded: chain E residue  604 LEU
Chi-restraints excluded: chain E residue  615 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0770
   chunk 22 optimal weight:    0.9980
   chunk 44 optimal weight:    0.4980
   chunk 35 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0040
   chunk 41 optimal weight:    0.0370
   chunk 50 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.2428

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

Flipped N/Q/H residues before XYZ refinement:
B 327 GLN
B 346 ASN
** B 454 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 = 0.3654 r_free = 0.3654 target = 0.126680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.117372 restraints weight = 9876.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 1.64
r_work: 0.3449 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3335 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.0998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6959  Z= 0.136
  Angle     :  0.615   8.232   9423  Z= 0.323
  Chirality :  0.045   0.167   1033
  Planarity :  0.005   0.051   1237
  Dihedral  : 11.986  73.320   1079
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.07 %
    Favored  : 90.81 %
  Rotamer:
    Outliers :  7.84 %
    Allowed  : 34.32 %
    Favored  : 57.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.12 (0.28), residues: 860
  helix: -1.03 (0.54), residues: 89
  sheet: -0.45 (0.32), residues: 287
  loop : -2.16 (0.27), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 264 
 HIS   0.003   0.001   HIS B 300 
 PHE   0.027   0.001   PHE B 440 
 TYR   0.016   0.001   TYR B 347 
 ARG   0.004   0.001   ARG B 242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04420 (  192)
  hydrogen bonds       : angle       7.27014 (  507)
  SS BOND              : bond        0.00235 (    7)
  SS BOND              : angle       0.86046 (   14)
  covalent geometry    : bond        0.00315 ( 6952)
  covalent geometry    : angle       0.61455 ( 9409)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 172
  time to evaluate  : 0.771 
Fit side-chains
REVERT: B  146 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.7020 (mt)
REVERT: B  384 GLU cc_start: 0.7312 (pp20) cc_final: 0.6962 (pp20)
REVERT: B  386 ARG cc_start: 0.6059 (mtt90) cc_final: 0.5789 (mpt90)
REVERT: E  216 ASP cc_start: 0.7198 (m-30) cc_final: 0.6994 (m-30)
REVERT: E  457 PHE cc_start: 0.7851 (p90) cc_final: 0.7522 (p90)
  outliers start: 58
  outliers final: 39
  residues processed: 218
  average time/residue: 1.1371
  time to fit residues: 263.5481
Evaluate side-chains
  206 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 166
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  125 ASN
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  152 ASP
Chi-restraints excluded: chain B residue  170 LYS
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  185 LYS
Chi-restraints excluded: chain B residue  191 MET
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  234 LYS
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  303 SER
Chi-restraints excluded: chain B residue  310 SER
Chi-restraints excluded: chain B residue  330 ILE
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  360 SER
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  458 ASP
Chi-restraints excluded: chain E residue  144 TRP
Chi-restraints excluded: chain E residue  177 ILE
Chi-restraints excluded: chain E residue  214 ILE
Chi-restraints excluded: chain E residue  233 LYS
Chi-restraints excluded: chain E residue  255 SER
Chi-restraints excluded: chain E residue  270 VAL
Chi-restraints excluded: chain E residue  279 THR
Chi-restraints excluded: chain E residue  291 MET
Chi-restraints excluded: chain E residue  366 VAL
Chi-restraints excluded: chain E residue  418 SER
Chi-restraints excluded: chain E residue  473 VAL
Chi-restraints excluded: chain E residue  502 CYS
Chi-restraints excluded: chain E residue  601 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 86 optimal weight:    0.0570
   chunk 3 optimal weight:    0.5980
   chunk 49 optimal weight:    0.6980
   chunk 50 optimal weight:    0.1980
   chunk 43 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 73 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
B 129 GLN
B 132 GLN
B 327 GLN
** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 236 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.124962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.115882 restraints weight = 9958.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 1.61
r_work: 0.3426 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3312 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.1219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6959  Z= 0.196
  Angle     :  0.636   8.576   9423  Z= 0.338
  Chirality :  0.047   0.170   1033
  Planarity :  0.005   0.049   1237
  Dihedral  :  8.972  59.275    992
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 10.00 %
    Favored  : 89.88 %
  Rotamer:
    Outliers :  9.86 %
    Allowed  : 33.38 %
    Favored  : 56.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.18 (0.28), residues: 860
  helix: -1.05 (0.53), residues: 89
  sheet: -0.38 (0.33), residues: 281
  loop : -2.26 (0.26), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 144 
 HIS   0.005   0.001   HIS B 218 
 PHE   0.026   0.002   PHE B 440 
 TYR   0.012   0.001   TYR B 142 
 ARG   0.006   0.001   ARG B 242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04525 (  192)
  hydrogen bonds       : angle       6.84856 (  507)
  SS BOND              : bond        0.00322 (    7)
  SS BOND              : angle       1.26852 (   14)
  covalent geometry    : bond        0.00462 ( 6952)
  covalent geometry    : angle       0.63435 ( 9409)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 177
  time to evaluate  : 0.702 
Fit side-chains
REVERT: B  384 GLU cc_start: 0.7417 (pp20) cc_final: 0.7057 (pp20)
  outliers start: 73
  outliers final: 46
  residues processed: 225
  average time/residue: 1.4785
  time to fit residues: 353.9230
Evaluate side-chains
  216 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 170
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  152 ASP
Chi-restraints excluded: chain B residue  170 LYS
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  185 LYS
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  234 LYS
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  279 LYS
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  310 SER
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  360 SER
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  458 ASP
Chi-restraints excluded: chain E residue  177 ILE
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  214 ILE
Chi-restraints excluded: chain E residue  233 LYS
Chi-restraints excluded: chain E residue  246 ILE
Chi-restraints excluded: chain E residue  255 SER
Chi-restraints excluded: chain E residue  270 VAL
Chi-restraints excluded: chain E residue  279 THR
Chi-restraints excluded: chain E residue  291 MET
Chi-restraints excluded: chain E residue  301 GLN
Chi-restraints excluded: chain E residue  348 SER
Chi-restraints excluded: chain E residue  366 VAL
Chi-restraints excluded: chain E residue  379 ASP
Chi-restraints excluded: chain E residue  400 LYS
Chi-restraints excluded: chain E residue  418 SER
Chi-restraints excluded: chain E residue  438 MET
Chi-restraints excluded: chain E residue  445 ASP
Chi-restraints excluded: chain E residue  473 VAL
Chi-restraints excluded: chain E residue  502 CYS
Chi-restraints excluded: chain E residue  562 LEU
Chi-restraints excluded: chain E residue  585 ILE
Chi-restraints excluded: chain E residue  601 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0870
   chunk 17 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   chunk 4 optimal weight:    0.3980
   chunk 60 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 68 optimal weight:    0.5980
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
B 129 GLN
B 327 GLN
** B 454 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 = 0.3631 r_free = 0.3631 target = 0.124877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.115730 restraints weight = 10033.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 1.62
r_work: 0.3424 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3308 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.1380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6959  Z= 0.197
  Angle     :  0.646   9.013   9423  Z= 0.342
  Chirality :  0.047   0.165   1033
  Planarity :  0.005   0.050   1237
  Dihedral  :  8.597  59.725    984
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.88 %
    Favored  : 90.00 %
  Rotamer:
    Outliers : 10.41 %
    Allowed  : 33.38 %
    Favored  : 56.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.22 (0.28), residues: 860
  helix: -1.09 (0.52), residues: 90
  sheet: -0.47 (0.33), residues: 268
  loop : -2.22 (0.26), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 144 
 HIS   0.005   0.001   HIS B 218 
 PHE   0.023   0.002   PHE B 440 
 TYR   0.011   0.002   TYR B 142 
 ARG   0.006   0.000   ARG B 378 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04134 (  192)
  hydrogen bonds       : angle       6.70252 (  507)
  SS BOND              : bond        0.00374 (    7)
  SS BOND              : angle       1.90800 (   14)
  covalent geometry    : bond        0.00473 ( 6952)
  covalent geometry    : angle       0.64187 ( 9409)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 175
  time to evaluate  : 0.727 
Fit side-chains
REVERT: B  144 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8072 (ttt)
REVERT: B  384 GLU cc_start: 0.7386 (pp20) cc_final: 0.7107 (pp20)
REVERT: E  145 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7647 (tmt-80)
REVERT: E  216 ASP cc_start: 0.7255 (m-30) cc_final: 0.7052 (m-30)
REVERT: E  305 TYR cc_start: 0.7747 (OUTLIER) cc_final: 0.6033 (m-80)
  outliers start: 77
  outliers final: 51
  residues processed: 228
  average time/residue: 1.0281
  time to fit residues: 248.8868
Evaluate side-chains
  223 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 169
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain B residue  152 ASP
Chi-restraints excluded: chain B residue  170 LYS
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  185 LYS
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  234 LYS
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  279 LYS
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  287 ARG
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  310 SER
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  360 SER
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  458 ASP
Chi-restraints excluded: chain E residue  145 ARG
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  214 ILE
Chi-restraints excluded: chain E residue  233 LYS
Chi-restraints excluded: chain E residue  246 ILE
Chi-restraints excluded: chain E residue  255 SER
Chi-restraints excluded: chain E residue  270 VAL
Chi-restraints excluded: chain E residue  279 THR
Chi-restraints excluded: chain E residue  291 MET
Chi-restraints excluded: chain E residue  301 GLN
Chi-restraints excluded: chain E residue  305 TYR
Chi-restraints excluded: chain E residue  309 SER
Chi-restraints excluded: chain E residue  348 SER
Chi-restraints excluded: chain E residue  357 GLN
Chi-restraints excluded: chain E residue  366 VAL
Chi-restraints excluded: chain E residue  379 ASP
Chi-restraints excluded: chain E residue  388 ILE
Chi-restraints excluded: chain E residue  400 LYS
Chi-restraints excluded: chain E residue  402 ILE
Chi-restraints excluded: chain E residue  409 ARG
Chi-restraints excluded: chain E residue  418 SER
Chi-restraints excluded: chain E residue  425 TRP
Chi-restraints excluded: chain E residue  438 MET
Chi-restraints excluded: chain E residue  445 ASP
Chi-restraints excluded: chain E residue  473 VAL
Chi-restraints excluded: chain E residue  502 CYS
Chi-restraints excluded: chain E residue  562 LEU
Chi-restraints excluded: chain E residue  585 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 6 optimal weight:    0.1980
   chunk 41 optimal weight:    0.8980
   chunk 76 optimal weight:    0.6980
   chunk 14 optimal weight:    0.3980
   chunk 16 optimal weight:    0.8980
   chunk 75 optimal weight:    0.0570
   chunk 47 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.4098

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

Flipped N/Q/H residues before XYZ refinement:
B 129 GLN
B 327 GLN
** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 236 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.125171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.116055 restraints weight = 9890.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 1.60
r_work: 0.3431 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.1427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6959  Z= 0.179
  Angle     :  0.637   9.618   9423  Z= 0.337
  Chirality :  0.047   0.175   1033
  Planarity :  0.005   0.050   1237
  Dihedral  :  8.275  59.213    981
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.77 %
    Favored  : 90.12 %
  Rotamer:
    Outliers : 10.14 %
    Allowed  : 33.38 %
    Favored  : 56.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.14 (0.28), residues: 860
  helix: -0.88 (0.52), residues: 90
  sheet: -0.39 (0.32), residues: 279
  loop : -2.24 (0.27), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 264 
 HIS   0.004   0.001   HIS B 218 
 PHE   0.020   0.002   PHE B 440 
 TYR   0.016   0.002   TYR B 136 
 ARG   0.006   0.000   ARG B 378 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03960 (  192)
  hydrogen bonds       : angle       6.54982 (  507)
  SS BOND              : bond        0.00425 (    7)
  SS BOND              : angle       1.75509 (   14)
  covalent geometry    : bond        0.00429 ( 6952)
  covalent geometry    : angle       0.63434 ( 9409)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 170
  time to evaluate  : 0.876 
Fit side-chains
REVERT: B  144 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8094 (ttt)
REVERT: B  384 GLU cc_start: 0.7421 (pp20) cc_final: 0.7113 (pp20)
REVERT: E  216 ASP cc_start: 0.7272 (m-30) cc_final: 0.7052 (m-30)
REVERT: E  305 TYR cc_start: 0.7745 (OUTLIER) cc_final: 0.6037 (m-80)
  outliers start: 75
  outliers final: 51
  residues processed: 223
  average time/residue: 1.1583
  time to fit residues: 275.3165
Evaluate side-chains
  216 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 163
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain B residue  145 ASP
Chi-restraints excluded: chain B residue  152 ASP
Chi-restraints excluded: chain B residue  170 LYS
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  185 LYS
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  234 LYS
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  279 LYS
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  287 ARG
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  310 SER
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  360 SER
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  401 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  458 ASP
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  214 ILE
Chi-restraints excluded: chain E residue  233 LYS
Chi-restraints excluded: chain E residue  246 ILE
Chi-restraints excluded: chain E residue  255 SER
Chi-restraints excluded: chain E residue  270 VAL
Chi-restraints excluded: chain E residue  279 THR
Chi-restraints excluded: chain E residue  291 MET
Chi-restraints excluded: chain E residue  301 GLN
Chi-restraints excluded: chain E residue  305 TYR
Chi-restraints excluded: chain E residue  323 VAL
Chi-restraints excluded: chain E residue  345 VAL
Chi-restraints excluded: chain E residue  348 SER
Chi-restraints excluded: chain E residue  357 GLN
Chi-restraints excluded: chain E residue  366 VAL
Chi-restraints excluded: chain E residue  379 ASP
Chi-restraints excluded: chain E residue  400 LYS
Chi-restraints excluded: chain E residue  402 ILE
Chi-restraints excluded: chain E residue  418 SER
Chi-restraints excluded: chain E residue  425 TRP
Chi-restraints excluded: chain E residue  473 VAL
Chi-restraints excluded: chain E residue  502 CYS
Chi-restraints excluded: chain E residue  562 LEU
Chi-restraints excluded: chain E residue  585 ILE
Chi-restraints excluded: chain E residue  601 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 45 optimal weight:    0.1980
   chunk 59 optimal weight:    0.5980
   chunk 78 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 68 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0980
   chunk 21 optimal weight:    1.9990
   chunk 83 optimal weight:    0.0770
   chunk 26 optimal weight:    1.9990
   chunk 67 optimal weight:    0.1980
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.2338

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

Flipped N/Q/H residues before XYZ refinement:
B 129 GLN
B 327 GLN
** B 454 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 = 0.3657 r_free = 0.3657 target = 0.126590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.117460 restraints weight = 9920.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 1.61
r_work: 0.3453 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3339 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.1562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6959  Z= 0.132
  Angle     :  0.606   8.790   9423  Z= 0.320
  Chirality :  0.045   0.171   1033
  Planarity :  0.005   0.050   1237
  Dihedral  :  7.929  59.073    981
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.07 %
    Favored  : 90.81 %
  Rotamer:
    Outliers :  7.57 %
    Allowed  : 35.54 %
    Favored  : 56.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.04 (0.28), residues: 860
  helix: -0.65 (0.53), residues: 90
  sheet: -0.40 (0.32), residues: 283
  loop : -2.17 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 264 
 HIS   0.004   0.001   HIS B 218 
 PHE   0.018   0.001   PHE B 440 
 TYR   0.015   0.001   TYR B 136 
 ARG   0.004   0.000   ARG B 378 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03614 (  192)
  hydrogen bonds       : angle       6.34543 (  507)
  SS BOND              : bond        0.00466 (    7)
  SS BOND              : angle       1.67760 (   14)
  covalent geometry    : bond        0.00314 ( 6952)
  covalent geometry    : angle       0.60339 ( 9409)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 169
  time to evaluate  : 0.768 
Fit side-chains
REVERT: B  144 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8086 (ttt)
REVERT: B  384 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7115 (pp20)
REVERT: E  305 TYR cc_start: 0.7697 (OUTLIER) cc_final: 0.6051 (m-80)
  outliers start: 56
  outliers final: 41
  residues processed: 207
  average time/residue: 0.9600
  time to fit residues: 211.4271
Evaluate side-chains
  212 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 168
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  125 ASN
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain B residue  152 ASP
Chi-restraints excluded: chain B residue  170 LYS
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  185 LYS
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  287 ARG
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  360 SER
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain E residue  214 ILE
Chi-restraints excluded: chain E residue  233 LYS
Chi-restraints excluded: chain E residue  246 ILE
Chi-restraints excluded: chain E residue  255 SER
Chi-restraints excluded: chain E residue  270 VAL
Chi-restraints excluded: chain E residue  279 THR
Chi-restraints excluded: chain E residue  291 MET
Chi-restraints excluded: chain E residue  301 GLN
Chi-restraints excluded: chain E residue  305 TYR
Chi-restraints excluded: chain E residue  357 GLN
Chi-restraints excluded: chain E residue  366 VAL
Chi-restraints excluded: chain E residue  379 ASP
Chi-restraints excluded: chain E residue  388 ILE
Chi-restraints excluded: chain E residue  400 LYS
Chi-restraints excluded: chain E residue  402 ILE
Chi-restraints excluded: chain E residue  418 SER
Chi-restraints excluded: chain E residue  425 TRP
Chi-restraints excluded: chain E residue  445 ASP
Chi-restraints excluded: chain E residue  473 VAL
Chi-restraints excluded: chain E residue  502 CYS
Chi-restraints excluded: chain E residue  565 CYS
Chi-restraints excluded: chain E residue  585 ILE
Chi-restraints excluded: chain E residue  601 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 16 optimal weight:    0.2980
   chunk 76 optimal weight:    0.0270
   chunk 42 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0980
   chunk 37 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0980
   chunk 62 optimal weight:    0.9980
   chunk 41 optimal weight:    0.2980
   chunk 0 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 78 optimal weight:    0.5980
   overall best weight:    0.1638

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

Flipped N/Q/H residues before XYZ refinement:
B 129 GLN
** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 236 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.127779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.118682 restraints weight = 9868.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 1.60
r_work: 0.3471 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3358 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6959  Z= 0.118
  Angle     :  0.594  10.828   9423  Z= 0.311
  Chirality :  0.045   0.168   1033
  Planarity :  0.004   0.048   1237
  Dihedral  :  7.220  59.873    974
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.72 %
    Favored  : 91.16 %
  Rotamer:
    Outliers :  7.16 %
    Allowed  : 36.35 %
    Favored  : 56.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.28), residues: 860
  helix: -0.52 (0.54), residues: 91
  sheet: -0.38 (0.32), residues: 283
  loop : -2.11 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 264 
 HIS   0.003   0.001   HIS B 218 
 PHE   0.015   0.001   PHE B 440 
 TYR   0.013   0.001   TYR B 136 
 ARG   0.004   0.000   ARG B 378 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03379 (  192)
  hydrogen bonds       : angle       6.11519 (  507)
  SS BOND              : bond        0.00445 (    7)
  SS BOND              : angle       1.51493 (   14)
  covalent geometry    : bond        0.00280 ( 6952)
  covalent geometry    : angle       0.59119 ( 9409)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 163
  time to evaluate  : 0.709 
Fit side-chains
REVERT: B  287 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8101 (ptm-80)
REVERT: B  384 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.7000 (pp20)
REVERT: E  305 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.6049 (m-80)
REVERT: E  331 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8184 (mtm)
REVERT: E  365 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7846 (mt-10)
  outliers start: 53
  outliers final: 35
  residues processed: 201
  average time/residue: 0.9953
  time to fit residues: 212.1178
Evaluate side-chains
  207 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 168
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  170 LYS
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  185 LYS
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  287 ARG
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  360 SER
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain E residue  177 ILE
Chi-restraints excluded: chain E residue  233 LYS
Chi-restraints excluded: chain E residue  255 SER
Chi-restraints excluded: chain E residue  279 THR
Chi-restraints excluded: chain E residue  291 MET
Chi-restraints excluded: chain E residue  301 GLN
Chi-restraints excluded: chain E residue  305 TYR
Chi-restraints excluded: chain E residue  323 VAL
Chi-restraints excluded: chain E residue  331 MET
Chi-restraints excluded: chain E residue  366 VAL
Chi-restraints excluded: chain E residue  379 ASP
Chi-restraints excluded: chain E residue  388 ILE
Chi-restraints excluded: chain E residue  400 LYS
Chi-restraints excluded: chain E residue  402 ILE
Chi-restraints excluded: chain E residue  407 ASN
Chi-restraints excluded: chain E residue  418 SER
Chi-restraints excluded: chain E residue  425 TRP
Chi-restraints excluded: chain E residue  445 ASP
Chi-restraints excluded: chain E residue  473 VAL
Chi-restraints excluded: chain E residue  502 CYS
Chi-restraints excluded: chain E residue  562 LEU
Chi-restraints excluded: chain E residue  565 CYS
Chi-restraints excluded: chain E residue  585 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   chunk 83 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9990
   chunk 79 optimal weight:    0.0970
   chunk 62 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0010
   chunk 23 optimal weight:    0.9990
   chunk 16 optimal weight:    0.4980
   chunk 73 optimal weight:    0.5980
   overall best weight:    0.3784

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

Flipped N/Q/H residues before XYZ refinement:
B 129 GLN
B 158 GLN
B 298 GLN
** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 237 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.126157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.117026 restraints weight = 10005.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 1.61
r_work: 0.3445 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6959  Z= 0.169
  Angle     :  0.628   9.447   9423  Z= 0.331
  Chirality :  0.046   0.173   1033
  Planarity :  0.005   0.046   1237
  Dihedral  :  7.200  59.287    969
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.19 %
    Favored  : 90.70 %
  Rotamer:
    Outliers :  7.30 %
    Allowed  : 36.35 %
    Favored  : 56.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (0.28), residues: 860
  helix: -0.57 (0.53), residues: 91
  sheet: -0.38 (0.32), residues: 281
  loop : -2.12 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E 209 
 HIS   0.005   0.001   HIS B 218 
 PHE   0.018   0.002   PHE B 440 
 TYR   0.012   0.001   TYR B 136 
 ARG   0.007   0.000   ARG B 378 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03640 (  192)
  hydrogen bonds       : angle       6.20287 (  507)
  SS BOND              : bond        0.00480 (    7)
  SS BOND              : angle       1.62998 (   14)
  covalent geometry    : bond        0.00407 ( 6952)
  covalent geometry    : angle       0.62554 ( 9409)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 172
  time to evaluate  : 0.692 
Fit side-chains
REVERT: B  144 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8072 (ttt)
REVERT: B  287 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8130 (ptm-80)
REVERT: B  384 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.7003 (pp20)
REVERT: E  305 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.6096 (m-80)
REVERT: E  331 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8243 (mtm)
  outliers start: 54
  outliers final: 41
  residues processed: 209
  average time/residue: 1.0577
  time to fit residues: 234.3411
Evaluate side-chains
  203 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 157
  time to evaluate  : 1.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain B residue  150 MET
Chi-restraints excluded: chain B residue  170 LYS
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  185 LYS
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  287 ARG
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  360 SER
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  458 ASP
Chi-restraints excluded: chain E residue  214 ILE
Chi-restraints excluded: chain E residue  233 LYS
Chi-restraints excluded: chain E residue  255 SER
Chi-restraints excluded: chain E residue  279 THR
Chi-restraints excluded: chain E residue  291 MET
Chi-restraints excluded: chain E residue  301 GLN
Chi-restraints excluded: chain E residue  305 TYR
Chi-restraints excluded: chain E residue  323 VAL
Chi-restraints excluded: chain E residue  331 MET
Chi-restraints excluded: chain E residue  345 VAL
Chi-restraints excluded: chain E residue  348 SER
Chi-restraints excluded: chain E residue  366 VAL
Chi-restraints excluded: chain E residue  379 ASP
Chi-restraints excluded: chain E residue  388 ILE
Chi-restraints excluded: chain E residue  400 LYS
Chi-restraints excluded: chain E residue  402 ILE
Chi-restraints excluded: chain E residue  418 SER
Chi-restraints excluded: chain E residue  445 ASP
Chi-restraints excluded: chain E residue  473 VAL
Chi-restraints excluded: chain E residue  502 CYS
Chi-restraints excluded: chain E residue  562 LEU
Chi-restraints excluded: chain E residue  565 CYS
Chi-restraints excluded: chain E residue  585 ILE
Chi-restraints excluded: chain E residue  601 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 43 optimal weight:    0.2980
   chunk 41 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 85 optimal weight:    0.2980
   chunk 67 optimal weight:    0.9980
   chunk 29 optimal weight:    0.3980
   chunk 24 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 129 GLN
** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 237 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.124517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.115476 restraints weight = 9966.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 1.60
r_work: 0.3421 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3305 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6959  Z= 0.228
  Angle     :  0.678   8.766   9423  Z= 0.357
  Chirality :  0.048   0.180   1033
  Planarity :  0.005   0.046   1237
  Dihedral  :  7.529  59.568    969
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.58 %
    Favored  : 89.42 %
  Rotamer:
    Outliers :  7.84 %
    Allowed  : 35.95 %
    Favored  : 56.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.28), residues: 860
  helix: -0.78 (0.52), residues: 91
  sheet: -0.42 (0.32), residues: 281
  loop : -2.19 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP E 144 
 HIS   0.004   0.001   HIS E 143 
 PHE   0.023   0.002   PHE B 440 
 TYR   0.013   0.002   TYR B 136 
 ARG   0.008   0.001   ARG B 378 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03944 (  192)
  hydrogen bonds       : angle       6.38277 (  507)
  SS BOND              : bond        0.00548 (    7)
  SS BOND              : angle       1.74339 (   14)
  covalent geometry    : bond        0.00547 ( 6952)
  covalent geometry    : angle       0.67518 ( 9409)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 159
  time to evaluate  : 1.096 
Fit side-chains
REVERT: B  144 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8074 (ttt)
REVERT: B  287 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8155 (ptm-80)
REVERT: B  384 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7167 (pp20)
REVERT: E  148 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7587 (ttm)
REVERT: E  305 TYR cc_start: 0.7753 (OUTLIER) cc_final: 0.6126 (m-80)
REVERT: E  331 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8226 (mtm)
REVERT: E  474 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7658 (m110)
  outliers start: 58
  outliers final: 45
  residues processed: 199
  average time/residue: 1.0518
  time to fit residues: 222.2704
Evaluate side-chains
  209 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 157
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain B residue  170 LYS
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  185 LYS
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  279 LYS
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  287 ARG
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  360 SER
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  458 ASP
Chi-restraints excluded: chain E residue  148 MET
Chi-restraints excluded: chain E residue  149 LYS
Chi-restraints excluded: chain E residue  214 ILE
Chi-restraints excluded: chain E residue  233 LYS
Chi-restraints excluded: chain E residue  246 ILE
Chi-restraints excluded: chain E residue  255 SER
Chi-restraints excluded: chain E residue  270 VAL
Chi-restraints excluded: chain E residue  279 THR
Chi-restraints excluded: chain E residue  291 MET
Chi-restraints excluded: chain E residue  301 GLN
Chi-restraints excluded: chain E residue  305 TYR
Chi-restraints excluded: chain E residue  323 VAL
Chi-restraints excluded: chain E residue  331 MET
Chi-restraints excluded: chain E residue  345 VAL
Chi-restraints excluded: chain E residue  348 SER
Chi-restraints excluded: chain E residue  366 VAL
Chi-restraints excluded: chain E residue  379 ASP
Chi-restraints excluded: chain E residue  388 ILE
Chi-restraints excluded: chain E residue  400 LYS
Chi-restraints excluded: chain E residue  402 ILE
Chi-restraints excluded: chain E residue  418 SER
Chi-restraints excluded: chain E residue  425 TRP
Chi-restraints excluded: chain E residue  445 ASP
Chi-restraints excluded: chain E residue  473 VAL
Chi-restraints excluded: chain E residue  474 ASN
Chi-restraints excluded: chain E residue  502 CYS
Chi-restraints excluded: chain E residue  562 LEU
Chi-restraints excluded: chain E residue  565 CYS
Chi-restraints excluded: chain E residue  585 ILE
Chi-restraints excluded: chain E residue  601 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.3980
   chunk 34 optimal weight:    0.0970
   chunk 8 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   chunk 82 optimal weight:    0.7980
   chunk 55 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 80 optimal weight:    0.4980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
B 129 GLN
** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 237 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.125268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.116088 restraints weight = 10090.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 1.63
r_work: 0.3429 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.1725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   6959  Z= 0.189
  Angle     :  0.658   8.979   9423  Z= 0.346
  Chirality :  0.047   0.173   1033
  Planarity :  0.005   0.049   1237
  Dihedral  :  7.488  58.864    969
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  7.16 %
    Allowed  : 37.16 %
    Favored  : 55.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.28), residues: 860
  helix: -0.78 (0.52), residues: 91
  sheet: -0.48 (0.33), residues: 271
  loop : -2.14 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 264 
 HIS   0.004   0.001   HIS B 218 
 PHE   0.021   0.002   PHE B 440 
 TYR   0.019   0.002   TYR B 136 
 ARG   0.008   0.000   ARG B 378 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03768 (  192)
  hydrogen bonds       : angle       6.36300 (  507)
  SS BOND              : bond        0.00503 (    7)
  SS BOND              : angle       1.61678 (   14)
  covalent geometry    : bond        0.00455 ( 6952)
  covalent geometry    : angle       0.65585 ( 9409)

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 159
  time to evaluate  : 0.786 
Fit side-chains
REVERT: B  144 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8071 (ttt)
REVERT: B  287 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8156 (ptm-80)
REVERT: B  384 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6964 (pp20)
REVERT: B  386 ARG cc_start: 0.6104 (mtt90) cc_final: 0.5841 (mtt90)
REVERT: E  148 MET cc_start: 0.7930 (ttm) cc_final: 0.7596 (ttp)
REVERT: E  220 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7387 (mt-10)
REVERT: E  236 ASN cc_start: 0.6727 (m110) cc_final: 0.6416 (m110)
REVERT: E  305 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.6119 (m-80)
REVERT: E  331 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8213 (mtm)
  outliers start: 53
  outliers final: 45
  residues processed: 198
  average time/residue: 1.0088
  time to fit residues: 211.9425
Evaluate side-chains
  212 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 162
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  139 ASP
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain B residue  150 MET
Chi-restraints excluded: chain B residue  170 LYS
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  185 LYS
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  287 ARG
Chi-restraints excluded: chain B residue  292 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  360 SER
Chi-restraints excluded: chain B residue  384 GLU
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  409 LEU
Chi-restraints excluded: chain B residue  458 ASP
Chi-restraints excluded: chain E residue  149 LYS
Chi-restraints excluded: chain E residue  214 ILE
Chi-restraints excluded: chain E residue  233 LYS
Chi-restraints excluded: chain E residue  255 SER
Chi-restraints excluded: chain E residue  279 THR
Chi-restraints excluded: chain E residue  291 MET
Chi-restraints excluded: chain E residue  301 GLN
Chi-restraints excluded: chain E residue  305 TYR
Chi-restraints excluded: chain E residue  323 VAL
Chi-restraints excluded: chain E residue  331 MET
Chi-restraints excluded: chain E residue  345 VAL
Chi-restraints excluded: chain E residue  348 SER
Chi-restraints excluded: chain E residue  366 VAL
Chi-restraints excluded: chain E residue  379 ASP
Chi-restraints excluded: chain E residue  388 ILE
Chi-restraints excluded: chain E residue  400 LYS
Chi-restraints excluded: chain E residue  402 ILE
Chi-restraints excluded: chain E residue  418 SER
Chi-restraints excluded: chain E residue  425 TRP
Chi-restraints excluded: chain E residue  445 ASP
Chi-restraints excluded: chain E residue  473 VAL
Chi-restraints excluded: chain E residue  502 CYS
Chi-restraints excluded: chain E residue  562 LEU
Chi-restraints excluded: chain E residue  565 CYS
Chi-restraints excluded: chain E residue  585 ILE
Chi-restraints excluded: chain E residue  601 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 15 optimal weight:    0.0980
   chunk 19 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   chunk 66 optimal weight:    0.4980
   chunk 36 optimal weight:    0.3980
   chunk 58 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
B 129 GLN
** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.125096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.115940 restraints weight = 10058.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.62
r_work: 0.3427 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3311 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   6959  Z= 0.196
  Angle     :  0.663   8.818   9423  Z= 0.349
  Chirality :  0.047   0.178   1033
  Planarity :  0.005   0.048   1237
  Dihedral  :  7.518  58.868    969
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.35 %
    Favored  : 89.65 %
  Rotamer:
    Outliers :  7.43 %
    Allowed  : 36.49 %
    Favored  : 56.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.14 (0.28), residues: 860
  helix: -0.86 (0.52), residues: 92
  sheet: -0.46 (0.32), residues: 281
  loop : -2.20 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 209 
 HIS   0.004   0.001   HIS B 218 
 PHE   0.021   0.002   PHE B 440 
 TYR   0.019   0.002   TYR B 136 
 ARG   0.008   0.001   ARG B 378 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03798 (  192)
  hydrogen bonds       : angle       6.38311 (  507)
  SS BOND              : bond        0.00510 (    7)
  SS BOND              : angle       1.69990 (   14)
  covalent geometry    : bond        0.00473 ( 6952)
  covalent geometry    : angle       0.66063 ( 9409)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7044.90 seconds
wall clock time: 125 minutes 13.08 seconds (7513.08 seconds total)