Starting phenix.real_space_refine
on Fri Aug 22 19:58:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wx3_37899/08_2025/8wx3_37899.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wx3_37899/08_2025/8wx3_37899.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wx3_37899/08_2025/8wx3_37899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wx3_37899/08_2025/8wx3_37899.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wx3_37899/08_2025/8wx3_37899.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wx3_37899/08_2025/8wx3_37899.cif"
  }
  resolution = 2.83
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.010
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      40      5.16       5
     C    4954      2.51       5
     N    1226      2.21       5
     O    1278      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7498
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 487, 3749
          Classifications: {'peptide': 487}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 466}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 487, 3749
          Classifications: {'peptide': 487}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 466}
          Chain breaks: 2
  Time building chain proxies: 2.00, per 1000 atoms: 0.27
  Number of scatterers: 7498
  At special positions: 0
  Unit cell: (83.415, 120.765, 83.415, 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      40     16.00
     O    1278      8.00
     N    1226      7.00
     C    4954      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  68 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 153 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  68 " - pdb=" SG  CYS B 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 133 " - pdb=" SG  CYS B 153 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 412.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1792

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 2 sheets defined
      77.7% alpha, 1.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 56
      removed outlier: 3.601A  pdb=" N   ILE A  54 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   SER A  56 " --> pdb=" O   TYR A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 63
    Processing helix  chain 'A' and resid 71 through 88
      removed outlier: 3.627A  pdb=" N   SER A  75 " --> pdb=" O   GLY A  71 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU A  78 " --> pdb=" O   ALA A  74 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   GLY A  83 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   TYR A  86 " --> pdb=" O   MET A  82 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLY A  88 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 99
    Processing helix  chain 'A' and resid 103 through 118
      removed outlier: 3.695A  pdb=" N   LEU A 118 " --> pdb=" O   LEU A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 125
    Processing helix  chain 'A' and resid 125 through 133
      removed outlier: 4.158A  pdb=" N   ALA A 130 " --> pdb=" O   PRO A 126 " (cutoff:3.500A)
      removed outlier: 5.328A  pdb=" N   ALA A 131 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   LEU A 132 " --> pdb=" O   THR A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 183
      removed outlier: 4.611A  pdb=" N   THR A 157 " --> pdb=" O   CYS A 153 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   ALA A 173 " --> pdb=" O   ALA A 169 " (cutoff:3.500A)
      Proline residue:  A 177  - end of helix
      removed outlier: 3.681A  pdb=" N   ALA A 180 " --> pdb=" O   THR A 176 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLN A 182 " --> pdb=" O   PHE A 178 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   VAL A 183 " --> pdb=" O   GLY A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 186
      No H-bonds generated for 'chain 'A' and resid 184 through 186'
    Processing helix  chain 'A' and resid 187 through 212
      removed outlier: 3.518A  pdb=" N   THR A 191 " --> pdb=" O   GLY A 187 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   TRP A 197 " --> pdb=" O   ARG A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 220
    Processing helix  chain 'A' and resid 221 through 244
      removed outlier: 3.634A  pdb=" N   GLY A 225 " --> pdb=" O   SER A 221 " (cutoff:3.500A)
      Proline residue:  A 229  - end of helix
    Processing helix  chain 'A' and resid 311 through 320
    Processing helix  chain 'A' and resid 321 through 328
    Processing helix  chain 'A' and resid 328 through 347
      removed outlier: 3.892A  pdb=" N   VAL A 343 " --> pdb=" O   GLN A 339 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU A 344 " --> pdb=" O   THR A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 359
      removed outlier: 3.825A  pdb=" N   THR A 358 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   THR A 359 " --> pdb=" O   SER A 355 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 354 through 359'
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 371 through 387
      removed outlier: 3.656A  pdb=" N   LEU A 376 " --> pdb=" O   PHE A 372 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU A 379 " --> pdb=" O   VAL A 375 " (cutoff:3.500A)
      Proline residue:  A 382  - end of helix
    Processing helix  chain 'A' and resid 387 through 395
    Processing helix  chain 'A' and resid 400 through 428
      removed outlier: 3.633A  pdb=" N   ARG A 404 " --> pdb=" O   SER A 400 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASN A 428 " --> pdb=" O   SER A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 453
    Processing helix  chain 'A' and resid 454 through 480
      removed outlier: 4.809A  pdb=" N   ILE A 470 " --> pdb=" O   ILE A 466 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ALA A 480 " --> pdb=" O   ALA A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 510
    Processing helix  chain 'A' and resid 531 through 563
      removed outlier: 3.880A  pdb=" N   HIS A 560 " --> pdb=" O   LYS A 556 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 56
      removed outlier: 3.802A  pdb=" N   VAL B  40 " --> pdb=" O   ALA B  36 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ILE B  54 " --> pdb=" O   ALA B  50 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   SER B  56 " --> pdb=" O   TYR B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 63
    Processing helix  chain 'B' and resid 70 through 88
    Processing helix  chain 'B' and resid 88 through 99
    Processing helix  chain 'B' and resid 102 through 118
      removed outlier: 3.514A  pdb=" N   LEU B 118 " --> pdb=" O   LEU B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 125
    Processing helix  chain 'B' and resid 125 through 133
      removed outlier: 4.323A  pdb=" N   ALA B 130 " --> pdb=" O   PRO B 126 " (cutoff:3.500A)
      removed outlier: 4.742A  pdb=" N   ALA B 131 " --> pdb=" O   ALA B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 182
      removed outlier: 3.972A  pdb=" N   THR B 176 " --> pdb=" O   LYS B 172 " (cutoff:3.500A)
      Proline residue:  B 177  - end of helix
      removed outlier: 3.809A  pdb=" N   GLN B 182 " --> pdb=" O   PHE B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 186
      removed outlier: 3.549A  pdb=" N   ARG B 186 " --> pdb=" O   VAL B 183 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 183 through 186'
    Processing helix  chain 'B' and resid 187 through 212
      removed outlier: 3.557A  pdb=" N   TRP B 197 " --> pdb=" O   ARG B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 220
    Processing helix  chain 'B' and resid 221 through 244
      removed outlier: 3.612A  pdb=" N   GLY B 225 " --> pdb=" O   SER B 221 " (cutoff:3.500A)
      Proline residue:  B 229  - end of helix
    Processing helix  chain 'B' and resid 311 through 320
      removed outlier: 3.684A  pdb=" N   LEU B 318 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LYS B 320 " --> pdb=" O   LYS B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 347
      Proline residue:  B 330  - end of helix
      removed outlier: 3.698A  pdb=" N   VAL B 343 " --> pdb=" O   GLN B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 371
      removed outlier: 4.280A  pdb=" N   LEU B 369 " --> pdb=" O   PRO B 365 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   THR B 370 " --> pdb=" O   ALA B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 387
      removed outlier: 3.571A  pdb=" N   LEU B 376 " --> pdb=" O   PHE B 372 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LEU B 379 " --> pdb=" O   VAL B 375 " (cutoff:3.500A)
      Proline residue:  B 382  - end of helix
    Processing helix  chain 'B' and resid 387 through 394
    Processing helix  chain 'B' and resid 400 through 430
      removed outlier: 3.585A  pdb=" N   ASN B 428 " --> pdb=" O   SER B 424 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 450 through 453
    Processing helix  chain 'B' and resid 454 through 479
      removed outlier: 3.679A  pdb=" N   ILE B 461 " --> pdb=" O   GLN B 457 " (cutoff:3.500A)
      removed outlier: 5.008A  pdb=" N   ILE B 470 " --> pdb=" O   ILE B 466 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ALA B 471 " --> pdb=" O   PHE B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 485 through 511
      removed outlier: 3.593A  pdb=" N   SER B 511 " --> pdb=" O   LEU B 507 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 531 through 559
      removed outlier: 3.539A  pdb=" N   TYR B 535 " --> pdb=" O   TYR B 531 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LYS B 556 " --> pdb=" O   ILE B 552 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 438
    Processing sheet with id=AA2, first strand: chain 'B' and resid 435 through 438

    510 hydrogen bonds defined for protein.
    1509 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: 1.19

  Time building geometry restraints manager: 0.87 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2301
        1.35 -     1.47: 1959
        1.47 -     1.59: 3366
        1.59 -     1.71: 0
        1.71 -     1.83: 60
  Bond restraints: 7686
  Sorted by residual:
  bond pdb=" C   SER A 154 "
       pdb=" N   PRO A 155 "
    ideal  model  delta    sigma   weight residual
    1.335  1.367 -0.031 1.36e-02 5.41e+03 5.24e+00
  bond pdb=" C   SER B 154 "
       pdb=" N   PRO B 155 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.026 1.36e-02 5.41e+03 3.55e+00
  bond pdb=" CA  ALA A  65 "
       pdb=" C   ALA A  65 "
    ideal  model  delta    sigma   weight residual
    1.524  1.540 -0.016 1.26e-02 6.30e+03 1.61e+00
  bond pdb=" N   ILE A 354 "
       pdb=" CA  ILE A 354 "
    ideal  model  delta    sigma   weight residual
    1.474  1.457  0.017 1.57e-02 4.06e+03 1.22e+00
  bond pdb=" CA  ALA B  65 "
       pdb=" C   ALA B  65 "
    ideal  model  delta    sigma   weight residual
    1.524  1.537 -0.013 1.26e-02 6.30e+03 1.07e+00
  ... (remaining 7681 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 10029
        1.47 -     2.93: 339
        2.93 -     4.40: 52
        4.40 -     5.86: 32
        5.86 -     7.33: 4
  Bond angle restraints: 10456
  Sorted by residual:
  angle pdb=" N   ILE A 263 "
        pdb=" CA  ILE A 263 "
        pdb=" C   ILE A 263 "
      ideal   model   delta    sigma   weight residual
     113.47  108.96    4.51 1.01e+00 9.80e-01 1.99e+01
  angle pdb=" N   ILE B 357 "
        pdb=" CA  ILE B 357 "
        pdb=" C   ILE B 357 "
      ideal   model   delta    sigma   weight residual
     112.96  108.70    4.26 1.00e+00 1.00e+00 1.81e+01
  angle pdb=" N   VAL B 246 "
        pdb=" CA  VAL B 246 "
        pdb=" C   VAL B 246 "
      ideal   model   delta    sigma   weight residual
     113.47  109.35    4.12 1.01e+00 9.80e-01 1.67e+01
  angle pdb=" N   ILE B 354 "
        pdb=" CA  ILE B 354 "
        pdb=" C   ILE B 354 "
      ideal   model   delta    sigma   weight residual
     106.21  109.92   -3.71 1.07e+00 8.73e-01 1.20e+01
  angle pdb=" C   ALA A  65 "
        pdb=" CA  ALA A  65 "
        pdb=" CB  ALA A  65 "
      ideal   model   delta    sigma   weight residual
     110.17  116.74   -6.57 1.97e+00 2.58e-01 1.11e+01
  ... (remaining 10451 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.45: 4081
       17.45 -    34.89: 334
       34.89 -    52.34: 35
       52.34 -    69.79: 5
       69.79 -    87.23: 7
  Dihedral angle restraints: 4462
    sinusoidal: 1670
      harmonic: 2792
  Sorted by residual:
  dihedral pdb=" CA  GLY A  83 "
           pdb=" C   GLY A  83 "
           pdb=" N   LEU A  84 "
           pdb=" CA  LEU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.87   21.13     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" SG  CYS B 133 "
           pdb=" CB  CYS B 153 "
           pdb=" SG  CYS B 153 "
           pdb=" CA  CYS B 153 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00   -6.70  -66.30     1      2.00e+01 2.50e-03 1.44e+01
  dihedral pdb=" CA  ALA B  65 "
           pdb=" C   ALA B  65 "
           pdb=" N   PRO B  66 "
           pdb=" CA  PRO B  66 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.20  -18.80     0      5.00e+00 4.00e-02 1.41e+01
  ... (remaining 4459 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 675
       0.028 -    0.056: 387
       0.056 -    0.084: 99
       0.084 -    0.111: 50
       0.111 -    0.139: 13
  Chirality restraints: 1224
  Sorted by residual:
  chirality pdb=" CA  VAL A 220 "
            pdb=" N   VAL A 220 "
            pdb=" C   VAL A 220 "
            pdb=" CB  VAL A 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.84e-01
  chirality pdb=" CA  ILE B 351 "
            pdb=" N   ILE B 351 "
            pdb=" C   ILE B 351 "
            pdb=" CB  ILE B 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.92e-01
  chirality pdb=" CA  VAL A 442 "
            pdb=" N   VAL A 442 "
            pdb=" C   VAL A 442 "
            pdb=" CB  VAL A 442 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.90e-01
  ... (remaining 1221 not shown)

  Planarity restraints: 1290
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B  65 "    0.048 5.00e-02 4.00e+02   7.05e-02 7.95e+00
        pdb=" N   PRO B  66 "   -0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO B  66 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B  66 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  65 "   -0.030 5.00e-02 4.00e+02   4.49e-02 3.23e+00
        pdb=" N   PRO A  66 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A  66 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A  66 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 174 "   -0.007 2.00e-02 2.50e+03   1.43e-02 2.05e+00
        pdb=" CG  ASN A 174 "    0.025 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 174 "   -0.009 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 174 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1287 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 611
        2.74 -     3.28: 7941
        3.28 -     3.82: 12732
        3.82 -     4.36: 14995
        4.36 -     4.90: 25762
  Nonbonded interactions: 62041
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 337 "
            pdb=" OH  TYR A 535 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" NH2 ARG B  33 "
            pdb=" OD1 ASP B 185 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" OE1 GLN B 345 "
            pdb=" NE2 GLN B 454 "
     model   vdw
     2.307 3.120
  nonbonded pdb=" O   LEU B 122 "
            pdb=" OG1 THR B 128 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" OD2 ASP A 259 "
            pdb=" NZ  LYS A 311 "
     model   vdw
     2.327 3.120
  ... (remaining 62036 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.870
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7003
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   0.044   7690  Z= 0.162
  Angle     :  0.701   7.328  10464  Z= 0.441
  Chirality :  0.039   0.139   1224
  Planarity :  0.004   0.070   1290
  Dihedral  : 12.635  87.232   2658
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.33 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.28), residues: 962
  helix:  1.13 (0.21), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.42 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 129 
 TYR   0.016   0.001   TYR A 335 
 PHE   0.012   0.001   PHE A  61 
 TRP   0.019   0.001   TRP A  69 
 HIS   0.001   0.000   HIS A 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 7686)
  covalent geometry    : angle       0.69964 (10456)
  SS BOND              : bond        0.00473 (    4)
  SS BOND              : angle       1.55551 (    8)
  hydrogen bonds       : bond        0.18286 (  510)
  hydrogen bonds       : angle       6.09367 ( 1509)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  104 ARG cc_start: 0.6756 (mtp85) cc_final: 0.6415 (mtp85)
REVERT: A  113 TYR cc_start: 0.8010 (t80) cc_final: 0.7802 (t80)
REVERT: A  129 ARG cc_start: 0.6549 (ttm110) cc_final: 0.6346 (ttm110)
REVERT: A  189 GLU cc_start: 0.6114 (pm20) cc_final: 0.5697 (tm-30)
REVERT: A  250 LYS cc_start: 0.7710 (ptmm) cc_final: 0.7021 (mttt)
REVERT: A  339 GLN cc_start: 0.7591 (mt0) cc_final: 0.7264 (mt0)
REVERT: A  353 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6639 (mm-30)
REVERT: A  482 LYS cc_start: 0.8005 (mppt) cc_final: 0.7395 (mmtp)
REVERT: A  484 MET cc_start: 0.6920 (mtm) cc_final: 0.6475 (mtp)
REVERT: B   34 ARG cc_start: 0.7112 (ttm170) cc_final: 0.6853 (ttp-170)
REVERT: B  112 LEU cc_start: 0.7687 (mt) cc_final: 0.7439 (mp)
REVERT: B  129 ARG cc_start: 0.6251 (ttm110) cc_final: 0.5963 (ttm110)
REVERT: B  242 CYS cc_start: 0.7997 (m) cc_final: 0.7194 (t)
REVERT: B  250 LYS cc_start: 0.7759 (mtpt) cc_final: 0.7284 (mttt)
REVERT: B  372 PHE cc_start: 0.5441 (t80) cc_final: 0.4774 (t80)
REVERT: B  386 LYS cc_start: 0.7396 (mmtt) cc_final: 0.6938 (mmtp)
REVERT: B  403 LYS cc_start: 0.7599 (mmtm) cc_final: 0.7258 (mmtm)
REVERT: B  409 MET cc_start: 0.8298 (mtp) cc_final: 0.8022 (mtt)
REVERT: B  482 LYS cc_start: 0.7791 (mppt) cc_final: 0.7220 (mmtp)
REVERT: B  501 PHE cc_start: 0.7032 (m-80) cc_final: 0.6785 (m-80)
REVERT: B  556 LYS cc_start: 0.7294 (mttt) cc_final: 0.6723 (mtpt)
REVERT: B  558 ASP cc_start: 0.7445 (m-30) cc_final: 0.7157 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.5152
  time to fit residues: 96.7482
Evaluate side-chains
  127 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 454 GLN
A 485 GLN
** B  73 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 = 0.3540 r_free = 0.3540 target = 0.139371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.102342 restraints weight = 8314.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 1.69
r_work: 0.2919 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2801 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.1403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7690  Z= 0.145
  Angle     :  0.590   7.962  10464  Z= 0.302
  Chirality :  0.040   0.206   1224
  Planarity :  0.005   0.070   1290
  Dihedral  :  3.958  20.220   1038
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.33 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  :  8.95 %
    Favored  : 88.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.28), residues: 962
  helix:  1.56 (0.20), residues: 684
  sheet:  None (None), residues: 0
  loop : -1.41 (0.36), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 129 
 TYR   0.024   0.002   TYR A 113 
 PHE   0.018   0.001   PHE A  67 
 TRP   0.011   0.001   TRP A  69 
 HIS   0.003   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 7686)
  covalent geometry    : angle       0.59010 (10456)
  SS BOND              : bond        0.00205 (    4)
  SS BOND              : angle       0.91578 (    8)
  hydrogen bonds       : bond        0.05116 (  510)
  hydrogen bonds       : angle       4.01974 ( 1509)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A  104 ARG cc_start: 0.7397 (mtp85) cc_final: 0.7067 (mtp85)
REVERT: A  129 ARG cc_start: 0.7277 (ttm110) cc_final: 0.6942 (ttm110)
REVERT: A  189 GLU cc_start: 0.6834 (pm20) cc_final: 0.6440 (tm-30)
REVERT: A  250 LYS cc_start: 0.8086 (ptmm) cc_final: 0.7522 (mttt)
REVERT: A  339 GLN cc_start: 0.8882 (mt0) cc_final: 0.8534 (mt0)
REVERT: A  353 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6913 (mm-30)
REVERT: A  482 LYS cc_start: 0.8272 (mppt) cc_final: 0.7740 (mmtp)
REVERT: A  484 MET cc_start: 0.7404 (mtm) cc_final: 0.7021 (mtp)
REVERT: B   84 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8638 (mt)
REVERT: B   97 ASP cc_start: 0.8718 (m-30) cc_final: 0.8384 (m-30)
REVERT: B  242 CYS cc_start: 0.8592 (m) cc_final: 0.7947 (t)
REVERT: B  250 LYS cc_start: 0.7937 (mtpt) cc_final: 0.7517 (mttt)
REVERT: B  386 LYS cc_start: 0.7899 (mmtt) cc_final: 0.7674 (mmtm)
REVERT: B  482 LYS cc_start: 0.8156 (mppt) cc_final: 0.7810 (mmtp)
  outliers start: 19
  outliers final: 10
  residues processed: 136
  average time/residue: 0.4272
  time to fit residues: 62.4277
Evaluate side-chains
  129 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  244 GLN
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  504 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 80 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0980
   chunk 79 optimal weight:    2.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.134173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.096248 restraints weight = 8275.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 1.68
r_work: 0.2847 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2728 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7690  Z= 0.160
  Angle     :  0.584   8.055  10464  Z= 0.299
  Chirality :  0.040   0.135   1224
  Planarity :  0.005   0.066   1290
  Dihedral  :  4.050  21.884   1038
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.64 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  :  9.97 %
    Favored  : 86.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.28), residues: 962
  helix:  1.55 (0.20), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.46 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 129 
 TYR   0.028   0.002   TYR A 113 
 PHE   0.019   0.002   PHE A  67 
 TRP   0.011   0.001   TRP A  69 
 HIS   0.005   0.001   HIS A 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 7686)
  covalent geometry    : angle       0.58421 (10456)
  SS BOND              : bond        0.00199 (    4)
  SS BOND              : angle       0.69070 (    8)
  hydrogen bonds       : bond        0.05058 (  510)
  hydrogen bonds       : angle       3.94263 ( 1509)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 114
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A  112 LEU cc_start: 0.8666 (mt) cc_final: 0.8408 (mp)
REVERT: A  129 ARG cc_start: 0.7366 (ttm110) cc_final: 0.6764 (ttm110)
REVERT: A  157 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8378 (m)
REVERT: A  186 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7309 (mtp85)
REVERT: A  189 GLU cc_start: 0.6882 (pm20) cc_final: 0.6441 (tm-30)
REVERT: A  250 LYS cc_start: 0.7920 (ptmm) cc_final: 0.7370 (mttt)
REVERT: A  339 GLN cc_start: 0.8922 (mt0) cc_final: 0.8597 (mt0)
REVERT: A  353 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6900 (mm-30)
REVERT: A  482 LYS cc_start: 0.8202 (mppt) cc_final: 0.7764 (mmtp)
REVERT: A  484 MET cc_start: 0.7614 (mtm) cc_final: 0.7345 (mtp)
REVERT: B   82 MET cc_start: 0.8468 (mmt) cc_final: 0.8153 (mmp)
REVERT: B   86 TYR cc_start: 0.8394 (m-80) cc_final: 0.7955 (m-80)
REVERT: B   97 ASP cc_start: 0.8692 (m-30) cc_final: 0.8386 (m-30)
REVERT: B  242 CYS cc_start: 0.8590 (m) cc_final: 0.7979 (t)
REVERT: B  250 LYS cc_start: 0.7967 (mtpt) cc_final: 0.7526 (mttt)
REVERT: B  320 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8069 (ttpp)
REVERT: B  386 LYS cc_start: 0.7965 (mmtt) cc_final: 0.7750 (mmtp)
REVERT: B  459 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8267 (mt)
REVERT: B  482 LYS cc_start: 0.8243 (mppt) cc_final: 0.7847 (mmtp)
  outliers start: 30
  outliers final: 15
  residues processed: 132
  average time/residue: 0.4291
  time to fit residues: 60.7641
Evaluate side-chains
  131 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  193 ARG
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  193 ARG
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  320 LYS
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  504 SER
Chi-restraints excluded: chain B residue  555 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   chunk 48 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 69 optimal weight:    6.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 244 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.133639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.095874 restraints weight = 8383.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 1.69
r_work: 0.2834 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2713 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7690  Z= 0.156
  Angle     :  0.577   8.271  10464  Z= 0.295
  Chirality :  0.040   0.134   1224
  Planarity :  0.005   0.065   1290
  Dihedral  :  4.071  22.056   1038
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.43 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 11.38 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.28), residues: 962
  helix:  1.56 (0.20), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.49 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 104 
 TYR   0.017   0.002   TYR B 335 
 PHE   0.020   0.002   PHE A  67 
 TRP   0.006   0.001   TRP A 517 
 HIS   0.004   0.001   HIS A 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 7686)
  covalent geometry    : angle       0.57677 (10456)
  SS BOND              : bond        0.00249 (    4)
  SS BOND              : angle       0.55303 (    8)
  hydrogen bonds       : bond        0.04831 (  510)
  hydrogen bonds       : angle       3.96001 ( 1509)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A  104 ARG cc_start: 0.7280 (mtp85) cc_final: 0.7000 (mtp85)
REVERT: A  129 ARG cc_start: 0.7210 (ttm110) cc_final: 0.6975 (ttm110)
REVERT: A  157 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8228 (t)
REVERT: A  186 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7312 (mtp85)
REVERT: A  189 GLU cc_start: 0.6882 (pm20) cc_final: 0.6410 (tm-30)
REVERT: A  250 LYS cc_start: 0.7907 (ptmm) cc_final: 0.7369 (mttt)
REVERT: A  339 GLN cc_start: 0.8893 (mt0) cc_final: 0.8565 (mt0)
REVERT: A  353 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6930 (mm-30)
REVERT: A  482 LYS cc_start: 0.8245 (mppt) cc_final: 0.7736 (mmtp)
REVERT: A  484 MET cc_start: 0.7616 (mtm) cc_final: 0.7402 (mtp)
REVERT: B   86 TYR cc_start: 0.8434 (m-80) cc_final: 0.7973 (m-80)
REVERT: B   97 ASP cc_start: 0.8703 (m-30) cc_final: 0.8379 (m-30)
REVERT: B  242 CYS cc_start: 0.8530 (m) cc_final: 0.8001 (t)
REVERT: B  250 LYS cc_start: 0.7962 (mtpt) cc_final: 0.7495 (mttt)
REVERT: B  320 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8452 (ptpp)
REVERT: B  386 LYS cc_start: 0.7950 (mmtt) cc_final: 0.7675 (mmtp)
REVERT: B  459 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8287 (mt)
REVERT: B  482 LYS cc_start: 0.8250 (mppt) cc_final: 0.7838 (mmtp)
  outliers start: 24
  outliers final: 15
  residues processed: 126
  average time/residue: 0.5135
  time to fit residues: 69.0182
Evaluate side-chains
  122 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  193 ARG
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  193 ARG
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  320 LYS
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  504 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0030
   chunk 82 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   overall best weight:    0.6590

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 217 GLN
** B  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 244 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.136307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.099039 restraints weight = 8398.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 1.68
r_work: 0.2883 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2763 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7690  Z= 0.118
  Angle     :  0.537   8.055  10464  Z= 0.272
  Chirality :  0.038   0.134   1224
  Planarity :  0.004   0.062   1290
  Dihedral  :  3.951  21.813   1038
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.81 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 11.76 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.27), residues: 962
  helix:  1.70 (0.20), residues: 692
  sheet:  None (None), residues: 0
  loop : -1.46 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 104 
 TYR   0.016   0.001   TYR B 335 
 PHE   0.017   0.001   PHE A  67 
 TRP   0.006   0.001   TRP B 197 
 HIS   0.002   0.000   HIS A 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 7686)
  covalent geometry    : angle       0.53729 (10456)
  SS BOND              : bond        0.00075 (    4)
  SS BOND              : angle       0.74941 (    8)
  hydrogen bonds       : bond        0.04261 (  510)
  hydrogen bonds       : angle       3.81968 ( 1509)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.317 
Fit side-chains
REVERT: A  104 ARG cc_start: 0.7197 (mtp85) cc_final: 0.6931 (mtp85)
REVERT: A  129 ARG cc_start: 0.7187 (ttm110) cc_final: 0.6664 (ttm110)
REVERT: A  157 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8260 (t)
REVERT: A  186 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7353 (mtp85)
REVERT: A  189 GLU cc_start: 0.6797 (pm20) cc_final: 0.6311 (OUTLIER)
REVERT: A  250 LYS cc_start: 0.7997 (ptmm) cc_final: 0.7500 (mttt)
REVERT: A  339 GLN cc_start: 0.8823 (mt0) cc_final: 0.8511 (mt0)
REVERT: A  353 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7013 (mm-30)
REVERT: A  482 LYS cc_start: 0.8245 (mppt) cc_final: 0.7727 (mmtp)
REVERT: A  484 MET cc_start: 0.7452 (mtm) cc_final: 0.7250 (mtp)
REVERT: B   82 MET cc_start: 0.8482 (mmt) cc_final: 0.8099 (mmp)
REVERT: B   86 TYR cc_start: 0.8488 (m-80) cc_final: 0.8049 (m-80)
REVERT: B   97 ASP cc_start: 0.8708 (m-30) cc_final: 0.8385 (m-30)
REVERT: B  222 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.5959 (t80)
REVERT: B  242 CYS cc_start: 0.8535 (m) cc_final: 0.7991 (t)
REVERT: B  250 LYS cc_start: 0.7906 (mtpt) cc_final: 0.7480 (mttt)
REVERT: B  320 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8438 (ptpp)
REVERT: B  338 MET cc_start: 0.8635 (mtm) cc_final: 0.8388 (ttp)
REVERT: B  459 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8180 (mt)
REVERT: B  482 LYS cc_start: 0.8242 (mppt) cc_final: 0.7837 (mmtp)
  outliers start: 26
  outliers final: 14
  residues processed: 127
  average time/residue: 0.5056
  time to fit residues: 68.5810
Evaluate side-chains
  121 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  193 ARG
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  193 ARG
Chi-restraints excluded: chain B residue  222 PHE
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  320 LYS
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  459 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 72 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 217 GLN
** B  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 244 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.135388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.097625 restraints weight = 8328.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 1.70
r_work: 0.2865 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2745 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7690  Z= 0.126
  Angle     :  0.542   8.069  10464  Z= 0.275
  Chirality :  0.039   0.135   1224
  Planarity :  0.004   0.062   1290
  Dihedral  :  3.941  21.771   1038
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.01 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 12.53 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.27), residues: 962
  helix:  1.77 (0.20), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.53 (0.35), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 129 
 TYR   0.015   0.001   TYR B 335 
 PHE   0.015   0.001   PHE A  67 
 TRP   0.005   0.001   TRP A 197 
 HIS   0.002   0.001   HIS A 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 7686)
  covalent geometry    : angle       0.54219 (10456)
  SS BOND              : bond        0.00158 (    4)
  SS BOND              : angle       0.48598 (    8)
  hydrogen bonds       : bond        0.04356 (  510)
  hydrogen bonds       : angle       3.81423 ( 1509)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.398 
Fit side-chains
REVERT: A  104 ARG cc_start: 0.7284 (mtp85) cc_final: 0.6952 (mtp85)
REVERT: A  129 ARG cc_start: 0.7225 (ttm110) cc_final: 0.6693 (ttm110)
REVERT: A  157 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8230 (t)
REVERT: A  186 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7360 (mtp85)
REVERT: A  189 GLU cc_start: 0.6807 (pm20) cc_final: 0.6312 (OUTLIER)
REVERT: A  250 LYS cc_start: 0.8096 (ptmm) cc_final: 0.7535 (mttt)
REVERT: A  339 GLN cc_start: 0.8876 (mt0) cc_final: 0.8524 (mt0)
REVERT: A  353 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7032 (mm-30)
REVERT: A  482 LYS cc_start: 0.8186 (mppt) cc_final: 0.7666 (mmtp)
REVERT: B   86 TYR cc_start: 0.8486 (m-80) cc_final: 0.7896 (m-80)
REVERT: B   97 ASP cc_start: 0.8693 (m-30) cc_final: 0.8393 (m-30)
REVERT: B  222 PHE cc_start: 0.6785 (OUTLIER) cc_final: 0.5919 (t80)
REVERT: B  242 CYS cc_start: 0.8540 (m) cc_final: 0.7974 (t)
REVERT: B  250 LYS cc_start: 0.7915 (mtpt) cc_final: 0.7486 (mttt)
REVERT: B  459 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8205 (mt)
REVERT: B  482 LYS cc_start: 0.8263 (mppt) cc_final: 0.7816 (mmtp)
  outliers start: 26
  outliers final: 16
  residues processed: 124
  average time/residue: 0.5200
  time to fit residues: 68.9657
Evaluate side-chains
  119 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  193 ARG
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  193 ARG
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  222 PHE
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  244 GLN
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  459 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 79 optimal weight:    0.4980
   chunk 76 optimal weight:    0.2980
   chunk 61 optimal weight:    7.9990
   chunk 44 optimal weight:    0.4980
   chunk 25 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 217 GLN
** B  73 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 = 0.3503 r_free = 0.3503 target = 0.136544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.099212 restraints weight = 8399.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 1.70
r_work: 0.2891 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2771 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   7690  Z= 0.116
  Angle     :  0.534   8.131  10464  Z= 0.269
  Chirality :  0.038   0.137   1224
  Planarity :  0.004   0.061   1290
  Dihedral  :  3.894  21.637   1038
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.91 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.32 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.28), residues: 962
  helix:  1.86 (0.20), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.50 (0.35), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 129 
 TYR   0.015   0.001   TYR B 335 
 PHE   0.013   0.001   PHE A  67 
 TRP   0.006   0.001   TRP A 197 
 HIS   0.002   0.000   HIS A 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 7686)
  covalent geometry    : angle       0.53401 (10456)
  SS BOND              : bond        0.00132 (    4)
  SS BOND              : angle       0.45076 (    8)
  hydrogen bonds       : bond        0.04143 (  510)
  hydrogen bonds       : angle       3.78878 ( 1509)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A  104 ARG cc_start: 0.7250 (mtp85) cc_final: 0.6919 (mtp85)
REVERT: A  129 ARG cc_start: 0.7176 (ttm110) cc_final: 0.6664 (ttm110)
REVERT: A  157 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8239 (t)
REVERT: A  186 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7366 (mtp85)
REVERT: A  189 GLU cc_start: 0.6776 (pm20) cc_final: 0.6295 (OUTLIER)
REVERT: A  250 LYS cc_start: 0.8088 (ptmm) cc_final: 0.7581 (mttt)
REVERT: A  339 GLN cc_start: 0.8825 (mt0) cc_final: 0.8474 (mt0)
REVERT: A  353 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7031 (mm-30)
REVERT: A  372 PHE cc_start: 0.8030 (m-10) cc_final: 0.6880 (t80)
REVERT: A  482 LYS cc_start: 0.8176 (mppt) cc_final: 0.7699 (mmtp)
REVERT: B   97 ASP cc_start: 0.8623 (m-30) cc_final: 0.8274 (m-30)
REVERT: B  222 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.5949 (t80)
REVERT: B  242 CYS cc_start: 0.8628 (m) cc_final: 0.7994 (t)
REVERT: B  244 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7866 (tp40)
REVERT: B  250 LYS cc_start: 0.7997 (mtpt) cc_final: 0.7598 (mttt)
REVERT: B  459 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8175 (mt)
REVERT: B  482 LYS cc_start: 0.8222 (mppt) cc_final: 0.7709 (mmtp)
  outliers start: 19
  outliers final: 14
  residues processed: 123
  average time/residue: 0.4918
  time to fit residues: 64.2881
Evaluate side-chains
  118 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  193 ARG
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  193 ARG
Chi-restraints excluded: chain B residue  222 PHE
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  244 GLN
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  459 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 8 optimal weight:    0.0670
   chunk 30 optimal weight:    0.0270
   chunk 28 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   chunk 75 optimal weight:    6.9990
   chunk 80 optimal weight:    0.8980
   chunk 21 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   overall best weight:    0.5376

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 217 GLN
** B  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 244 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.137307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.100166 restraints weight = 8422.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 1.69
r_work: 0.2905 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2784 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7690  Z= 0.113
  Angle     :  0.535   8.253  10464  Z= 0.267
  Chirality :  0.038   0.137   1224
  Planarity :  0.004   0.061   1290
  Dihedral  :  3.854  21.464   1038
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.81 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 14.32 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.55 (0.28), residues: 962
  helix:  1.98 (0.20), residues: 682
  sheet:  None (None), residues: 0
  loop : -1.45 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 129 
 TYR   0.015   0.001   TYR B 335 
 PHE   0.012   0.001   PHE A  67 
 TRP   0.005   0.001   TRP A 197 
 HIS   0.002   0.000   HIS A 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 7686)
  covalent geometry    : angle       0.53509 (10456)
  SS BOND              : bond        0.00138 (    4)
  SS BOND              : angle       0.41748 (    8)
  hydrogen bonds       : bond        0.04037 (  510)
  hydrogen bonds       : angle       3.73910 ( 1509)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A  129 ARG cc_start: 0.7177 (ttm110) cc_final: 0.6691 (ttm110)
REVERT: A  157 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8239 (t)
REVERT: A  186 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7356 (mtp85)
REVERT: A  189 GLU cc_start: 0.6757 (pm20) cc_final: 0.6289 (OUTLIER)
REVERT: A  250 LYS cc_start: 0.7995 (ptmm) cc_final: 0.7568 (mttt)
REVERT: A  339 GLN cc_start: 0.8767 (mt0) cc_final: 0.8422 (mt0)
REVERT: A  353 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7023 (mm-30)
REVERT: A  372 PHE cc_start: 0.7985 (m-10) cc_final: 0.6944 (t80)
REVERT: A  482 LYS cc_start: 0.8171 (mppt) cc_final: 0.7703 (mmtp)
REVERT: B   86 TYR cc_start: 0.8345 (m-80) cc_final: 0.7972 (m-80)
REVERT: B   97 ASP cc_start: 0.8635 (m-30) cc_final: 0.8290 (m-30)
REVERT: B  222 PHE cc_start: 0.6972 (OUTLIER) cc_final: 0.6181 (t80)
REVERT: B  242 CYS cc_start: 0.8547 (m) cc_final: 0.8005 (t)
REVERT: B  244 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7984 (tp40)
REVERT: B  250 LYS cc_start: 0.7974 (mtpt) cc_final: 0.7557 (mttt)
REVERT: B  409 MET cc_start: 0.9198 (mtt) cc_final: 0.8959 (mtm)
REVERT: B  459 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8211 (mt)
REVERT: B  482 LYS cc_start: 0.8215 (mppt) cc_final: 0.7701 (mmtp)
  outliers start: 23
  outliers final: 14
  residues processed: 120
  average time/residue: 0.4857
  time to fit residues: 62.2642
Evaluate side-chains
  117 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  193 ARG
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  193 ARG
Chi-restraints excluded: chain B residue  222 PHE
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  244 GLN
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  465 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 9 optimal weight:    0.1980
   chunk 81 optimal weight:    0.6980
   chunk 93 optimal weight:    0.9990
   chunk 42 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0270
   chunk 47 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 217 GLN
** B  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 244 GLN
B 457 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.137571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.100580 restraints weight = 8345.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 1.69
r_work: 0.2907 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2786 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7690  Z= 0.114
  Angle     :  0.536   8.350  10464  Z= 0.267
  Chirality :  0.038   0.138   1224
  Planarity :  0.004   0.060   1290
  Dihedral  :  3.834  21.362   1038
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.01 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 15.22 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.58 (0.28), residues: 962
  helix:  2.00 (0.20), residues: 682
  sheet:  None (None), residues: 0
  loop : -1.42 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 129 
 TYR   0.014   0.001   TYR B 335 
 PHE   0.012   0.001   PHE A  67 
 TRP   0.005   0.001   TRP A 197 
 HIS   0.002   0.000   HIS A 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 7686)
  covalent geometry    : angle       0.53577 (10456)
  SS BOND              : bond        0.00133 (    4)
  SS BOND              : angle       0.40416 (    8)
  hydrogen bonds       : bond        0.04010 (  510)
  hydrogen bonds       : angle       3.71410 ( 1509)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A  129 ARG cc_start: 0.7161 (ttm110) cc_final: 0.6678 (ttm110)
REVERT: A  157 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8266 (t)
REVERT: A  186 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7378 (mtp85)
REVERT: A  189 GLU cc_start: 0.6764 (pm20) cc_final: 0.6291 (OUTLIER)
REVERT: A  250 LYS cc_start: 0.8020 (ptmm) cc_final: 0.7391 (mttt)
REVERT: A  339 GLN cc_start: 0.8755 (mt0) cc_final: 0.8396 (mt0)
REVERT: A  353 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7031 (mm-30)
REVERT: A  372 PHE cc_start: 0.7973 (m-10) cc_final: 0.6962 (t80)
REVERT: A  482 LYS cc_start: 0.8167 (mppt) cc_final: 0.7699 (mmtp)
REVERT: B   86 TYR cc_start: 0.8307 (m-80) cc_final: 0.7903 (m-80)
REVERT: B   97 ASP cc_start: 0.8639 (m-30) cc_final: 0.8290 (m-30)
REVERT: B  104 ARG cc_start: 0.7642 (ttm110) cc_final: 0.7102 (mtp85)
REVERT: B  222 PHE cc_start: 0.6959 (OUTLIER) cc_final: 0.6078 (t80)
REVERT: B  242 CYS cc_start: 0.8564 (m) cc_final: 0.7933 (t)
REVERT: B  244 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8198 (tp40)
REVERT: B  250 LYS cc_start: 0.7997 (mtpt) cc_final: 0.7565 (mttt)
REVERT: B  338 MET cc_start: 0.8672 (mtp) cc_final: 0.8240 (mtp)
REVERT: B  459 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8213 (mt)
REVERT: B  482 LYS cc_start: 0.8216 (mppt) cc_final: 0.7699 (mmtp)
  outliers start: 21
  outliers final: 16
  residues processed: 119
  average time/residue: 0.5039
  time to fit residues: 63.9314
Evaluate side-chains
  119 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  193 ARG
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  193 ARG
Chi-restraints excluded: chain B residue  222 PHE
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  244 GLN
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  465 GLU
Chi-restraints excluded: chain B residue  504 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 3 optimal weight:    6.9990
   chunk 85 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 52 optimal weight:    9.9990
   chunk 76 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0980
   overall best weight:    1.6188

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 217 GLN
** B  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 244 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.133370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.095892 restraints weight = 8336.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 1.68
r_work: 0.2841 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2720 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7690  Z= 0.167
  Angle     :  0.586   8.786  10464  Z= 0.296
  Chirality :  0.041   0.142   1224
  Planarity :  0.004   0.060   1290
  Dihedral  :  3.987  22.029   1038
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.53 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 14.96 %
    Favored  : 82.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.28), residues: 962
  helix:  1.82 (0.20), residues: 684
  sheet:  None (None), residues: 0
  loop : -1.39 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 129 
 TYR   0.014   0.002   TYR A 335 
 PHE   0.013   0.002   PHE A  67 
 TRP   0.005   0.001   TRP A 517 
 HIS   0.004   0.001   HIS A 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 7686)
  covalent geometry    : angle       0.58612 (10456)
  SS BOND              : bond        0.00229 (    4)
  SS BOND              : angle       0.41791 (    8)
  hydrogen bonds       : bond        0.04694 (  510)
  hydrogen bonds       : angle       3.87679 ( 1509)

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A  129 ARG cc_start: 0.7213 (ttm110) cc_final: 0.6668 (ttm110)
REVERT: A  157 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8334 (m)
REVERT: A  161 LEU cc_start: 0.8274 (mt) cc_final: 0.8065 (mt)
REVERT: A  186 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7843 (mtt180)
REVERT: A  189 GLU cc_start: 0.6851 (pm20) cc_final: 0.6389 (OUTLIER)
REVERT: A  250 LYS cc_start: 0.8005 (ptmm) cc_final: 0.7534 (mttt)
REVERT: A  339 GLN cc_start: 0.8866 (mt0) cc_final: 0.8479 (mt0)
REVERT: A  353 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7026 (mm-30)
REVERT: A  372 PHE cc_start: 0.8049 (m-10) cc_final: 0.6970 (t80)
REVERT: A  482 LYS cc_start: 0.8192 (mppt) cc_final: 0.7652 (mmtp)
REVERT: B   86 TYR cc_start: 0.8356 (m-80) cc_final: 0.7980 (m-80)
REVERT: B   97 ASP cc_start: 0.8650 (m-30) cc_final: 0.8295 (m-30)
REVERT: B  222 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.5997 (t80)
REVERT: B  250 LYS cc_start: 0.8064 (mtpt) cc_final: 0.7582 (mttt)
REVERT: B  459 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8290 (mt)
REVERT: B  482 LYS cc_start: 0.8240 (mppt) cc_final: 0.7708 (mmtp)
  outliers start: 22
  outliers final: 17
  residues processed: 109
  average time/residue: 0.4812
  time to fit residues: 55.9741
Evaluate side-chains
  112 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  193 ARG
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  484 MET
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  193 ARG
Chi-restraints excluded: chain B residue  222 PHE
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  459 LEU
Chi-restraints excluded: chain B residue  465 GLU
Chi-restraints excluded: chain B residue  504 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 94 optimal weight:    0.9980
   chunk 87 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 91 optimal weight:    0.0030
   chunk 55 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.7390

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 217 GLN
** B  73 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 = 0.3489 r_free = 0.3489 target = 0.135522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.098065 restraints weight = 8347.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 1.70
r_work: 0.2889 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2767 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7690  Z= 0.121
  Angle     :  0.548   8.598  10464  Z= 0.274
  Chirality :  0.039   0.139   1224
  Planarity :  0.004   0.059   1290
  Dihedral  :  3.905  21.557   1038
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.01 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 15.09 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.27), residues: 962
  helix:  1.88 (0.20), residues: 686
  sheet:  None (None), residues: 0
  loop : -1.44 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 129 
 TYR   0.014   0.001   TYR B 335 
 PHE   0.012   0.001   PHE A  67 
 TRP   0.005   0.001   TRP A 197 
 HIS   0.002   0.001   HIS A 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 7686)
  covalent geometry    : angle       0.54760 (10456)
  SS BOND              : bond        0.00159 (    4)
  SS BOND              : angle       0.40611 (    8)
  hydrogen bonds       : bond        0.04207 (  510)
  hydrogen bonds       : angle       3.79743 ( 1509)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2759.04 seconds
wall clock time: 47 minutes 48.28 seconds (2868.28 seconds total)