Starting phenix.real_space_refine
on Wed Mar 12 07:31:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wx3_37899/03_2025/8wx3_37899.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wx3_37899/03_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_37899/03_2025/8wx3_37899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wx3_37899/03_2025/8wx3_37899.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wx3_37899/03_2025/8wx3_37899.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wx3_37899/03_2025/8wx3_37899.cif"
  }
  resolution = 2.83
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.010
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.48, per 1000 atoms: 0.60
  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: 1.62
  Conformation dependent library (CDL) restraints added in 946.4 milliseconds
  

  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: 0.63
  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: 1.96

  Time building geometry restraints manager: 1.96 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: 0.04
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:             0.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.770
  Find NCS groups from input model:        0.210
  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:             0.010
  Load rotamer database and sin/cos tables:10.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.220
-------------------------------------------------------------------------------
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   7686  Z= 0.205
  Angle     :  0.700   7.328  10456  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.019   0.001   TRP A  69 
 HIS   0.001   0.000   HIS A 521 
 PHE   0.012   0.001   PHE A  61 
 TYR   0.016   0.001   TYR A 335 
 ARG   0.010   0.000   ARG B 129 

*********************** 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  : 0.786 
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: 1.0184
  time to fit residues: 191.9593
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  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0050
   chunk 24 optimal weight:    0.0050
   chunk 49 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0870
   chunk 29 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9990
   overall best weight:    0.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 339 GLN
A 454 GLN
A 485 GLN
** B  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.141165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.104165 restraints weight = 8267.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3088 rms_B_bonded: 1.70
r_work: 0.2970 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.1334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7686  Z= 0.178
  Angle     :  0.571   7.770  10456  Z= 0.291
  Chirality :  0.039   0.181   1224
  Planarity :  0.005   0.069   1290
  Dihedral  :  3.880  19.787   1038
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.22 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  :  9.34 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.28), residues: 962
  helix:  1.64 (0.20), residues: 682
  sheet:  None (None), residues: 0
  loop : -1.58 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  69 
 HIS   0.003   0.001   HIS A 559 
 PHE   0.017   0.001   PHE A  67 
 TYR   0.021   0.001   TYR A 113 
 ARG   0.004   0.000   ARG B 129 

*********************** 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
  146 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 130
  time to evaluate  : 0.863 
Fit side-chains
REVERT: A  104 ARG cc_start: 0.7338 (mtp85) cc_final: 0.7006 (mtp85)
REVERT: A  129 ARG cc_start: 0.7285 (ttm110) cc_final: 0.7002 (ttm110)
REVERT: A  189 GLU cc_start: 0.6798 (pm20) cc_final: 0.6408 (tm-30)
REVERT: A  250 LYS cc_start: 0.8059 (ptmm) cc_final: 0.7509 (mttt)
REVERT: A  339 GLN cc_start: 0.8765 (mt0) cc_final: 0.8446 (mt0)
REVERT: A  353 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6928 (mm-30)
REVERT: A  482 LYS cc_start: 0.8256 (mppt) cc_final: 0.7740 (mmtp)
REVERT: A  484 MET cc_start: 0.7298 (mtm) cc_final: 0.6884 (mtp)
REVERT: B   84 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8600 (mt)
REVERT: B  129 ARG cc_start: 0.6754 (ttm110) cc_final: 0.6501 (ttm110)
REVERT: B  242 CYS cc_start: 0.8578 (m) cc_final: 0.7918 (t)
REVERT: B  250 LYS cc_start: 0.7830 (mtpt) cc_final: 0.7493 (mttt)
REVERT: B  386 LYS cc_start: 0.7899 (mmtt) cc_final: 0.7672 (mmtp)
REVERT: B  482 LYS cc_start: 0.8177 (mppt) cc_final: 0.7832 (mmtp)
  outliers start: 16
  outliers final: 7
  residues processed: 139
  average time/residue: 1.0793
  time to fit residues: 161.7499
Evaluate side-chains
  129 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 121
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 36 optimal weight:    8.9990
   chunk 46 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 76 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 174 ASN
A 339 GLN
** B  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 244 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.131565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.093592 restraints weight = 8404.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.2923 rms_B_bonded: 1.69
r_work: 0.2805 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2686 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.2126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   7686  Z= 0.346
  Angle     :  0.645   8.561  10456  Z= 0.332
  Chirality :  0.043   0.136   1224
  Planarity :  0.005   0.067   1290
  Dihedral  :  4.244  22.597   1038
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.53 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  :  9.59 %
    Favored  : 86.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.27), residues: 962
  helix:  1.36 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop : -1.58 (0.35), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  69 
 HIS   0.006   0.001   HIS A 563 
 PHE   0.019   0.002   PHE A  67 
 TYR   0.036   0.002   TYR A 113 
 ARG   0.006   0.000   ARG B 129 

*********************** 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
  143 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 115
  time to evaluate  : 0.840 
Fit side-chains
REVERT: A  112 LEU cc_start: 0.8686 (mt) cc_final: 0.8407 (mp)
REVERT: A  189 GLU cc_start: 0.6881 (pm20) cc_final: 0.6415 (tm-30)
REVERT: A  250 LYS cc_start: 0.7884 (ptmm) cc_final: 0.7370 (mttt)
REVERT: A  339 GLN cc_start: 0.8996 (mt0) cc_final: 0.8702 (mt0)
REVERT: A  353 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6936 (mm-30)
REVERT: A  482 LYS cc_start: 0.8223 (mppt) cc_final: 0.7785 (mmtp)
REVERT: A  484 MET cc_start: 0.7894 (mtm) cc_final: 0.7670 (mtp)
REVERT: B   86 TYR cc_start: 0.8442 (m-80) cc_final: 0.8002 (m-80)
REVERT: B   97 ASP cc_start: 0.8648 (m-30) cc_final: 0.8249 (m-30)
REVERT: B  129 ARG cc_start: 0.7081 (ttm110) cc_final: 0.6811 (ttm110)
REVERT: B  242 CYS cc_start: 0.8595 (m) cc_final: 0.7987 (t)
REVERT: B  250 LYS cc_start: 0.8016 (mtpt) cc_final: 0.7610 (mttt)
REVERT: B  386 LYS cc_start: 0.7954 (mmtt) cc_final: 0.7744 (mmtp)
REVERT: B  459 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8305 (mt)
REVERT: B  482 LYS cc_start: 0.8257 (mppt) cc_final: 0.7852 (mmtp)
REVERT: B  553 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8483 (mt)
  outliers start: 28
  outliers final: 19
  residues processed: 132
  average time/residue: 0.8647
  time to fit residues: 123.1567
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  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 THR
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  442 VAL
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  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  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  553 ILE
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 60 optimal weight:    2.9990
   chunk 84 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0270
   chunk 49 optimal weight:    0.8980
   chunk 83 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 72 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 35 optimal weight:    5.9990
   overall best weight:    0.8640

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3486 r_free = 0.3486 target = 0.135018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.097771 restraints weight = 8332.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.2980 rms_B_bonded: 1.67
r_work: 0.2860 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2741 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.2198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7686  Z= 0.196
  Angle     :  0.567  10.863  10456  Z= 0.285
  Chirality :  0.039   0.135   1224
  Planarity :  0.004   0.064   1290
  Dihedral  :  4.059  21.421   1038
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.70 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 10.87 %
    Favored  : 85.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.27), residues: 962
  helix:  1.58 (0.20), residues: 692
  sheet:  None (None), residues: 0
  loop : -1.62 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 197 
 HIS   0.002   0.001   HIS A 563 
 PHE   0.021   0.001   PHE A  67 
 TYR   0.016   0.001   TYR B 335 
 ARG   0.005   0.000   ARG A 129 

*********************** 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
  137 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.729 
Fit side-chains
REVERT: A  104 ARG cc_start: 0.7234 (mtp85) cc_final: 0.6956 (mtp85)
REVERT: A  157 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8252 (t)
REVERT: A  186 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7276 (mtp85)
REVERT: A  189 GLU cc_start: 0.6858 (pm20) cc_final: 0.6408 (tm-30)
REVERT: A  250 LYS cc_start: 0.7902 (ptmm) cc_final: 0.7408 (mttt)
REVERT: A  339 GLN cc_start: 0.8857 (mt0) cc_final: 0.8527 (mt0)
REVERT: A  353 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6908 (mm-30)
REVERT: A  482 LYS cc_start: 0.8237 (mppt) cc_final: 0.7734 (mmtp)
REVERT: A  484 MET cc_start: 0.7522 (mtm) cc_final: 0.7298 (mtp)
REVERT: B   97 ASP cc_start: 0.8659 (m-30) cc_final: 0.8266 (m-30)
REVERT: B  129 ARG cc_start: 0.7176 (ttm110) cc_final: 0.6816 (ttm110)
REVERT: B  222 PHE cc_start: 0.6744 (OUTLIER) cc_final: 0.6097 (t80)
REVERT: B  242 CYS cc_start: 0.8535 (m) cc_final: 0.7999 (t)
REVERT: B  250 LYS cc_start: 0.7945 (mtpt) cc_final: 0.7505 (mttt)
REVERT: B  386 LYS cc_start: 0.7959 (mmtt) cc_final: 0.7686 (mmtp)
REVERT: B  409 MET cc_start: 0.9237 (mtt) cc_final: 0.8978 (mtm)
REVERT: B  459 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8254 (mt)
REVERT: B  482 LYS cc_start: 0.8250 (mppt) cc_final: 0.7842 (mmtp)
  outliers start: 26
  outliers final: 14
  residues processed: 127
  average time/residue: 0.9298
  time to fit residues: 126.6941
Evaluate side-chains
  120 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
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  442 VAL
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  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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 48 optimal weight:   10.0000
   chunk 93 optimal weight:    4.9990
   chunk 67 optimal weight:    0.0570
   chunk 50 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9990
   chunk 4 optimal weight:    9.9990
   overall best weight:    0.6500

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3500 r_free = 0.3500 target = 0.136322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.099026 restraints weight = 8304.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 1.69
r_work: 0.2885 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2764 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7686  Z= 0.175
  Angle     :  0.546   8.912  10456  Z= 0.273
  Chirality :  0.038   0.134   1224
  Planarity :  0.004   0.062   1290
  Dihedral  :  3.937  21.888   1038
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.33 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 12.02 %
    Favored  : 85.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.27), residues: 962
  helix:  1.71 (0.20), residues: 692
  sheet:  None (None), residues: 0
  loop : -1.54 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 197 
 HIS   0.002   0.001   HIS A 563 
 PHE   0.016   0.001   PHE A  67 
 TYR   0.017   0.001   TYR B 335 
 ARG   0.003   0.000   ARG A 129 

*********************** 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
  138 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.824 
Fit side-chains
REVERT: A  104 ARG cc_start: 0.7195 (mtp85) cc_final: 0.6915 (mtp85)
REVERT: A  157 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8241 (t)
REVERT: A  186 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7282 (mtp85)
REVERT: A  189 GLU cc_start: 0.6777 (pm20) cc_final: 0.6291 (OUTLIER)
REVERT: A  250 LYS cc_start: 0.8093 (ptmm) cc_final: 0.7572 (mttt)
REVERT: A  339 GLN cc_start: 0.8826 (mt0) cc_final: 0.8502 (mt0)
REVERT: A  353 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7032 (mm-30)
REVERT: A  372 PHE cc_start: 0.8013 (m-10) cc_final: 0.6890 (t80)
REVERT: A  482 LYS cc_start: 0.8236 (mppt) cc_final: 0.7721 (mmtp)
REVERT: B   55 THR cc_start: 0.8098 (p) cc_final: 0.7834 (p)
REVERT: B   86 TYR cc_start: 0.8370 (m-80) cc_final: 0.8094 (m-80)
REVERT: B   97 ASP cc_start: 0.8640 (m-30) cc_final: 0.8243 (m-30)
REVERT: B  129 ARG cc_start: 0.7094 (ttm110) cc_final: 0.6726 (ttm110)
REVERT: B  242 CYS cc_start: 0.8542 (m) cc_final: 0.7972 (t)
REVERT: B  250 LYS cc_start: 0.7906 (mtpt) cc_final: 0.7495 (mttt)
REVERT: B  459 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8177 (mt)
REVERT: B  482 LYS cc_start: 0.8254 (mppt) cc_final: 0.7804 (mmtp)
  outliers start: 23
  outliers final: 14
  residues processed: 128
  average time/residue: 0.8996
  time to fit residues: 123.9051
Evaluate side-chains
  125 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
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  442 VAL
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  176 THR
Chi-restraints excluded: chain B residue  193 ARG
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  443 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 59 optimal weight:    4.9990
   chunk 58 optimal weight:    8.9990
   chunk 93 optimal weight:    3.9990
   chunk 81 optimal weight:    0.8980
   chunk 60 optimal weight:    4.9990
   chunk 23 optimal weight:    6.9990
   chunk 73 optimal weight:    0.0030
   chunk 87 optimal weight:    3.9990
   chunk 4 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   overall best weight:    1.9594

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3437 r_free = 0.3437 target = 0.131334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.093594 restraints weight = 8380.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 1.68
r_work: 0.2813 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2691 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7686  Z= 0.307
  Angle     :  0.615   8.636  10456  Z= 0.312
  Chirality :  0.042   0.139   1224
  Planarity :  0.005   0.061   1290
  Dihedral  :  4.180  22.662   1038
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.64 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 12.92 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.27), residues: 962
  helix:  1.57 (0.20), residues: 686
  sheet:  None (None), residues: 0
  loop : -1.63 (0.35), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 517 
 HIS   0.005   0.001   HIS A 563 
 PHE   0.016   0.002   PHE A  67 
 TYR   0.017   0.002   TYR A 335 
 ARG   0.004   0.000   ARG B 129 

*********************** 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
  127 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 100
  time to evaluate  : 0.745 
Fit side-chains
REVERT: A  186 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7265 (mtp85)
REVERT: A  189 GLU cc_start: 0.6835 (pm20) cc_final: 0.6366 (OUTLIER)
REVERT: A  250 LYS cc_start: 0.7847 (ptmm) cc_final: 0.7394 (mttt)
REVERT: A  339 GLN cc_start: 0.8944 (mt0) cc_final: 0.8569 (mt0)
REVERT: A  353 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6947 (mm-30)
REVERT: A  482 LYS cc_start: 0.8254 (mppt) cc_final: 0.7722 (mmtp)
REVERT: B   86 TYR cc_start: 0.8379 (m-80) cc_final: 0.8019 (m-80)
REVERT: B   97 ASP cc_start: 0.8613 (m-30) cc_final: 0.8194 (m-30)
REVERT: B  129 ARG cc_start: 0.7257 (ttm110) cc_final: 0.6909 (ttm110)
REVERT: B  222 PHE cc_start: 0.7240 (OUTLIER) cc_final: 0.6240 (t80)
REVERT: B  242 CYS cc_start: 0.8570 (m) cc_final: 0.8009 (t)
REVERT: B  244 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8119 (tp40)
REVERT: B  250 LYS cc_start: 0.7902 (mtpt) cc_final: 0.7442 (mttt)
REVERT: B  459 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8339 (mt)
REVERT: B  482 LYS cc_start: 0.8289 (mppt) cc_final: 0.7760 (mmtp)
  outliers start: 27
  outliers final: 23
  residues processed: 118
  average time/residue: 0.9583
  time to fit residues: 121.4199
Evaluate side-chains
  121 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
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  220 VAL
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  442 VAL
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   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  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
Chi-restraints excluded: chain B residue  465 GLU
Chi-restraints excluded: chain B residue  504 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 10 optimal weight:    0.0020
   chunk 31 optimal weight:    0.8980
   chunk 23 optimal weight:    6.9990
   chunk 6 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   overall best weight:    0.7188

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.134288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.096496 restraints weight = 8307.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 1.71
r_work: 0.2857 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2735 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7686  Z= 0.182
  Angle     :  0.556   8.473  10456  Z= 0.279
  Chirality :  0.039   0.136   1224
  Planarity :  0.004   0.059   1290
  Dihedral  :  4.033  22.193   1038
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.12 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 13.94 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.27), residues: 962
  helix:  1.74 (0.20), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.59 (0.35), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 197 
 HIS   0.002   0.001   HIS A 521 
 PHE   0.014   0.001   PHE A  67 
 TYR   0.015   0.001   TYR B 335 
 ARG   0.004   0.000   ARG A 129 

*********************** 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
  127 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.986 
Fit side-chains
REVERT: A  157 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8351 (m)
REVERT: A  186 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7270 (mtp85)
REVERT: A  189 GLU cc_start: 0.6729 (pm20) cc_final: 0.6231 (OUTLIER)
REVERT: A  250 LYS cc_start: 0.7862 (ptmm) cc_final: 0.7379 (mttt)
REVERT: A  339 GLN cc_start: 0.8793 (mt0) cc_final: 0.8435 (mt0)
REVERT: A  353 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7002 (mm-30)
REVERT: A  372 PHE cc_start: 0.8031 (m-10) cc_final: 0.6922 (t80)
REVERT: A  482 LYS cc_start: 0.8235 (mppt) cc_final: 0.7704 (mmtp)
REVERT: B   86 TYR cc_start: 0.8308 (m-80) cc_final: 0.8012 (m-80)
REVERT: B   97 ASP cc_start: 0.8634 (m-30) cc_final: 0.8261 (m-30)
REVERT: B  129 ARG cc_start: 0.7187 (ttm110) cc_final: 0.6876 (ttm110)
REVERT: B  222 PHE cc_start: 0.7088 (OUTLIER) cc_final: 0.6088 (t80)
REVERT: B  242 CYS cc_start: 0.8657 (m) cc_final: 0.8013 (t)
REVERT: B  244 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7933 (tp40)
REVERT: B  250 LYS cc_start: 0.7896 (mtpt) cc_final: 0.7423 (mttt)
REVERT: B  459 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8258 (mt)
REVERT: B  482 LYS cc_start: 0.8229 (mppt) cc_final: 0.7695 (mmtp)
  outliers start: 25
  outliers final: 18
  residues processed: 118
  average time/residue: 0.9938
  time to fit residues: 126.3858
Evaluate side-chains
  118 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
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  442 VAL
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  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
Chi-restraints excluded: chain B residue  465 GLU
Chi-restraints excluded: chain B residue  504 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 58 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 82 optimal weight:    7.9990
   chunk 85 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 83 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3480 r_free = 0.3480 target = 0.134691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.097296 restraints weight = 8428.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.2980 rms_B_bonded: 1.69
r_work: 0.2861 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7686  Z= 0.189
  Angle     :  0.554   8.293  10456  Z= 0.277
  Chirality :  0.039   0.138   1224
  Planarity :  0.004   0.060   1290
  Dihedral  :  3.978  21.665   1038
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.12 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 14.19 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.27), residues: 962
  helix:  1.80 (0.20), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.54 (0.35), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 197 
 HIS   0.002   0.001   HIS A 563 
 PHE   0.013   0.001   PHE A  67 
 TYR   0.014   0.001   TYR B 335 
 ARG   0.003   0.000   ARG A 129 

*********************** 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
  126 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 0.745 
Fit side-chains
REVERT: A  157 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8419 (m)
REVERT: A  186 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7330 (mtp85)
REVERT: A  189 GLU cc_start: 0.6743 (pm20) cc_final: 0.6260 (OUTLIER)
REVERT: A  250 LYS cc_start: 0.8033 (ptmm) cc_final: 0.7525 (mttt)
REVERT: A  339 GLN cc_start: 0.8799 (mt0) cc_final: 0.8429 (mt0)
REVERT: A  353 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7044 (mm-30)
REVERT: A  372 PHE cc_start: 0.8031 (m-10) cc_final: 0.6933 (t80)
REVERT: A  482 LYS cc_start: 0.8179 (mppt) cc_final: 0.7653 (mmtp)
REVERT: A  484 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7823 (ptp)
REVERT: B   86 TYR cc_start: 0.8336 (m-80) cc_final: 0.8096 (m-80)
REVERT: B   97 ASP cc_start: 0.8625 (m-30) cc_final: 0.8228 (m-30)
REVERT: B  129 ARG cc_start: 0.7204 (ttm110) cc_final: 0.6617 (ttm110)
REVERT: B  222 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.6085 (t80)
REVERT: B  242 CYS cc_start: 0.8552 (m) cc_final: 0.8010 (t)
REVERT: B  244 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8086 (tp40)
REVERT: B  250 LYS cc_start: 0.7885 (mtpt) cc_final: 0.7417 (mttt)
REVERT: B  459 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8196 (mt)
REVERT: B  482 LYS cc_start: 0.8248 (mppt) cc_final: 0.7722 (mmtp)
  outliers start: 24
  outliers final: 18
  residues processed: 117
  average time/residue: 0.9249
  time to fit residues: 116.2877
Evaluate side-chains
  120 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
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  442 VAL
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  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
Chi-restraints excluded: chain B residue  465 GLU
Chi-restraints excluded: chain B residue  504 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 82 optimal weight:    0.6980
   chunk 69 optimal weight:    0.4980
   chunk 76 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 80 optimal weight:    0.5980
   chunk 41 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3497 r_free = 0.3497 target = 0.135978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.099086 restraints weight = 8421.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 1.68
r_work: 0.2880 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2757 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7686  Z= 0.171
  Angle     :  0.547   8.169  10456  Z= 0.273
  Chirality :  0.038   0.138   1224
  Planarity :  0.004   0.059   1290
  Dihedral  :  3.935  21.483   1038
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.22 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 13.81 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.27), residues: 962
  helix:  1.85 (0.20), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.52 (0.35), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 197 
 HIS   0.002   0.000   HIS A 563 
 PHE   0.012   0.001   PHE A  67 
 TYR   0.015   0.001   TYR B 335 
 ARG   0.003   0.000   ARG A 129 

*********************** 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
  131 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 0.758 
Fit side-chains
REVERT: A  157 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8417 (m)
REVERT: A  186 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7330 (mtp85)
REVERT: A  189 GLU cc_start: 0.6732 (pm20) cc_final: 0.6254 (OUTLIER)
REVERT: A  250 LYS cc_start: 0.7991 (ptmm) cc_final: 0.7535 (mttt)
REVERT: A  339 GLN cc_start: 0.8769 (mt0) cc_final: 0.8386 (mt0)
REVERT: A  353 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7038 (mm-30)
REVERT: A  372 PHE cc_start: 0.7983 (m-10) cc_final: 0.6895 (t80)
REVERT: A  482 LYS cc_start: 0.8170 (mppt) cc_final: 0.7656 (mmtp)
REVERT: A  484 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7797 (ptp)
REVERT: B   86 TYR cc_start: 0.8340 (m-80) cc_final: 0.8083 (m-80)
REVERT: B   97 ASP cc_start: 0.8635 (m-30) cc_final: 0.8244 (m-30)
REVERT: B  104 ARG cc_start: 0.7683 (ttm110) cc_final: 0.7135 (mtp85)
REVERT: B  129 ARG cc_start: 0.7173 (ttm110) cc_final: 0.6485 (ttm110)
REVERT: B  222 PHE cc_start: 0.6949 (OUTLIER) cc_final: 0.5913 (t80)
REVERT: B  242 CYS cc_start: 0.8379 (m) cc_final: 0.7696 (t)
REVERT: B  250 LYS cc_start: 0.7876 (mtpt) cc_final: 0.7390 (mttt)
REVERT: B  338 MET cc_start: 0.8686 (mtm) cc_final: 0.8352 (mtp)
REVERT: B  459 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8190 (mt)
REVERT: B  482 LYS cc_start: 0.8243 (mppt) cc_final: 0.7717 (mmtp)
  outliers start: 27
  outliers final: 19
  residues processed: 121
  average time/residue: 0.9395
  time to fit residues: 122.1304
Evaluate side-chains
  124 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
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  442 VAL
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  220 VAL
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  443 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 67 optimal weight:    0.0040
   chunk 79 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 91 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 11 optimal weight:    8.9990
   chunk 87 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3491 r_free = 0.3491 target = 0.135625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.098470 restraints weight = 8355.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 1.68
r_work: 0.2881 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2760 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7686  Z= 0.176
  Angle     :  0.549   8.507  10456  Z= 0.272
  Chirality :  0.039   0.139   1224
  Planarity :  0.004   0.059   1290
  Dihedral  :  3.906  21.442   1038
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.12 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 14.45 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.28), residues: 962
  helix:  1.87 (0.20), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.47 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 197 
 HIS   0.002   0.001   HIS A 563 
 PHE   0.012   0.001   PHE A  67 
 TYR   0.014   0.001   TYR B 335 
 ARG   0.003   0.000   ARG A 129 

********************** 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
  128 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.804 
Fit side-chains
REVERT: A  157 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8422 (m)
REVERT: A  186 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7899 (mtt180)
REVERT: A  189 GLU cc_start: 0.6742 (pm20) cc_final: 0.6262 (OUTLIER)
REVERT: A  250 LYS cc_start: 0.7975 (ptmm) cc_final: 0.7524 (mttt)
REVERT: A  339 GLN cc_start: 0.8757 (mt0) cc_final: 0.8374 (mt0)
REVERT: A  353 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7033 (mm-30)
REVERT: A  372 PHE cc_start: 0.7962 (m-10) cc_final: 0.6844 (t80)
REVERT: A  482 LYS cc_start: 0.8169 (mppt) cc_final: 0.7649 (mmtp)
REVERT: A  484 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7794 (ptp)
REVERT: B   55 THR cc_start: 0.8272 (p) cc_final: 0.8023 (p)
REVERT: B   86 TYR cc_start: 0.8341 (m-80) cc_final: 0.7860 (m-80)
REVERT: B   97 ASP cc_start: 0.8615 (m-30) cc_final: 0.8239 (m-30)
REVERT: B  104 ARG cc_start: 0.7694 (ttm110) cc_final: 0.7141 (mtp85)
REVERT: B  129 ARG cc_start: 0.7126 (ttm110) cc_final: 0.6443 (ttm110)
REVERT: B  222 PHE cc_start: 0.6932 (OUTLIER) cc_final: 0.5898 (t80)
REVERT: B  242 CYS cc_start: 0.8569 (m) cc_final: 0.7943 (t)
REVERT: B  250 LYS cc_start: 0.7890 (mtpt) cc_final: 0.7382 (mttt)
REVERT: B  459 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8185 (mt)
REVERT: B  482 LYS cc_start: 0.8240 (mppt) cc_final: 0.7720 (mmtp)
  outliers start: 23
  outliers final: 19
  residues processed: 119
  average time/residue: 0.9057
  time to fit residues: 115.9975
Evaluate side-chains
  125 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
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  442 VAL
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  220 VAL
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  443 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 82 optimal weight:    0.5980
   chunk 50 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0570
   chunk 57 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9980
   chunk 58 optimal weight:    7.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    0.7302

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

Flipped N/Q/H residues before XYZ refinement:
A 174 ASN
** 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 = 0.3493 r_free = 0.3493 target = 0.135746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.098586 restraints weight = 8346.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 1.69
r_work: 0.2899 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2778 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.2583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7686  Z= 0.177
  Angle     :  0.547   8.369  10456  Z= 0.271
  Chirality :  0.039   0.139   1224
  Planarity :  0.004   0.059   1290
  Dihedral  :  3.886  21.376   1038
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.33 %
    Favored  : 96.47 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.28), residues: 962
  helix:  1.89 (0.20), residues: 684
  sheet:  None (None), residues: 0
  loop : -1.43 (0.36), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 197 
 HIS   0.002   0.001   HIS A 563 
 PHE   0.012   0.001   PHE A  67 
 TYR   0.015   0.001   TYR B 113 
 ARG   0.003   0.000   ARG A 129 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5393.99 seconds
wall clock time: 92 minutes 37.92 seconds (5557.92 seconds total)