Starting phenix.real_space_refine
on Mon Mar 11 06:59:09 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx3_37899/03_2024/8wx3_37899.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx3_37899/03_2024/8wx3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx3_37899/03_2024/8wx3_37899.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx3_37899/03_2024/8wx3_37899.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx3_37899/03_2024/8wx3_37899.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx3_37899/03_2024/8wx3_37899.pdb"
  }
  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
    Residue "A TYR   52": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  158": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  181": "OD1" <-> "OD2"
    Residue "A ASP  185": "OD1" <-> "OD2"
    Residue "A PHE  194": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  215": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  385": "OD1" <-> "OD2"
    Residue "A TYR  444": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  448": "OD1" <-> "OD2"
    Residue "B TYR   52": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU   70": "OE1" <-> "OE2"
    Residue "B TYR   86": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  194": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  215": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  226": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  535": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  557": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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  - 3.50
        Amino acid           : False - 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: 3.01
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  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: 0.58
  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: 2.02

  Time building geometry restraints manager: 3.28 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:
       99.13 -   106.12: 173
      106.12 -   113.10: 4155
      113.10 -   120.08: 2881
      120.08 -   127.06: 3156
      127.06 -   134.05: 91
  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 2.440
  nonbonded pdb=" NH2 ARG B  33 "
            pdb=" OD1 ASP B 185 "
     model   vdw
     2.263 2.520
  nonbonded pdb=" OE1 GLN B 345 "
            pdb=" NE2 GLN B 454 "
     model   vdw
     2.307 2.520
  nonbonded pdb=" O   LEU B 122 "
            pdb=" OG1 THR B 128 "
     model   vdw
     2.313 2.440
  nonbonded pdb=" OD2 ASP A 259 "
            pdb=" NZ  LYS A 311 "
     model   vdw
     2.327 2.520
  ... (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
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:             0.330
  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:          2.210
  Check model and map are aligned:         0.110
  Set scattering table:                    0.070
  Process input model:                     23.280
  Find NCS groups from input model:        0.410
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.420
-------------------------------------------------------------------------------
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 fitting.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.710 
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: 1.0137
  time to fit residues: 191.0844
Evaluate side-chains
  127 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 72 optimal weight:    3.9990
   chunk 40 optimal weight:    0.2980
   chunk 24 optimal weight:    0.0670
   chunk 49 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.5518

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
moved from start:          0.1342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7686  Z= 0.182
  Angle     :  0.574   8.071  10456  Z= 0.291
  Chirality :  0.039   0.192   1224
  Planarity :  0.005   0.070   1290
  Dihedral  :  3.902  20.087   1038
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.43 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  :  8.95 %
    Favored  : 88.75 %
  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:  1.03 (0.28), residues: 962
  helix:  1.54 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop : -1.59 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   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   0.003   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
  144 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.879 
Fit side-chains
REVERT: A  104 ARG cc_start: 0.6591 (mtp85) cc_final: 0.6298 (mtp85)
REVERT: A  129 ARG cc_start: 0.6545 (ttm110) cc_final: 0.6252 (ttm110)
REVERT: A  189 GLU cc_start: 0.6208 (pm20) cc_final: 0.5779 (tm-30)
REVERT: A  250 LYS cc_start: 0.7850 (ptmm) cc_final: 0.7177 (mttt)
REVERT: A  339 GLN cc_start: 0.7579 (mt0) cc_final: 0.7318 (mt0)
REVERT: A  353 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6629 (mm-30)
REVERT: A  482 LYS cc_start: 0.8010 (mppt) cc_final: 0.7246 (mmtp)
REVERT: A  484 MET cc_start: 0.6626 (mtm) cc_final: 0.6155 (mtp)
REVERT: B  129 ARG cc_start: 0.6534 (ttm110) cc_final: 0.6306 (ttm110)
REVERT: B  242 CYS cc_start: 0.8000 (m) cc_final: 0.7191 (t)
REVERT: B  250 LYS cc_start: 0.7831 (mtpt) cc_final: 0.7339 (mttt)
REVERT: B  377 ILE cc_start: 0.7436 (mm) cc_final: 0.7185 (mt)
REVERT: B  386 LYS cc_start: 0.7175 (mmtt) cc_final: 0.6846 (mmtp)
REVERT: B  482 LYS cc_start: 0.7835 (mppt) cc_final: 0.7305 (mmtp)
  outliers start: 18
  outliers final: 9
  residues processed: 135
  average time/residue: 0.8822
  time to fit residues: 128.5005
Evaluate side-chains
  128 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  244 GLN
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  511 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 48 optimal weight:   10.0000
   chunk 27 optimal weight:    1.9990
   chunk 72 optimal weight:    5.9990
   chunk 59 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 94 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 70 optimal weight:    0.7980
   overall best weight:    1.1586

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7053
moved from start:          0.1849

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= 0.223
  Angle     :  0.571   8.456  10456  Z= 0.291
  Chirality :  0.039   0.134   1224
  Planarity :  0.005   0.068   1290
  Dihedral  :  3.944  21.624   1038
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.64 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 10.10 %
    Favored  : 86.45 %
  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:  1.16 (0.28), residues: 962
  helix:  1.65 (0.20), residues: 686
  sheet:  None (None), residues: 0
  loop : -1.53 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  69 
 HIS   0.004   0.001   HIS A 563 
 PHE   0.020   0.001   PHE A  67 
 TYR   0.027   0.002   TYR A 113 
 ARG   0.005   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
  147 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 120
  time to evaluate  : 0.896 
Fit side-chains
REVERT: A   44 GLU cc_start: 0.6920 (tp30) cc_final: 0.6691 (tp30)
REVERT: A  112 LEU cc_start: 0.7477 (mt) cc_final: 0.7230 (mp)
REVERT: A  129 ARG cc_start: 0.6484 (ttm110) cc_final: 0.6026 (ttm110)
REVERT: A  157 THR cc_start: 0.7711 (OUTLIER) cc_final: 0.7503 (m)
REVERT: A  189 GLU cc_start: 0.6109 (pm20) cc_final: 0.5656 (tm-30)
REVERT: A  250 LYS cc_start: 0.7904 (ptmm) cc_final: 0.7257 (mttt)
REVERT: A  339 GLN cc_start: 0.7539 (mt0) cc_final: 0.7291 (mt0)
REVERT: A  353 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6618 (mm-30)
REVERT: A  482 LYS cc_start: 0.7876 (mppt) cc_final: 0.7314 (mmtp)
REVERT: A  484 MET cc_start: 0.6838 (mtm) cc_final: 0.6565 (mtp)
REVERT: B   82 MET cc_start: 0.7566 (mmt) cc_final: 0.7201 (mmp)
REVERT: B   84 LEU cc_start: 0.7821 (mt) cc_final: 0.7594 (tp)
REVERT: B   86 TYR cc_start: 0.7220 (m-80) cc_final: 0.6767 (m-80)
REVERT: B   97 ASP cc_start: 0.7910 (m-30) cc_final: 0.7371 (m-30)
REVERT: B  242 CYS cc_start: 0.7993 (m) cc_final: 0.7229 (t)
REVERT: B  250 LYS cc_start: 0.7862 (mtpt) cc_final: 0.7335 (mttt)
REVERT: B  386 LYS cc_start: 0.7181 (mmtt) cc_final: 0.6860 (mmtp)
REVERT: B  459 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7142 (mt)
REVERT: B  482 LYS cc_start: 0.7840 (mppt) cc_final: 0.7274 (mmtp)
REVERT: B  558 ASP cc_start: 0.6933 (m-30) cc_final: 0.6667 (m-30)
  outliers start: 27
  outliers final: 14
  residues processed: 137
  average time/residue: 0.9087
  time to fit residues: 134.0069
Evaluate side-chains
  127 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
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  443 VAL
Chi-restraints excluded: chain A residue  511 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  224 THR
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  511 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 87 optimal weight:    0.9980
   chunk 92 optimal weight:    6.9990
   chunk 83 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 77 optimal weight:    0.6980
   overall best weight:    1.0582

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7054
moved from start:          0.2081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7686  Z= 0.208
  Angle     :  0.545   7.875  10456  Z= 0.277
  Chirality :  0.039   0.137   1224
  Planarity :  0.004   0.066   1290
  Dihedral  :  3.932  21.748   1038
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.22 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 11.38 %
    Favored  : 85.68 %
  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:  1.24 (0.27), residues: 962
  helix:  1.72 (0.20), residues: 686
  sheet:  None (None), residues: 0
  loop : -1.53 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 197 
 HIS   0.003   0.001   HIS A 563 
 PHE   0.019   0.001   PHE A  67 
 TYR   0.015   0.001   TYR B 335 
 ARG   0.006   0.000   ARG B 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
  140 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 0.820 
Fit side-chains
REVERT: A   44 GLU cc_start: 0.6866 (tp30) cc_final: 0.6635 (tp30)
REVERT: A  104 ARG cc_start: 0.6322 (mtp85) cc_final: 0.6029 (mtp85)
REVERT: A  129 ARG cc_start: 0.6342 (ttm110) cc_final: 0.5992 (ttm110)
REVERT: A  186 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.6771 (mtp85)
REVERT: A  189 GLU cc_start: 0.6105 (pm20) cc_final: 0.5637 (tm-30)
REVERT: A  250 LYS cc_start: 0.7766 (ptmm) cc_final: 0.7219 (mttt)
REVERT: A  339 GLN cc_start: 0.7512 (mt0) cc_final: 0.7243 (mt0)
REVERT: A  353 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6765 (mm-30)
REVERT: A  482 LYS cc_start: 0.7880 (mppt) cc_final: 0.7266 (mmtp)
REVERT: A  484 MET cc_start: 0.6859 (mtm) cc_final: 0.6630 (mtp)
REVERT: B   82 MET cc_start: 0.7661 (mmt) cc_final: 0.7155 (mmp)
REVERT: B   84 LEU cc_start: 0.7779 (mt) cc_final: 0.7564 (tp)
REVERT: B   86 TYR cc_start: 0.7359 (m-80) cc_final: 0.6875 (m-80)
REVERT: B   97 ASP cc_start: 0.7877 (m-30) cc_final: 0.7355 (m-30)
REVERT: B  129 ARG cc_start: 0.6562 (ttm110) cc_final: 0.6321 (ttm110)
REVERT: B  242 CYS cc_start: 0.7951 (m) cc_final: 0.7241 (t)
REVERT: B  250 LYS cc_start: 0.7890 (mtpt) cc_final: 0.7350 (mttt)
REVERT: B  338 MET cc_start: 0.7222 (mtp) cc_final: 0.7015 (ttp)
REVERT: B  386 LYS cc_start: 0.7157 (mmtt) cc_final: 0.6836 (mmtp)
REVERT: B  459 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.6994 (mt)
REVERT: B  482 LYS cc_start: 0.7835 (mppt) cc_final: 0.7267 (mmtp)
REVERT: B  558 ASP cc_start: 0.6982 (m-30) cc_final: 0.6720 (m-30)
  outliers start: 23
  outliers final: 15
  residues processed: 133
  average time/residue: 0.8879
  time to fit residues: 127.1644
Evaluate side-chains
  123 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  193 ARG
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  511 SER
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  193 ARG
Chi-restraints excluded: chain B residue  224 THR
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  511 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 52 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 79 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 47 optimal weight:    4.9990
   chunk 83 optimal weight:    0.6980
   chunk 23 optimal weight:    0.4980
   chunk 31 optimal weight:    0.7980
   overall best weight:    1.1582

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7686  Z= 0.215
  Angle     :  0.550   7.084  10456  Z= 0.279
  Chirality :  0.039   0.135   1224
  Planarity :  0.004   0.064   1290
  Dihedral  :  3.942  22.175   1038
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.43 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 11.64 %
    Favored  : 84.65 %
  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:  1.28 (0.27), residues: 962
  helix:  1.71 (0.20), residues: 692
  sheet:  None (None), residues: 0
  loop : -1.48 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 197 
 HIS   0.003   0.001   HIS A 563 
 PHE   0.017   0.001   PHE A  67 
 TYR   0.016   0.001   TYR B 335 
 ARG   0.005   0.000   ARG B 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
  137 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 108
  time to evaluate  : 0.821 
Fit side-chains
REVERT: A  104 ARG cc_start: 0.6430 (mtp85) cc_final: 0.6108 (mtp85)
REVERT: A  157 THR cc_start: 0.7675 (OUTLIER) cc_final: 0.7367 (t)
REVERT: A  185 ASP cc_start: 0.7359 (p0) cc_final: 0.7154 (p0)
REVERT: A  186 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.6760 (mtp85)
REVERT: A  189 GLU cc_start: 0.6105 (pm20) cc_final: 0.5639 (tm-30)
REVERT: A  250 LYS cc_start: 0.7757 (ptmm) cc_final: 0.7213 (mttt)
REVERT: A  339 GLN cc_start: 0.7517 (mt0) cc_final: 0.7216 (mt0)
REVERT: A  353 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6765 (mm-30)
REVERT: A  482 LYS cc_start: 0.7886 (mppt) cc_final: 0.7251 (mmtp)
REVERT: B   82 MET cc_start: 0.7679 (mmt) cc_final: 0.7172 (mmp)
REVERT: B   84 LEU cc_start: 0.7770 (mt) cc_final: 0.7558 (tp)
REVERT: B   86 TYR cc_start: 0.7400 (m-80) cc_final: 0.6833 (m-80)
REVERT: B   97 ASP cc_start: 0.7851 (m-30) cc_final: 0.7377 (m-30)
REVERT: B  222 PHE cc_start: 0.5574 (OUTLIER) cc_final: 0.4811 (t80)
REVERT: B  242 CYS cc_start: 0.7951 (m) cc_final: 0.7236 (t)
REVERT: B  250 LYS cc_start: 0.7948 (mtpt) cc_final: 0.7379 (mttt)
REVERT: B  338 MET cc_start: 0.7491 (mtp) cc_final: 0.7068 (ttm)
REVERT: B  386 LYS cc_start: 0.7142 (mmtt) cc_final: 0.6924 (mmtm)
REVERT: B  459 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7110 (mt)
REVERT: B  482 LYS cc_start: 0.7836 (mppt) cc_final: 0.7263 (mmtp)
REVERT: B  558 ASP cc_start: 0.6978 (m-30) cc_final: 0.6710 (m-30)
  outliers start: 29
  outliers final: 19
  residues processed: 125
  average time/residue: 1.0358
  time to fit residues: 138.7192
Evaluate side-chains
  130 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  193 ARG
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  511 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  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
Chi-restraints excluded: chain B residue  511 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 83 optimal weight:    0.9990
   chunk 18 optimal weight:    8.9990
   chunk 54 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 92 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9980
   chunk 43 optimal weight:    0.3980
   chunk 7 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0970
   chunk 48 optimal weight:   10.0000
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
B 244 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7035
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      :  0.002   0.039   7686  Z= 0.167
  Angle     :  0.524   7.669  10456  Z= 0.264
  Chirality :  0.038   0.136   1224
  Planarity :  0.004   0.062   1290
  Dihedral  :  3.850  21.411   1038
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.70 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 13.30 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.93 (0.20), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.58 (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 563 
 PHE   0.015   0.001   PHE A  67 
 TYR   0.016   0.001   TYR B 335 
 ARG   0.006   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
  141 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 114
  time to evaluate  : 0.797 
Fit side-chains
REVERT: A  104 ARG cc_start: 0.6330 (mtp85) cc_final: 0.6078 (mtp85)
REVERT: A  157 THR cc_start: 0.7695 (OUTLIER) cc_final: 0.7403 (t)
REVERT: A  185 ASP cc_start: 0.7407 (p0) cc_final: 0.7201 (p0)
REVERT: A  186 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.6795 (mtp85)
REVERT: A  189 GLU cc_start: 0.5955 (pm20) cc_final: 0.5480 (tm-30)
REVERT: A  250 LYS cc_start: 0.7810 (ptmm) cc_final: 0.7233 (mttt)
REVERT: A  339 GLN cc_start: 0.7396 (mt0) cc_final: 0.7101 (mt0)
REVERT: A  353 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6724 (mm-30)
REVERT: A  372 PHE cc_start: 0.7230 (m-10) cc_final: 0.5898 (t80)
REVERT: A  378 LEU cc_start: 0.8447 (mt) cc_final: 0.8095 (mt)
REVERT: A  409 MET cc_start: 0.8106 (mtt) cc_final: 0.7811 (mtm)
REVERT: A  482 LYS cc_start: 0.7835 (mppt) cc_final: 0.7196 (mmtp)
REVERT: B   82 MET cc_start: 0.7620 (mmt) cc_final: 0.7150 (mmp)
REVERT: B   84 LEU cc_start: 0.7738 (mt) cc_final: 0.7528 (tp)
REVERT: B   86 TYR cc_start: 0.7416 (m-80) cc_final: 0.6937 (m-80)
REVERT: B   97 ASP cc_start: 0.7887 (m-30) cc_final: 0.7408 (m-30)
REVERT: B  222 PHE cc_start: 0.5758 (OUTLIER) cc_final: 0.5066 (t80)
REVERT: B  242 CYS cc_start: 0.7953 (m) cc_final: 0.7218 (t)
REVERT: B  250 LYS cc_start: 0.8002 (mtpt) cc_final: 0.7501 (mttt)
REVERT: B  338 MET cc_start: 0.7325 (mtp) cc_final: 0.6937 (ttm)
REVERT: B  459 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.6995 (mt)
REVERT: B  482 LYS cc_start: 0.7831 (mppt) cc_final: 0.7257 (mmtp)
  outliers start: 27
  outliers final: 16
  residues processed: 132
  average time/residue: 0.8704
  time to fit residues: 124.0568
Evaluate side-chains
  127 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  193 ARG
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  511 SER
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  193 ARG
Chi-restraints excluded: chain B residue  222 PHE
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  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
Chi-restraints excluded: chain B residue  511 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 10 optimal weight:    0.0770
   chunk 52 optimal weight:   10.0000
   chunk 67 optimal weight:    0.6980
   chunk 78 optimal weight:    0.0980
   chunk 51 optimal weight:    4.9990
   chunk 92 optimal weight:    8.9990
   chunk 57 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 42 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.5742

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7686  Z= 0.163
  Angle     :  0.521   7.592  10456  Z= 0.262
  Chirality :  0.038   0.138   1224
  Planarity :  0.004   0.062   1290
  Dihedral  :  3.793  21.581   1038
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.22 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 13.30 %
    Favored  : 82.99 %
  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:  1.59 (0.28), residues: 962
  helix:  2.01 (0.20), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.52 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 197 
 HIS   0.002   0.000   HIS A 563 
 PHE   0.013   0.001   PHE A  67 
 TYR   0.015   0.001   TYR B 335 
 ARG   0.002   0.000   ARG B 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
  141 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 112
  time to evaluate  : 0.780 
Fit side-chains
REVERT: A  104 ARG cc_start: 0.6389 (mtp85) cc_final: 0.6078 (mtp85)
REVERT: A  157 THR cc_start: 0.7682 (OUTLIER) cc_final: 0.7400 (t)
REVERT: A  186 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.6819 (mtp85)
REVERT: A  189 GLU cc_start: 0.6059 (pm20) cc_final: 0.5603 (OUTLIER)
REVERT: A  250 LYS cc_start: 0.7844 (ptmm) cc_final: 0.7163 (mttt)
REVERT: A  339 GLN cc_start: 0.7437 (mt0) cc_final: 0.6985 (mt0)
REVERT: A  353 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6719 (mm-30)
REVERT: A  372 PHE cc_start: 0.7186 (m-10) cc_final: 0.5879 (t80)
REVERT: A  482 LYS cc_start: 0.7835 (mppt) cc_final: 0.7189 (mmtp)
REVERT: B   86 TYR cc_start: 0.7389 (m-80) cc_final: 0.6888 (m-80)
REVERT: B   97 ASP cc_start: 0.7964 (m-30) cc_final: 0.7484 (m-30)
REVERT: B  129 ARG cc_start: 0.6247 (ttm110) cc_final: 0.5971 (ttm110)
REVERT: B  222 PHE cc_start: 0.5722 (OUTLIER) cc_final: 0.4950 (t80)
REVERT: B  242 CYS cc_start: 0.7955 (m) cc_final: 0.7212 (t)
REVERT: B  250 LYS cc_start: 0.7949 (mtpt) cc_final: 0.7450 (mttt)
REVERT: B  409 MET cc_start: 0.8062 (mtt) cc_final: 0.7769 (mtm)
REVERT: B  459 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7046 (mt)
REVERT: B  482 LYS cc_start: 0.7794 (mppt) cc_final: 0.7165 (mmtp)
  outliers start: 29
  outliers final: 18
  residues processed: 128
  average time/residue: 0.8750
  time to fit residues: 120.7020
Evaluate side-chains
  126 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  193 ARG
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  511 SER
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  193 ARG
Chi-restraints excluded: chain B residue  222 PHE
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  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
Chi-restraints excluded: chain B residue  511 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 58 optimal weight:   10.0000
   chunk 63 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0020
   chunk 8 optimal weight:    0.8980
   chunk 72 optimal weight:    0.6980
   chunk 84 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   chunk 80 optimal weight:    0.8980
   overall best weight:    0.6588

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7028
moved from start:          0.2401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7686  Z= 0.173
  Angle     :  0.531   8.130  10456  Z= 0.265
  Chirality :  0.038   0.138   1224
  Planarity :  0.004   0.062   1290
  Dihedral  :  3.771  21.436   1038
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.01 %
    Favored  : 96.78 %
  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:  1.58 (0.28), residues: 962
  helix:  1.99 (0.20), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.48 (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 113 
 ARG   0.002   0.000   ARG B 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
  135 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.829 
Fit side-chains
REVERT: A  104 ARG cc_start: 0.6381 (mtp85) cc_final: 0.6072 (mtp85)
REVERT: A  157 THR cc_start: 0.7724 (OUTLIER) cc_final: 0.7455 (t)
REVERT: A  186 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.6782 (mtp85)
REVERT: A  189 GLU cc_start: 0.6061 (pm20) cc_final: 0.5605 (OUTLIER)
REVERT: A  250 LYS cc_start: 0.7844 (ptmm) cc_final: 0.7174 (mttt)
REVERT: A  339 GLN cc_start: 0.7547 (mt0) cc_final: 0.7197 (mt0)
REVERT: A  353 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6716 (mm-30)
REVERT: A  372 PHE cc_start: 0.7287 (m-10) cc_final: 0.6088 (t80)
REVERT: A  409 MET cc_start: 0.8167 (mtt) cc_final: 0.7898 (mtm)
REVERT: A  482 LYS cc_start: 0.7837 (mppt) cc_final: 0.7175 (mmtp)
REVERT: B   86 TYR cc_start: 0.7382 (m-80) cc_final: 0.6856 (m-80)
REVERT: B   97 ASP cc_start: 0.7965 (m-30) cc_final: 0.7486 (m-30)
REVERT: B  129 ARG cc_start: 0.6255 (ttm110) cc_final: 0.6007 (ttm110)
REVERT: B  222 PHE cc_start: 0.5931 (OUTLIER) cc_final: 0.5141 (t80)
REVERT: B  242 CYS cc_start: 0.7957 (m) cc_final: 0.7207 (t)
REVERT: B  250 LYS cc_start: 0.8041 (mtpt) cc_final: 0.7453 (mttt)
REVERT: B  459 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7042 (mt)
REVERT: B  482 LYS cc_start: 0.7804 (mppt) cc_final: 0.7139 (mmtp)
  outliers start: 24
  outliers final: 20
  residues processed: 124
  average time/residue: 0.9326
  time to fit residues: 124.5307
Evaluate side-chains
  128 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  193 ARG
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  484 MET
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  511 SER
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  193 ARG
Chi-restraints excluded: chain B residue  222 PHE
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  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
Chi-restraints excluded: chain B residue  511 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 37 optimal weight:    0.0270
   chunk 67 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 77 optimal weight:    0.0980
   chunk 81 optimal weight:    0.6980
   chunk 85 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.5238

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7016
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7686  Z= 0.160
  Angle     :  0.527   8.536  10456  Z= 0.261
  Chirality :  0.038   0.138   1224
  Planarity :  0.004   0.062   1290
  Dihedral  :  3.740  21.426   1038
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.22 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 14.71 %
    Favored  : 82.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.67 (0.28), residues: 962
  helix:  2.08 (0.20), residues: 684
  sheet:  None (None), residues: 0
  loop : -1.45 (0.36), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 197 
 HIS   0.001   0.000   HIS A 563 
 PHE   0.012   0.001   PHE A  67 
 TYR   0.015   0.001   TYR B 335 
 ARG   0.001   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
  132 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.751 
Fit side-chains
REVERT: A  157 THR cc_start: 0.7750 (OUTLIER) cc_final: 0.7453 (t)
REVERT: A  186 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.6823 (mtp85)
REVERT: A  189 GLU cc_start: 0.6059 (pm20) cc_final: 0.5601 (OUTLIER)
REVERT: A  250 LYS cc_start: 0.7789 (ptmm) cc_final: 0.7084 (mttt)
REVERT: A  339 GLN cc_start: 0.7516 (mt0) cc_final: 0.7116 (mt0)
REVERT: A  353 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6709 (mm-30)
REVERT: A  372 PHE cc_start: 0.7454 (m-10) cc_final: 0.6195 (t80)
REVERT: A  409 MET cc_start: 0.8159 (mtt) cc_final: 0.7893 (mtm)
REVERT: A  482 LYS cc_start: 0.7834 (mppt) cc_final: 0.7196 (mmtp)
REVERT: A  546 THR cc_start: 0.8081 (p) cc_final: 0.7580 (t)
REVERT: B   86 TYR cc_start: 0.7404 (m-80) cc_final: 0.6978 (m-80)
REVERT: B   97 ASP cc_start: 0.7947 (m-30) cc_final: 0.7454 (m-30)
REVERT: B  129 ARG cc_start: 0.6275 (ttm110) cc_final: 0.6028 (ttm110)
REVERT: B  222 PHE cc_start: 0.5855 (OUTLIER) cc_final: 0.5011 (t80)
REVERT: B  242 CYS cc_start: 0.7959 (m) cc_final: 0.7199 (t)
REVERT: B  250 LYS cc_start: 0.7989 (mtpt) cc_final: 0.7442 (mttt)
REVERT: B  338 MET cc_start: 0.7382 (mtm) cc_final: 0.6973 (mtp)
REVERT: B  409 MET cc_start: 0.8109 (mtt) cc_final: 0.7851 (mtm)
REVERT: B  459 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7038 (mt)
REVERT: B  482 LYS cc_start: 0.7800 (mppt) cc_final: 0.7133 (mmtp)
REVERT: B  558 ASP cc_start: 0.6921 (m-30) cc_final: 0.6652 (m-30)
  outliers start: 24
  outliers final: 18
  residues processed: 122
  average time/residue: 0.8758
  time to fit residues: 115.3257
Evaluate side-chains
  125 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
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  435 ILE
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  484 MET
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  511 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  193 ARG
Chi-restraints excluded: chain B residue  222 PHE
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  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
Chi-restraints excluded: chain B residue  511 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 43 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 88 optimal weight:    0.0970
   chunk 76 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0570
   chunk 46 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9990
   chunk 81 optimal weight:    0.5980
   overall best weight:    0.4696

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7010
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7686  Z= 0.156
  Angle     :  0.527   8.553  10456  Z= 0.260
  Chirality :  0.038   0.140   1224
  Planarity :  0.004   0.062   1290
  Dihedral  :  3.710  20.961   1038
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.01 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 14.45 %
    Favored  : 82.35 %
  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:  1.75 (0.28), residues: 962
  helix:  2.16 (0.20), residues: 682
  sheet:  None (None), residues: 0
  loop : -1.46 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 197 
 HIS   0.001   0.000   HIS A 563 
 PHE   0.011   0.001   PHE A  67 
 TYR   0.015   0.001   TYR B 335 
 ARG   0.002   0.000   ARG B 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
  135 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.822 
Fit side-chains
REVERT: A  157 THR cc_start: 0.7745 (OUTLIER) cc_final: 0.7523 (m)
REVERT: A  186 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6786 (mtp85)
REVERT: A  189 GLU cc_start: 0.6051 (pm20) cc_final: 0.5606 (OUTLIER)
REVERT: A  250 LYS cc_start: 0.7779 (ptmm) cc_final: 0.7084 (mttt)
REVERT: A  339 GLN cc_start: 0.7495 (mt0) cc_final: 0.7026 (mt0)
REVERT: A  353 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6700 (mm-30)
REVERT: A  372 PHE cc_start: 0.7436 (m-10) cc_final: 0.6174 (t80)
REVERT: A  409 MET cc_start: 0.8158 (mtt) cc_final: 0.7895 (mtm)
REVERT: A  482 LYS cc_start: 0.7822 (mppt) cc_final: 0.7185 (mmtp)
REVERT: A  546 THR cc_start: 0.8072 (p) cc_final: 0.7581 (t)
REVERT: B   86 TYR cc_start: 0.7388 (m-80) cc_final: 0.7051 (m-80)
REVERT: B   97 ASP cc_start: 0.7952 (m-30) cc_final: 0.7489 (m-30)
REVERT: B  129 ARG cc_start: 0.6279 (ttm110) cc_final: 0.6035 (ttm110)
REVERT: B  222 PHE cc_start: 0.5747 (OUTLIER) cc_final: 0.4881 (t80)
REVERT: B  242 CYS cc_start: 0.7962 (m) cc_final: 0.7193 (t)
REVERT: B  250 LYS cc_start: 0.7987 (mtpt) cc_final: 0.7442 (mttt)
REVERT: B  338 MET cc_start: 0.7331 (mtm) cc_final: 0.7013 (mtp)
REVERT: B  409 MET cc_start: 0.8108 (mtt) cc_final: 0.7837 (mtm)
REVERT: B  459 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7052 (mt)
REVERT: B  482 LYS cc_start: 0.7801 (mppt) cc_final: 0.7132 (mmtp)
REVERT: B  558 ASP cc_start: 0.6916 (m-30) cc_final: 0.6646 (m-30)
  outliers start: 25
  outliers final: 20
  residues processed: 125
  average time/residue: 0.8880
  time to fit residues: 119.8489
Evaluate side-chains
  128 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
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  333 THR
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  484 MET
Chi-restraints excluded: chain A residue  504 SER
Chi-restraints excluded: chain A residue  511 SER
Chi-restraints excluded: chain B residue   89 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  154 SER
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  193 ARG
Chi-restraints excluded: chain B residue  222 PHE
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  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
Chi-restraints excluded: chain B residue  511 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 23 optimal weight:    0.0670
   chunk 70 optimal weight:    0.0050
   chunk 11 optimal weight:    0.0970
   chunk 21 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0980
   chunk 9 optimal weight:    0.0980
   chunk 14 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0870
   overall best weight:    0.0708

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 395 HIS
** 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 = 0.3583 r_free = 0.3583 target = 0.143338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.107218 restraints weight = 8301.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 1.69
r_work: 0.3016 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7686  Z= 0.137
  Angle     :  0.517   8.326  10456  Z= 0.252
  Chirality :  0.037   0.141   1224
  Planarity :  0.004   0.063   1290
  Dihedral  :  3.611  19.890   1038
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.81 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.60 %
    Favored  : 82.35 %
  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:  1.89 (0.28), residues: 962
  helix:  2.28 (0.20), residues: 680
  sheet:  None (None), residues: 0
  loop : -1.43 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 197 
 HIS   0.001   0.000   HIS A 348 
 PHE   0.011   0.001   PHE A  67 
 TYR   0.016   0.001   TYR B 335 
 ARG   0.002   0.000   ARG B  48 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2854.09 seconds
wall clock time: 51 minutes 18.48 seconds (3078.48 seconds total)