Starting phenix.real_space_refine
on Fri Dec  8 06:36:12 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx3_37899/12_2023/8wx3_37899.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx3_37899/12_2023/8wx3_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_37899/12_2023/8wx3_37899.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx3_37899/12_2023/8wx3_37899.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx3_37899/12_2023/8wx3_37899.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wx3_37899/12_2023/8wx3_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-1.21rc1-5172/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: 4.37, per 1000 atoms: 0.58
  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: 2.90
  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: 0.72
  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: 2.17

  Time building geometry restraints manager: 3.16 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:             0.390
  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:          2.310
  Check model and map are aligned:         0.100
  Set scattering table:                    0.070
  Process input model:                     23.420
  Find NCS groups from input model:        0.400
  Set up NCS constraints:                  0.040
  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:14.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.900
-------------------------------------------------------------------------------
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  : 0.830 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 1.0240
  time to fit residues: 192.8659
Evaluate side-chains
  120 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.802 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0841
-------------------------------------------------------------------------------
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:    0.5980
   chunk 72 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0010
   chunk 49 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   overall best weight:    1.0790

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

Flipped N/Q/H residues before XYZ refinement:
A 454 GLN
A 485 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.1579

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= 0.225
  Angle     :  0.594   7.930  10456  Z= 0.304
  Chirality :  0.040   0.211   1224
  Planarity :  0.005   0.070   1290
  Dihedral  :  3.978  20.374   1038
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.33 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 10.49 %
    Favored  : 86.70 %
  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:  0.94 (0.28), residues: 962
  helix:  1.47 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop : -1.61 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP A  69 
   HIS   0.003   0.001   HIS A 521 
   PHE   0.024   0.001   PHE B 372 
   TYR   0.018   0.002   TYR B 113 
   ARG   0.006   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
  142 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 0.820 
Fit side-chains
  outliers start: 22
  outliers final: 13
  residues processed: 130
  average time/residue: 0.8640
  time to fit residues: 121.2057
Evaluate side-chains
  127 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.736 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 6
  residues processed: 7
  average time/residue: 0.2757
  time to fit residues: 3.3313
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    6.9990
   chunk 72 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 70 optimal weight:    0.0060
   overall best weight:    0.9000

-------------------------------------------------------------------------------
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: 0.7043
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7686  Z= 0.197
  Angle     :  0.551   7.909  10456  Z= 0.279
  Chirality :  0.039   0.132   1224
  Planarity :  0.004   0.068   1290
  Dihedral  :  3.915  21.112   1038
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.33 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 11.64 %
    Favored  : 84.78 %
  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:  1.19 (0.28), residues: 962
  helix:  1.70 (0.20), residues: 684
  sheet:  None (None), residues: 0
  loop : -1.57 (0.36), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP A  69 
   HIS   0.003   0.001   HIS A 563 
   PHE   0.020   0.001   PHE A  67 
   TYR   0.020   0.001   TYR B 335 
   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
  142 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 114
  time to evaluate  : 0.826 
Fit side-chains
  outliers start: 28
  outliers final: 19
  residues processed: 132
  average time/residue: 0.8370
  time to fit residues: 119.6299
Evaluate side-chains
  120 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.801 
Switching outliers to nearest non-outliers
  outliers start: 19
  outliers final: 13
  residues processed: 6
  average time/residue: 0.2461
  time to fit residues: 2.9144
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 58 optimal weight:    8.9990
   chunk 87 optimal weight:    0.5980
   chunk 92 optimal weight:    7.9990
   chunk 83 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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: 0.7053
moved from start:          0.2211

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= 0.212
  Angle     :  0.561  10.448  10456  Z= 0.281
  Chirality :  0.039   0.135   1224
  Planarity :  0.004   0.066   1290
  Dihedral  :  3.923  21.504   1038
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.12 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 12.15 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.23 (0.28), residues: 962
  helix:  1.70 (0.20), residues: 686
  sheet:  None (None), residues: 0
  loop : -1.52 (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   0.017   0.001   PHE A  67 
   TYR   0.016   0.001   TYR B 335 
   ARG   0.004   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
  139 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 110
  time to evaluate  : 0.798 
Fit side-chains
  outliers start: 29
  outliers final: 18
  residues processed: 128
  average time/residue: 0.8378
  time to fit residues: 116.1450
Evaluate side-chains
  118 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.809 
Switching outliers to nearest non-outliers
  outliers start: 18
  outliers final: 13
  residues processed: 5
  average time/residue: 0.0691
  time to fit residues: 1.7756
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
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: 0.7076
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7686  Z= 0.282
  Angle     :  0.598   9.010  10456  Z= 0.301
  Chirality :  0.041   0.137   1224
  Planarity :  0.005   0.064   1290
  Dihedral  :  4.077  22.542   1038
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.53 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 12.92 %
    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:  1.10 (0.27), residues: 962
  helix:  1.59 (0.20), residues: 690
  sheet:  None (None), residues: 0
  loop : -1.55 (0.35), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP A 517 
   HIS   0.004   0.001   HIS A 563 
   PHE   0.015   0.002   PHE A  67 
   TYR   0.016   0.002   TYR B 335 
   ARG   0.002   0.000   ARG B 102 

*********************** 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
  132 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 102
  time to evaluate  : 0.839 
Fit side-chains
  outliers start: 30
  outliers final: 23
  residues processed: 122
  average time/residue: 0.8767
  time to fit residues: 115.7825
Evaluate side-chains
  116 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.823 
Switching outliers to nearest non-outliers
  outliers start: 23
  outliers final: 16
  residues processed: 7
  average time/residue: 0.4232
  time to fit residues: 4.5407
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 18 optimal weight:    8.9990
   chunk 54 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0060
   chunk 92 optimal weight:    4.9990
   chunk 77 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0060
   chunk 7 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 48 optimal weight:   10.0000
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.5412

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7038
moved from start:          0.2470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7686  Z= 0.162
  Angle     :  0.542   8.633  10456  Z= 0.272
  Chirality :  0.038   0.135   1224
  Planarity :  0.004   0.061   1290
  Dihedral  :  3.917  21.474   1038
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.70 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 15.35 %
    Favored  : 81.71 %
  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:  1.32 (0.28), residues: 962
  helix:  1.80 (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 B 197 
   HIS   0.001   0.000   HIS A 521 
   PHE   0.012   0.001   PHE A  67 
   TYR   0.016   0.001   TYR B 335 
   ARG   0.005   0.000   ARG B 104 

*********************** 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
  131 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.671 
Fit side-chains
  outliers start: 23
  outliers final: 16
  residues processed: 126
  average time/residue: 0.8392
  time to fit residues: 114.4965
Evaluate side-chains
  113 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.814 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 15
  residues processed: 1
  average time/residue: 1.7214
  time to fit residues: 2.8923
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 52 optimal weight:   10.0000
   chunk 67 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 92 optimal weight:    0.1980
   chunk 57 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 42 optimal weight:    6.9990
   chunk 36 optimal weight:    0.1980
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.2784

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7060
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7686  Z= 0.228
  Angle     :  0.570   8.397  10456  Z= 0.287
  Chirality :  0.040   0.140   1224
  Planarity :  0.004   0.060   1290
  Dihedral  :  3.960  22.217   1038
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.22 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 15.22 %
    Favored  : 81.46 %
  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 (0.28), residues: 962
  helix:  1.75 (0.20), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.53 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP A 197 
   HIS   0.003   0.001   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 104 

*********************** 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
  123 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 97
  time to evaluate  : 0.818 
Fit side-chains
  outliers start: 26
  outliers final: 22
  residues processed: 115
  average time/residue: 0.9675
  time to fit residues: 119.3779
Evaluate side-chains
  114 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.785 
Switching outliers to nearest non-outliers
  outliers start: 22
  outliers final: 16
  residues processed: 6
  average time/residue: 0.6290
  time to fit residues: 5.2605
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 18 optimal weight:    8.9990
   chunk 17 optimal weight:    2.9990
   chunk 58 optimal weight:    9.9990
   chunk 63 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 72 optimal weight:    0.0980
   chunk 84 optimal weight:    5.9990
   chunk 88 optimal weight:    4.9990
   chunk 80 optimal weight:    0.7980
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7686  Z= 0.233
  Angle     :  0.575   8.190  10456  Z= 0.290
  Chirality :  0.040   0.140   1224
  Planarity :  0.004   0.060   1290
  Dihedral  :  3.999  22.041   1038
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.22 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 16.37 %
    Favored  : 80.95 %
  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:  1.26 (0.28), residues: 962
  helix:  1.72 (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   0.006   0.001   TRP A 197 
   HIS   0.003   0.001   HIS A 563 
   PHE   0.014   0.001   PHE B 222 
   TYR   0.014   0.001   TYR B 335 
   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
  113 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.801 
Fit side-chains
  outliers start: 21
  outliers final: 18
  residues processed: 111
  average time/residue: 0.9831
  time to fit residues: 117.0175
Evaluate side-chains
  107 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.833 
Switching outliers to nearest non-outliers
  outliers start: 18
  outliers final: 17
  residues processed: 1
  average time/residue: 1.6884
  time to fit residues: 2.8634
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0070
   chunk 67 optimal weight:    0.0470
   chunk 26 optimal weight:    0.9980
   chunk 77 optimal weight:    0.5980
   chunk 81 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 91 optimal weight:    0.3980
   overall best weight:    0.4096

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7018
moved from start:          0.2622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   7686  Z= 0.157
  Angle     :  0.537   8.072  10456  Z= 0.267
  Chirality :  0.038   0.140   1224
  Planarity :  0.004   0.059   1290
  Dihedral  :  3.844  21.039   1038
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.91 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 16.62 %
    Favored  : 80.82 %
  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:  1.48 (0.28), residues: 962
  helix:  1.92 (0.20), residues: 686
  sheet:  None (None), residues: 0
  loop : -1.50 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP A 197 
   HIS   0.001   0.000   HIS A 521 
   PHE   0.009   0.001   PHE A  67 
   TYR   0.015   0.001   TYR B 335 
   ARG   0.002   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
  129 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.891 
Fit side-chains
  outliers start: 20
  outliers final: 17
  residues processed: 126
  average time/residue: 0.9125
  time to fit residues: 123.9089
Evaluate side-chains
  115 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.832 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 17
  residues processed: 0
  time to fit residues: 1.1309
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9980
   chunk 76 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   chunk 60 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 457 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7686  Z= 0.219
  Angle     :  0.574   8.711  10456  Z= 0.285
  Chirality :  0.039   0.144   1224
  Planarity :  0.004   0.060   1290
  Dihedral  :  3.896  21.445   1038
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.22 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.26 %
    Favored  : 80.18 %
  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:  1.45 (0.28), residues: 962
  helix:  1.89 (0.20), residues: 684
  sheet:  None (None), residues: 0
  loop : -1.44 (0.36), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP A 197 
   HIS   0.003   0.001   HIS A 563 
   PHE   0.011   0.001   PHE B 492 
   TYR   0.014   0.001   TYR B 335 
   ARG   0.005   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
  120 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.813 
Fit side-chains
  outliers start: 20
  outliers final: 17
  residues processed: 117
  average time/residue: 0.9643
  time to fit residues: 121.5060
Evaluate side-chains
  111 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.756 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 16
  residues processed: 1
  average time/residue: 1.7395
  time to fit residues: 2.8705
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 70 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 21 optimal weight:   10.0000
   chunk 76 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0870
   chunk 66 optimal weight:    1.9990
   chunk 4 optimal weight:    8.9990
   overall best weight:    0.6958

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.136041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.098984 restraints weight = 8263.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 1.68
r_work: 0.2896 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2775 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7686  Z= 0.175
  Angle     :  0.557   8.480  10456  Z= 0.276
  Chirality :  0.039   0.140   1224
  Planarity :  0.004   0.058   1290
  Dihedral  :  3.872  21.321   1038
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.12 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.65 %
    Favored  : 80.18 %
  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:  1.45 (0.28), residues: 962
  helix:  1.87 (0.20), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.46 (0.36), residues: 274

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   0.014   0.001   PHE B 222 
   TYR   0.015   0.001   TYR B 335 
   ARG   0.004   0.000   ARG B 129 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2781.90 seconds
wall clock time: 50 minutes 13.42 seconds (3013.42 seconds total)