Starting phenix.real_space_refine
on Fri Dec  8 00:07:22 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3n_23658/12_2023/7m3n_23658.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3n_23658/12_2023/7m3n_23658.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3n_23658/12_2023/7m3n_23658.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3n_23658/12_2023/7m3n_23658.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3n_23658/12_2023/7m3n_23658.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3n_23658/12_2023/7m3n_23658.pdb"
  }
  resolution = 2.4
  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
-------------------------------------------------------------------------------
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=   0.005 sd=   0.047
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      23      5.16       5
     C    3813      2.51       5
     N    1024      2.21       5
     O    1144      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "L ASP    1": "OD1" <-> "OD2"
    Residue "L ASP   17": "OD1" <-> "OD2"
    Residue "L ASP   28": "OD1" <-> "OD2"
    Residue "L ARG   61": "NH1" <-> "NH2"
    Residue "L ASP   70": "OD1" <-> "OD2"
    Residue "L GLU   81": "OE1" <-> "OE2"
    Residue "L TYR   86": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H ASP   33": "OD1" <-> "OD2"
    Residue "H GLU   46": "OE1" <-> "OE2"
    Residue "H PHE   52": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR   60": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H PHE   64": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H GLU   88": "OE1" <-> "OE2"
    Residue "H ASP   89": "OD1" <-> "OD2"
    Residue "H ARG   98": "NH1" <-> "NH2"
    Residue "A GLU   50": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A GLU  135": "OE1" <-> "OE2"
    Residue "A GLU  155": "OE1" <-> "OE2"
    Residue "A ASP  178": "OD1" <-> "OD2"
    Residue "A GLU  193": "OE1" <-> "OE2"
    Residue "A TYR  210": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  259": "OD1" <-> "OD2"
    Residue "A GLU  260": "OE1" <-> "OE2"
    Residue "A PHE  353": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  361": "NH1" <-> "NH2"
    Residue "A ASP  373": "OD1" <-> "OD2"
    Residue "A GLU  396": "OE1" <-> "OE2"
    Residue "A ASP  405": "OD1" <-> "OD2"
    Residue "A TYR  444": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  473": "OE1" <-> "OE2"
    Residue "A ASP  475": "OD1" <-> "OD2"
    Residue "A GLU  509": "OE1" <-> "OE2"
    Residue "A ASP  511": "OD1" <-> "OD2"
    Residue "A ASP  526": "OD1" <-> "OD2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 6004
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "L"
      Number of atoms: 842
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 842
          Classifications: {'peptide': 108}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 924
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 924
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "A"
      Number of atoms: 4238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 532, 4238
          Classifications: {'peptide': 532}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 492}
          Chain breaks: 2
  Time building chain proxies: 3.78, per 1000 atoms: 0.63
  Number of scatterers: 6004
  At special positions: 0
  Unit cell: (82.5, 113.3, 105.6, 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      23     16.00
     O    1144      8.00
     N    1024      7.00
     C    3813      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 490 " - pdb=" SG  CYS A 494 " distance=2.04

  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: 2.00
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1400

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 17 sheets defined
      9.6% alpha, 36.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.611A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 91
    Processing helix  chain 'A' and resid 95 through 99
    Processing helix  chain 'A' and resid 116 through 120
      removed outlier: 3.533A  pdb=" N   VAL A 119 " --> pdb=" O   ALA A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 132
    Processing helix  chain 'A' and resid 187 through 191
      removed outlier: 3.979A  pdb=" N   MET A 190 " --> pdb=" O   PRO A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 241
      removed outlier: 3.853A  pdb=" N   VAL A 241 " --> pdb=" O   PRO A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 285
      removed outlier: 4.037A  pdb=" N   LEU A 285 " --> pdb=" O   ASN A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 313
      removed outlier: 4.099A  pdb=" N   ARG A 313 " --> pdb=" O   GLN A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 385
      removed outlier: 4.192A  pdb=" N   GLY A 385 " --> pdb=" O   ARG A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 413
      removed outlier: 3.556A  pdb=" N   ASP A 413 " --> pdb=" O   PRO A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 448
      removed outlier: 3.722A  pdb=" N   PHE A 448 " --> pdb=" O   THR A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 561
      removed outlier: 3.692A  pdb=" N   ASN A 560 " --> pdb=" O   ASN A 557 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR A 561 " --> pdb=" O   GLN A 558 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 557 through 561'
    Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 6
      removed outlier: 5.687A  pdb=" N   THR L  69 " --> pdb=" O   ALA L  25 " (cutoff:3.500A)
      removed outlier: 10.148A  pdb=" N   GLN L  27 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
      removed outlier: 9.651A  pdb=" N   SER L  67 " --> pdb=" O   GLN L  27 " (cutoff:3.500A)
      removed outlier: 11.685A  pdb=" N   VAL L  29 " --> pdb=" O   SER L  65 " (cutoff:3.500A)
      removed outlier: 11.526A  pdb=" N   SER L  65 " --> pdb=" O   VAL L  29 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 11
      removed outlier: 6.443A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 11
      removed outlier: 3.979A  pdb=" N   THR L  97 " --> pdb=" O   GLN L  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA5, first strand: chain 'H' and resid 57 through 60
      removed outlier: 6.655A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   TRP H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   MET H  34 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 57 through 60
      removed outlier: 6.655A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   TRP H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   MET H  34 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 49 through 53
      removed outlier: 6.761A  pdb=" N   TYR A 524 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   VAL A 149 " --> pdb=" O   TYR A 524 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   ASP A 526 " --> pdb=" O   ASN A 147 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   ASN A 147 " --> pdb=" O   ASP A 526 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   TRP A 528 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   ILE A 145 " --> pdb=" O   TRP A 528 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   LYS A 530 " --> pdb=" O   GLN A 143 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   GLN A 143 " --> pdb=" O   LYS A 530 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   LYS A 532 " --> pdb=" O   PHE A 141 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   PHE A 141 " --> pdb=" O   LYS A 532 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   VAL A 534 " --> pdb=" O   VAL A 139 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   LYS A 538 " --> pdb=" O   GLU A 135 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   GLU A 135 " --> pdb=" O   LYS A 538 " (cutoff:3.500A)
      removed outlier: 5.105A  pdb=" N   GLN A 143 " --> pdb=" O   GLY A 264 " (cutoff:3.500A)
      removed outlier: 5.332A  pdb=" N   GLY A 264 " --> pdb=" O   GLN A 143 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   ILE A 145 " --> pdb=" O   ALA A 262 " (cutoff:3.500A)
      removed outlier: 5.393A  pdb=" N   ALA A 262 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 164 through 167
    Processing sheet with id=AA9, first strand: chain 'A' and resid 80 through 84
      removed outlier: 4.235A  pdb=" N   ALA A 103 " --> pdb=" O   PHE A 212 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   TRP A 208 " --> pdb=" O   THR A 107 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   TRP A 109 " --> pdb=" O   THR A 206 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   THR A 206 " --> pdb=" O   TRP A 109 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 80 through 84
      removed outlier: 5.963A  pdb=" N   VAL A 502 " --> pdb=" O   PRO A 108 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLN A 497 " --> pdb=" O   ASP A 178 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 215 through 218
      removed outlier: 6.336A  pdb=" N   ASP A 215 " --> pdb=" O   HIS A 234 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 276 through 278
    Processing sheet with id=AB4, first strand: chain 'A' and resid 335 through 336
      removed outlier: 6.357A  pdb=" N   GLU A 335 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'A' and resid 345 through 348
    Processing sheet with id=AB6, first strand: chain 'A' and resid 377 through 380
    Processing sheet with id=AB7, first strand: chain 'A' and resid 415 through 416
    Processing sheet with id=AB8, first strand: chain 'A' and resid 470 through 472
      removed outlier: 6.555A  pdb=" N   ASP A 471 " --> pdb=" O   CYS A 490 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8

    167 hydrogen bonds defined for protein.
    387 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.85

  Time building geometry restraints manager: 2.21 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1949
        1.34 -     1.46: 1564
        1.46 -     1.58: 2622
        1.58 -     1.70: 0
        1.70 -     1.82: 38
  Bond restraints: 6173
  Sorted by residual:
  bond pdb=" CA  ILE A 219 "
       pdb=" CB  ILE A 219 "
    ideal  model  delta    sigma   weight residual
    1.537  1.522  0.015 1.29e-02 6.01e+03 1.36e+00
  bond pdb=" CG1 ILE A 101 "
       pdb=" CD1 ILE A 101 "
    ideal  model  delta    sigma   weight residual
    1.513  1.472  0.041 3.90e-02 6.57e+02 1.09e+00
  bond pdb=" CA  ASP A 269 "
       pdb=" C   ASP A 269 "
    ideal  model  delta    sigma   weight residual
    1.530  1.519  0.011 1.08e-02 8.57e+03 1.04e+00
  bond pdb=" CB  THR A 230 "
       pdb=" CG2 THR A 230 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.49e-01
  bond pdb=" CB  GLN A 143 "
       pdb=" CG  GLN A 143 "
    ideal  model  delta    sigma   weight residual
    1.520  1.493  0.027 3.00e-02 1.11e+03 7.83e-01
  ... (remaining 6168 not shown)

  Histogram of bond angle deviations from ideal:
       99.68 -   106.56: 222
      106.56 -   113.43: 3265
      113.43 -   120.31: 2160
      120.31 -   127.18: 2674
      127.18 -   134.06: 99
  Bond angle restraints: 8420
  Sorted by residual:
  angle pdb=" C   GLY H  54 "
        pdb=" N   ASP H  55 "
        pdb=" CA  ASP H  55 "
      ideal   model   delta    sigma   weight residual
     121.54  127.42   -5.88 1.91e+00 2.74e-01 9.48e+00
  angle pdb=" N   ALA L  32 "
        pdb=" CA  ALA L  32 "
        pdb=" C   ALA L  32 "
      ideal   model   delta    sigma   weight residual
     111.30  114.69   -3.39 1.36e+00 5.41e-01 6.21e+00
  angle pdb=" N   PRO A 423 "
        pdb=" CA  PRO A 423 "
        pdb=" C   PRO A 423 "
      ideal   model   delta    sigma   weight residual
     112.47  107.54    4.93 2.06e+00 2.36e-01 5.73e+00
  angle pdb=" C   LYS H  74 "
        pdb=" N   SER H  75 "
        pdb=" CA  SER H  75 "
      ideal   model   delta    sigma   weight residual
     121.54  125.91   -4.37 1.91e+00 2.74e-01 5.23e+00
  angle pdb=" CA  ASN H  83 "
        pdb=" C   ASN H  83 "
        pdb=" N   ARG H  84 "
      ideal   model   delta    sigma   weight residual
     114.17  117.47   -3.30 1.45e+00 4.76e-01 5.18e+00
  ... (remaining 8415 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.94: 3131
       16.94 -    33.88: 353
       33.88 -    50.82: 86
       50.82 -    67.76: 30
       67.76 -    84.70: 6
  Dihedral angle restraints: 3606
    sinusoidal: 1417
      harmonic: 2189
  Sorted by residual:
  dihedral pdb=" CB  CYS A 490 "
           pdb=" SG  CYS A 490 "
           pdb=" SG  CYS A 494 "
           pdb=" CB  CYS A 494 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.65   55.35     1      1.00e+01 1.00e-02 4.14e+01
  dihedral pdb=" CA  THR L  31 "
           pdb=" C   THR L  31 "
           pdb=" N   ALA L  32 "
           pdb=" CA  ALA L  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.43   28.57     0      5.00e+00 4.00e-02 3.26e+01
  dihedral pdb=" CA  ASN A 421 "
           pdb=" C   ASN A 421 "
           pdb=" N   LEU A 422 "
           pdb=" CA  LEU A 422 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.12  -23.88     0      5.00e+00 4.00e-02 2.28e+01
  ... (remaining 3603 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 483
       0.028 -    0.057: 256
       0.057 -    0.085: 99
       0.085 -    0.113: 52
       0.113 -    0.141: 17
  Chirality restraints: 907
  Sorted by residual:
  chirality pdb=" CA  ILE L  39 "
            pdb=" N   ILE L  39 "
            pdb=" C   ILE L  39 "
            pdb=" CB  ILE L  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.98e-01
  chirality pdb=" CA  ILE A 357 "
            pdb=" N   ILE A 357 "
            pdb=" C   ILE A 357 "
            pdb=" CB  ILE A 357 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.35e-01
  chirality pdb=" CA  ILE A 306 "
            pdb=" N   ILE A 306 "
            pdb=" C   ILE A 306 "
            pdb=" CB  ILE A 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.31e-01
  ... (remaining 904 not shown)

  Planarity restraints: 1096
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 122 "    0.040 5.00e-02 4.00e+02   6.05e-02 5.85e+00
        pdb=" N   PRO A 123 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 123 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 123 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 464 "   -0.040 5.00e-02 4.00e+02   6.01e-02 5.78e+00
        pdb=" N   PRO A 465 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A 465 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 465 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP H  55 "    0.009 2.00e-02 2.50e+03   1.71e-02 2.91e+00
        pdb=" C   ASP H  55 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ASP H  55 "    0.011 2.00e-02 2.50e+03
        pdb=" N   GLY H  56 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1093 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 259
        2.71 -     3.26: 5360
        3.26 -     3.81: 9281
        3.81 -     4.35: 11759
        4.35 -     4.90: 20009
  Nonbonded interactions: 46668
  Sorted by model distance:
  nonbonded pdb=" OG  SER L  43 "
            pdb=" O   GLY H 110 "
     model   vdw
     2.168 2.440
  nonbonded pdb=" NH2 ARG A 382 "
            pdb=" O   GLY A 392 "
     model   vdw
     2.220 2.520
  nonbonded pdb=" OG  SER A  65 "
            pdb=" O   VAL A 119 "
     model   vdw
     2.287 2.440
  nonbonded pdb=" O   THR A 301 "
            pdb=" OG1 THR A 301 "
     model   vdw
     2.324 2.440
  nonbonded pdb=" ND2 ASN A 443 "
            pdb=" OG1 THR A 445 "
     model   vdw
     2.346 2.520
  ... (remaining 46663 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.840
  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:          19.370
  Check model and map are aligned:         0.100
  Set scattering table:                    0.060
  Process input model:                     20.310
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   57.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
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      :  0.005   0.044   6173  Z= 0.303
  Angle     :  0.630   8.042   8420  Z= 0.358
  Chirality :  0.044   0.141    907
  Planarity :  0.005   0.060   1096
  Dihedral  : 15.949  84.702   2197
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.27 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 22.48 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.53 (0.26), residues: 749
  helix: -2.08 (1.08), residues: 10
  sheet: -1.02 (0.30), residues: 248
  loop : -2.14 (0.22), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP H  50 
   HIS   0.007   0.001   HIS L  91 
   PHE   0.015   0.002   PHE A 535 
   TYR   0.019   0.002   TYR A 342 
   ARG   0.012   0.001   ARG H  84 

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 654 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 155
  time to evaluate  : 0.708 
Fit side-chains
  outliers start: 28
  outliers final: 13
  residues processed: 175
  average time/residue: 0.9801
  time to fit residues: 181.2581
Evaluate side-chains
  162 residues out of total 654 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 149
  time to evaluate  : 0.686 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 9
  residues processed: 4
  average time/residue: 0.5654
  time to fit residues: 3.4854
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 56 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0770
   chunk 22 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.8940

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

Flipped N/Q/H residues before XYZ refinement:
L  37 GLN
L  42 GLN
L  53 ASN
L  89 GLN
H  39 GLN
H  43 GLN
H  81 GLN
A  72 ASN
A  93 ASN
A 104 GLN
A 137 HIS
A 143 GLN
A 222 HIS
A 242 GLN
A 280 GLN
A 296 GLN
A 302 ASN
A 309 GLN
A 384 HIS
A 404 GLN
A 417 ASN
A 428 ASN
A 443 ASN
A 446 ASN
A 458 ASN
A 459 ASN
A 468 GLN
A 560 ASN

Total number of N/Q/H flips: 28

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.1211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6173  Z= 0.179
  Angle     :  0.519   8.066   8420  Z= 0.268
  Chirality :  0.043   0.146    907
  Planarity :  0.004   0.065   1096
  Dihedral  :  4.780  26.457    821
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.74 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 24.46 %
    Favored  : 70.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -1.71 (0.27), residues: 749
  helix: -2.03 (0.87), residues: 16
  sheet: -0.37 (0.31), residues: 243
  loop : -1.59 (0.24), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.001   TRP H  50 
   HIS   0.004   0.001   HIS L  91 
   PHE   0.008   0.001   PHE A 535 
   TYR   0.010   0.001   TYR A 342 
   ARG   0.004   0.000   ARG H  84 

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 654 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 155
  time to evaluate  : 0.742 
Fit side-chains
  outliers start: 32
  outliers final: 17
  residues processed: 173
  average time/residue: 0.9489
  time to fit residues: 173.3564
Evaluate side-chains
  166 residues out of total 654 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 149
  time to evaluate  : 0.599 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 11
  residues processed: 7
  average time/residue: 0.5198
  time to fit residues: 4.7818
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 37 optimal weight:    0.1980
   chunk 20 optimal weight:    0.0170
   chunk 55 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 18 optimal weight:    7.9990
   chunk 67 optimal weight:    7.9990
   chunk 72 optimal weight:    0.0030
   chunk 59 optimal weight:    5.9990
   chunk 66 optimal weight:    0.6980
   chunk 22 optimal weight:    6.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.3628

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

Flipped N/Q/H residues before XYZ refinement:
L  89 GLN
A 137 HIS
A 404 GLN
A 459 ASN
A 466 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6173  Z= 0.124
  Angle     :  0.475   6.975   8420  Z= 0.243
  Chirality :  0.042   0.146    907
  Planarity :  0.004   0.067   1096
  Dihedral  :  4.298  22.591    821
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 25.84 %
    Favored  : 69.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -1.22 (0.28), residues: 749
  helix: -1.45 (1.00), residues: 16
  sheet: -0.15 (0.32), residues: 255
  loop : -1.19 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP H  50 
   HIS   0.003   0.001   HIS L  91 
   PHE   0.010   0.001   PHE L  73 
   TYR   0.008   0.001   TYR H  60 
   ARG   0.002   0.000   ARG H  84 

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 654 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 153
  time to evaluate  : 0.698 
Fit side-chains
  outliers start: 31
  outliers final: 13
  residues processed: 173
  average time/residue: 0.9495
  time to fit residues: 173.6396
Evaluate side-chains
  161 residues out of total 654 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 148
  time to evaluate  : 0.683 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 10
  residues processed: 3
  average time/residue: 0.5847
  time to fit residues: 2.8217
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 66 optimal weight:    0.0270
   chunk 50 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 67 optimal weight:    9.9990
   chunk 71 optimal weight:    0.1980
   chunk 35 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.8444

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

Flipped N/Q/H residues before XYZ refinement:
L   8 HIS
L  89 GLN
A 137 HIS
A 404 GLN
A 459 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6173  Z= 0.169
  Angle     :  0.494   6.961   8420  Z= 0.253
  Chirality :  0.043   0.160    907
  Planarity :  0.004   0.068   1096
  Dihedral  :  4.352  22.653    821
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 26.15 %
    Favored  : 70.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.28), residues: 749
  helix: -1.42 (0.97), residues: 16
  sheet:  0.02 (0.32), residues: 255
  loop : -1.07 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP A 126 
   HIS   0.004   0.001   HIS L  91 
   PHE   0.014   0.001   PHE L  73 
   TYR   0.012   0.001   TYR A 342 
   ARG   0.001   0.000   ARG H  84 

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 654 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 152
  time to evaluate  : 0.673 
Fit side-chains
  outliers start: 25
  outliers final: 17
  residues processed: 168
  average time/residue: 1.0333
  time to fit residues: 183.5522
Evaluate side-chains
  165 residues out of total 654 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 0.709 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 12
  residues processed: 5
  average time/residue: 0.7540
  time to fit residues: 4.9515
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 53 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    2.9990
   chunk 64 optimal weight:    6.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
L  89 GLN
A 137 HIS
A 167 ASN
A 404 GLN
A 459 ASN
A 483 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.1668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.082   6173  Z= 0.541
  Angle     :  0.631   7.897   8420  Z= 0.326
  Chirality :  0.049   0.178    907
  Planarity :  0.005   0.075   1096
  Dihedral  :  5.269  29.485    821
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.81 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 25.54 %
    Favored  : 69.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.28), residues: 749
  helix: -1.45 (0.96), residues: 16
  sheet:  0.13 (0.33), residues: 243
  loop : -1.22 (0.25), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.002   TRP A 470 
   HIS   0.011   0.002   HIS L  91 
   PHE   0.019   0.002   PHE A 398 
   TYR   0.029   0.002   TYR A 342 
   ARG   0.005   0.001   ARG A 581 

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 654 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 147
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
  outliers start: 33
  outliers final: 26
  residues processed: 164
  average time/residue: 1.0294
  time to fit residues: 178.0389
Evaluate side-chains
  171 residues out of total 654 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 145
  time to evaluate  : 0.658 
Switching outliers to nearest non-outliers
  outliers start: 26
  outliers final: 15
  residues processed: 11
  average time/residue: 0.1704
  time to fit residues: 3.3344
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 14 optimal weight:    8.9990
   chunk 41 optimal weight:    0.6980
   chunk 17 optimal weight:    7.9990
   chunk 71 optimal weight:    0.4980
   chunk 59 optimal weight:    0.1980
   chunk 33 optimal weight:    6.9990
   chunk 5 optimal weight:    0.3980
   chunk 23 optimal weight:    5.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
L  89 GLN
H  81 GLN
A 137 HIS
A 404 GLN
A 459 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6173  Z= 0.134
  Angle     :  0.484   6.521   8420  Z= 0.247
  Chirality :  0.042   0.149    907
  Planarity :  0.004   0.067   1096
  Dihedral  :  4.425  22.900    821
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 25.54 %
    Favored  : 70.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.29), residues: 749
  helix: -1.49 (0.93), residues: 16
  sheet:  0.19 (0.32), residues: 255
  loop : -0.95 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP H  50 
   HIS   0.003   0.001   HIS L  91 
   PHE   0.006   0.001   PHE L  73 
   TYR   0.010   0.001   TYR H  60 
   ARG   0.002   0.000   ARG H  98 

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 654 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 152
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
  outliers start: 27
  outliers final: 20
  residues processed: 168
  average time/residue: 1.0605
  time to fit residues: 187.7141
Evaluate side-chains
  159 residues out of total 654 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.688 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 15
  residues processed: 5
  average time/residue: 0.7893
  time to fit residues: 5.1238
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 52 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0570
   chunk 44 optimal weight:    6.9990
   chunk 43 optimal weight:    0.4980
   chunk 32 optimal weight:    0.0470
   chunk 28 optimal weight:    7.9990
   overall best weight:    1.1200

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

Flipped N/Q/H residues before XYZ refinement:
L  89 GLN
A 137 HIS
A 404 GLN
A 459 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6173  Z= 0.207
  Angle     :  0.508   6.903   8420  Z= 0.260
  Chirality :  0.043   0.177    907
  Planarity :  0.004   0.065   1096
  Dihedral  :  4.478  23.801    821
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.41 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 26.15 %
    Favored  : 70.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -0.71 (0.29), residues: 749
  helix: -1.20 (1.01), residues: 16
  sheet:  0.41 (0.33), residues: 239
  loop : -0.94 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP H  50 
   HIS   0.005   0.001   HIS L  91 
   PHE   0.011   0.001   PHE A 535 
   TYR   0.015   0.001   TYR A 342 
   ARG   0.002   0.000   ARG A 581 

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 654 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
  outliers start: 24
  outliers final: 20
  residues processed: 157
  average time/residue: 1.1285
  time to fit residues: 186.2320
Evaluate side-chains
  154 residues out of total 654 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 0.686 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 17
  residues processed: 3
  average time/residue: 0.0729
  time to fit residues: 1.2886
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 48 optimal weight:    6.9990
   chunk 35 optimal weight:    0.8980
   chunk 6 optimal weight:    9.9990
   chunk 56 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
L  89 GLN
A 137 HIS
A 404 GLN
A 459 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6173  Z= 0.230
  Angle     :  0.517   6.785   8420  Z= 0.265
  Chirality :  0.043   0.153    907
  Planarity :  0.004   0.066   1096
  Dihedral  :  4.580  24.762    821
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.27 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 26.15 %
    Favored  : 69.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -0.66 (0.29), residues: 749
  helix: -1.12 (1.05), residues: 16
  sheet:  0.44 (0.33), residues: 239
  loop : -0.89 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP H  50 
   HIS   0.005   0.001   HIS L  91 
   PHE   0.011   0.001   PHE A 535 
   TYR   0.016   0.001   TYR A 342 
   ARG   0.002   0.000   ARG A 581 

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 654 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 141
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
  outliers start: 26
  outliers final: 21
  residues processed: 161
  average time/residue: 1.0611
  time to fit residues: 179.8882
Evaluate side-chains
  160 residues out of total 654 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 139
  time to evaluate  : 0.636 
Switching outliers to nearest non-outliers
  outliers start: 21
  outliers final: 17
  residues processed: 4
  average time/residue: 0.8588
  time to fit residues: 4.4848
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 28 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0370
   chunk 20 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0070
   chunk 70 optimal weight:    0.0060
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.3092

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

Flipped N/Q/H residues before XYZ refinement:
L  89 GLN
A 137 HIS
A 404 GLN
A 459 ASN
A 468 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6173  Z= 0.119
  Angle     :  0.476   6.028   8420  Z= 0.242
  Chirality :  0.042   0.145    907
  Planarity :  0.004   0.063   1096
  Dihedral  :  4.155  21.032    821
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 27.22 %
    Favored  : 69.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 (0.29), residues: 749
  helix: -0.89 (1.10), residues: 16
  sheet:  0.37 (0.33), residues: 257
  loop : -0.72 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP H  47 
   HIS   0.003   0.000   HIS L  91 
   PHE   0.008   0.001   PHE A 266 
   TYR   0.010   0.001   TYR H  60 
   ARG   0.001   0.000   ARG A 520 

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 654 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.685 
Fit side-chains
  outliers start: 21
  outliers final: 16
  residues processed: 161
  average time/residue: 1.0717
  time to fit residues: 181.3685
Evaluate side-chains
  153 residues out of total 654 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 137
  time to evaluate  : 0.704 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 14
  residues processed: 2
  average time/residue: 0.0550
  time to fit residues: 1.1134
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 33 optimal weight:    8.9990
   chunk 48 optimal weight:    3.9990
   chunk 73 optimal weight:    0.6980
   chunk 67 optimal weight:    7.9990
   chunk 58 optimal weight:    7.9990
   chunk 6 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9990
   chunk 35 optimal weight:    6.9990
   chunk 46 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 17 optimal weight:    9.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
L  89 GLN
A 137 HIS
A 404 GLN
A 459 ASN
A 468 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   6173  Z= 0.344
  Angle     :  0.582   6.692   8420  Z= 0.298
  Chirality :  0.046   0.182    907
  Planarity :  0.004   0.068   1096
  Dihedral  :  4.794  26.246    821
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.27 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 28.90 %
    Favored  : 68.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -0.57 (0.29), residues: 749
  helix: -1.18 (1.04), residues: 16
  sheet:  0.49 (0.33), residues: 239
  loop : -0.82 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP H  50 
   HIS   0.007   0.001   HIS L  91 
   PHE   0.019   0.002   PHE L  73 
   TYR   0.022   0.002   TYR A 342 
   ARG   0.003   0.001   ARG A 581 

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 654 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 144
  time to evaluate  : 0.748 
Fit side-chains
  outliers start: 17
  outliers final: 16
  residues processed: 159
  average time/residue: 0.9986
  time to fit residues: 167.2248
Evaluate side-chains
  155 residues out of total 654 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 0.733 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 14
  residues processed: 2
  average time/residue: 0.0903
  time to fit residues: 1.2811
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0370
   chunk 58 optimal weight:    0.2980
   chunk 24 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 42 optimal weight:    4.9990
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
L  89 GLN
A 137 HIS
A 302 ASN
A 404 GLN
A 459 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.126563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.113384 restraints weight = 7849.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 1.57
r_work: 0.3454 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6173  Z= 0.146
  Angle     :  0.496   6.024   8420  Z= 0.254
  Chirality :  0.043   0.147    907
  Planarity :  0.004   0.063   1096
  Dihedral  :  4.340  23.005    821
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 28.75 %
    Favored  : 68.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -0.46 (0.30), residues: 749
  helix: -0.85 (1.13), residues: 16
  sheet:  0.40 (0.32), residues: 255
  loop : -0.69 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP H  50 
   HIS   0.003   0.001   HIS L  91 
   PHE   0.013   0.001   PHE L  73 
   TYR   0.010   0.001   TYR A 573 
   ARG   0.001   0.000   ARG A 520 

===============================================================================
Job complete
usr+sys time: 3525.16 seconds
wall clock time: 62 minutes 52.78 seconds (3772.78 seconds total)