Starting phenix.real_space_refine
on Sat Aug 23 15:21:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c1b_16377/08_2025/8c1b_16377.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c1b_16377/08_2025/8c1b_16377.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c1b_16377/08_2025/8c1b_16377.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c1b_16377/08_2025/8c1b_16377.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c1b_16377/08_2025/8c1b_16377.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c1b_16377/08_2025/8c1b_16377.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.057
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: 5
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    4105      2.51       5
     N    1119      2.21       5
     O    1318      1.98       5
     H    6106      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12675
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "H"
      Number of atoms: 4913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 319, 4913
          Classifications: {'peptide': 319}
          Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 296}
    Chain: "R"
      Number of atoms: 2646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 169, 2646
          Classifications: {'peptide': 169}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 162}
    Chain: "X"
      Number of atoms: 4913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 319, 4913
          Classifications: {'peptide': 319}
          Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 296}
    Chain: "A"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "B"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "R"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   GLY H 315 " occ=0.00
      ... (5 atoms not shown)
      pdb=" HA3 GLY H 315 " occ=0.00
    residue:
      pdb=" N   HIS H 316 " occ=0.00
      ... (15 atoms not shown)
      pdb=" HE2 HIS H 316 " occ=0.00
    residue:
      pdb=" N   GLY X 315 " occ=0.00
      ... (5 atoms not shown)
      pdb=" HA3 GLY X 315 " occ=0.00
    residue:
      pdb=" N   HIS X 316 " occ=0.00
      ... (15 atoms not shown)
      pdb=" HE2 HIS X 316 " occ=0.00
  Time building chain proxies: 2.46, per 1000 atoms: 0.19
  Number of scatterers: 12675
  At special positions: 0
  Unit cell: (96.3713, 122.278, 103.625, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      27     16.00
     O    1318      8.00
     N    1119      7.00
     C    4105      6.00
     H    6106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS H 237 " - pdb=" SG  CYS X 325 " distance=2.06
    Simple disulfide: pdb=" SG  CYS H 251 " - pdb=" SG  CYS H 309 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 325 " - pdb=" SG  CYS X 237 " distance=2.05
    Simple disulfide: pdb=" SG  CYS H 355 " - pdb=" SG  CYS H 415 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 461 " - pdb=" SG  CYS H 521 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  26 " - pdb=" SG  CYS R  68 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 107 " - pdb=" SG  CYS R 151 " distance=2.04
    Simple disulfide: pdb=" SG  CYS X 251 " - pdb=" SG  CYS X 309 " distance=2.04
    Simple disulfide: pdb=" SG  CYS X 355 " - pdb=" SG  CYS X 415 " distance=2.03
    Simple disulfide: pdb=" SG  CYS X 461 " - pdb=" SG  CYS X 521 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Atom "HETATM12645  O5  NAG R 501 .*.     O  " rejected from bonding due to valence issues.
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA A   3 " - " MAN A   4 "
      " BMA C   3 " - " MAN C   4 "
    ALPHA1-4
      " NAG B   2 " - " MAN B   3 "
    ALPHA1-6
      " BMA A   3 " - " MAN A   5 "
      " BMA C   3 " - " MAN C   5 "
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
      " NAG A   2 " - " BMA A   3 "
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
    NAG-ASN
      " NAG A   1 " - " ASN H 391 "
      " NAG B   1 " - " ASN R  42 "
      " NAG C   1 " - " ASN X 391 "
      " NAG R 501 " - " ASN R 166 "
      " NAG R 502 " - " ASN R  21 "
      " NAG R 503 " - " ASN R 135 "
  Time building additional restraints: 1.13
  Conformation dependent library (CDL) restraints added in 389.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1524

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 19 sheets defined
      9.9% alpha, 48.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'H' and resid 273 through 275
      No H-bonds generated for 'chain 'H' and resid 273 through 275'
    Processing helix  chain 'H' and resid 298 through 303
    Processing helix  chain 'H' and resid 341 through 347
    Processing helix  chain 'H' and resid 403 through 409
    Processing helix  chain 'H' and resid 483 through 485
      No H-bonds generated for 'chain 'H' and resid 483 through 485'
    Processing helix  chain 'H' and resid 509 through 516
    Processing helix  chain 'R' and resid 59 through 63
    Processing helix  chain 'R' and resid 111 through 113
      No H-bonds generated for 'chain 'R' and resid 111 through 113'
    Processing helix  chain 'R' and resid 142 through 146
      removed outlier: 3.698A  pdb=" N   SER R 146 " --> pdb=" O   VAL R 143 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 273 through 275
      No H-bonds generated for 'chain 'X' and resid 273 through 275'
    Processing helix  chain 'X' and resid 298 through 303
    Processing helix  chain 'X' and resid 341 through 347
    Processing helix  chain 'X' and resid 403 through 409
    Processing helix  chain 'X' and resid 483 through 485
      No H-bonds generated for 'chain 'X' and resid 483 through 485'
    Processing helix  chain 'X' and resid 510 through 516
    Processing sheet with id=AA1, first strand: chain 'H' and resid 277 through 284
      removed outlier: 6.381A  pdb=" N   ALA H 288 " --> pdb=" O   GLY H 255 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   GLY H 255 " --> pdb=" O   ALA H 288 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   GLN H 248 " --> pdb=" O   SER H 235 " (cutoff:3.500A)
      removed outlier: 5.854A  pdb=" N   ALA X 288 " --> pdb=" O   GLY X 255 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 270 through 271
    Processing sheet with id=AA3, first strand: chain 'H' and resid 334 through 337
      removed outlier: 4.712A  pdb=" N   ASP H 359 " --> pdb=" O   LEU H 394 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   LEU H 394 " --> pdb=" O   ASP H 359 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 368 through 373
    Processing sheet with id=AA5, first strand: chain 'H' and resid 441 through 446
      removed outlier: 5.532A  pdb=" N   PHE H 500 " --> pdb=" O   ASN H 465 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 441 through 446
      removed outlier: 5.532A  pdb=" N   PHE H 500 " --> pdb=" O   ASN H 465 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 480 through 481
    Processing sheet with id=AA8, first strand: chain 'R' and resid 6 through 10
    Processing sheet with id=AA9, first strand: chain 'R' and resid 15 through 17
      removed outlier: 6.568A  pdb=" N   ILE R  16 " --> pdb=" O   PHE R  84 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'R' and resid 44 through 46
      removed outlier: 4.480A  pdb=" N   TRP R  39 " --> pdb=" O   SER R  46 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 88 through 92
    Processing sheet with id=AB3, first strand: chain 'R' and resid 96 through 98
      removed outlier: 6.709A  pdb=" N   VAL R  97 " --> pdb=" O   ILE R 170 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   THR R 148 " --> pdb=" O   LYS R 122 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   LYS R 122 " --> pdb=" O   THR R 148 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   TYR R 150 " --> pdb=" O   TYR R 120 " (cutoff:3.500A)
      removed outlier: 4.935A  pdb=" N   TYR R 120 " --> pdb=" O   TYR R 150 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   THR R 152 " --> pdb=" O   VAL R 118 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   VAL R 118 " --> pdb=" O   THR R 152 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LYS R 128 " --> pdb=" O   TYR R 120 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   LYS R 122 " --> pdb=" O   ALA R 126 " (cutoff:3.500A)
      removed outlier: 5.679A  pdb=" N   ALA R 126 " --> pdb=" O   LYS R 122 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'R' and resid 96 through 98
      removed outlier: 6.709A  pdb=" N   VAL R  97 " --> pdb=" O   ILE R 170 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'X' and resid 270 through 271
    Processing sheet with id=AB6, first strand: chain 'X' and resid 334 through 337
      removed outlier: 3.774A  pdb=" N   ASP X 359 " --> pdb=" O   LEU X 394 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   LEU X 394 " --> pdb=" O   ASP X 359 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'X' and resid 368 through 373
    Processing sheet with id=AB8, first strand: chain 'X' and resid 441 through 446
      removed outlier: 5.418A  pdb=" N   PHE X 500 " --> pdb=" O   ASN X 465 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'X' and resid 441 through 446
      removed outlier: 5.418A  pdb=" N   PHE X 500 " --> pdb=" O   ASN X 465 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'X' and resid 480 through 481

    292 hydrogen bonds defined for protein.
    747 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: 2.98

  Time building geometry restraints manager: 1.55 seconds

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

  Histogram of bond lengths:
        0.83 -     1.04: 6106
        1.04 -     1.24: 798
        1.24 -     1.44: 2168
        1.44 -     1.64: 3731
        1.64 -     1.84: 34
  Bond restraints: 12837
  Sorted by residual:
  bond pdb=" N   ASP X 224 "
       pdb=" H1  ASP X 224 "
    ideal  model  delta    sigma   weight residual
    0.960  0.860  0.100 2.00e-02 2.50e+03 2.50e+01
  bond pdb=" N   ASP H 224 "
       pdb=" H1  ASP H 224 "
    ideal  model  delta    sigma   weight residual
    0.960  0.860  0.100 2.00e-02 2.50e+03 2.49e+01
  bond pdb=" C1  NAG R 501 "
       pdb=" O5  NAG R 501 "
    ideal  model  delta    sigma   weight residual
    1.406  1.483 -0.077 2.00e-02 2.50e+03 1.49e+01
  bond pdb=" CA  VAL R  22 "
       pdb=" CB  VAL R  22 "
    ideal  model  delta    sigma   weight residual
    1.540  1.590 -0.050 1.36e-02 5.41e+03 1.35e+01
  bond pdb=" C1  NAG R 502 "
       pdb=" O5  NAG R 502 "
    ideal  model  delta    sigma   weight residual
    1.406  1.456 -0.050 2.00e-02 2.50e+03 6.25e+00
  ... (remaining 12832 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 22002
        2.49 -     4.97: 891
        4.97 -     7.46: 139
        7.46 -     9.95: 15
        9.95 -    12.43: 4
  Bond angle restraints: 23051
  Sorted by residual:
  angle pdb=" C   ASN R 166 "
        pdb=" CA  ASN R 166 "
        pdb=" CB  ASN R 166 "
      ideal   model   delta    sigma   weight residual
     109.84  121.81  -11.97 1.63e+00 3.76e-01 5.39e+01
  angle pdb=" CA  GLN R 157 "
        pdb=" CB  GLN R 157 "
        pdb=" CG  GLN R 157 "
      ideal   model   delta    sigma   weight residual
     114.10  126.53  -12.43 2.00e+00 2.50e-01 3.87e+01
  angle pdb=" N   VAL R  22 "
        pdb=" CA  VAL R  22 "
        pdb=" CB  VAL R  22 "
      ideal   model   delta    sigma   weight residual
     111.23  119.92   -8.69 1.65e+00 3.67e-01 2.77e+01
  angle pdb=" C   GLU H 319 "
        pdb=" CA  GLU H 319 "
        pdb=" CB  GLU H 319 "
      ideal   model   delta    sigma   weight residual
     110.62  101.26    9.36 1.86e+00 2.89e-01 2.53e+01
  angle pdb=" C   GLY R  64 "
        pdb=" N   GLU R  65 "
        pdb=" CA  GLU R  65 "
      ideal   model   delta    sigma   weight residual
     120.82  127.56   -6.74 1.41e+00 5.03e-01 2.29e+01
  ... (remaining 23046 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.05: 5853
       22.05 -    44.10: 402
       44.10 -    66.15: 84
       66.15 -    88.20: 27
       88.20 -   110.26: 10
  Dihedral angle restraints: 6376
    sinusoidal: 3601
      harmonic: 2775
  Sorted by residual:
  dihedral pdb=" CB  CYS H 325 "
           pdb=" SG  CYS H 325 "
           pdb=" SG  CYS X 237 "
           pdb=" CB  CYS X 237 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -167.92   81.92     1      1.00e+01 1.00e-02 8.25e+01
  dihedral pdb=" CB  CYS H 237 "
           pdb=" SG  CYS H 237 "
           pdb=" SG  CYS X 325 "
           pdb=" CB  CYS X 325 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.28  -73.28     1      1.00e+01 1.00e-02 6.84e+01
  dihedral pdb=" C   ASN R 166 "
           pdb=" N   ASN R 166 "
           pdb=" CA  ASN R 166 "
           pdb=" CB  ASN R 166 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.35   16.75     0      2.50e+00 1.60e-01 4.49e+01
  ... (remaining 6373 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.115: 980
       0.115 -    0.229: 85
       0.229 -    0.344: 6
       0.344 -    0.458: 1
       0.458 -    0.572: 1
  Chirality restraints: 1073
  Sorted by residual:
  chirality pdb=" CA  ASN R 166 "
            pdb=" N   ASN R 166 "
            pdb=" C   ASN R 166 "
            pdb=" CB  ASN R 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.94    0.57 2.00e-01 2.50e+01 8.19e+00
  chirality pdb=" CG  LEU R  90 "
            pdb=" CB  LEU R  90 "
            pdb=" CD1 LEU R  90 "
            pdb=" CD2 LEU R  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.24   -0.34 2.00e-01 2.50e+01 2.97e+00
  chirality pdb=" CA  GLN R 157 "
            pdb=" N   GLN R 157 "
            pdb=" C   GLN R 157 "
            pdb=" CB  GLN R 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.56e+00
  ... (remaining 1070 not shown)

  Planarity restraints: 1911
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN R 166 "   -0.005 2.00e-02 2.50e+03   9.57e-02 1.15e+02
        pdb=" CG  ASN R 166 "   -0.119 2.00e-02 2.50e+03
        pdb=" OD1 ASN R 166 "    0.117 2.00e-02 2.50e+03
        pdb=" ND2 ASN R 166 "   -0.091 2.00e-02 2.50e+03
        pdb=" C1  NAG R 501 "    0.098 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN R 166 "    0.029 2.00e-02 2.50e+03   5.82e-02 3.39e+01
        pdb=" CG  ASN R 166 "   -0.101 2.00e-02 2.50e+03
        pdb=" OD1 ASN R 166 "    0.039 2.00e-02 2.50e+03
        pdb=" ND2 ASN R 166 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR X 257 "    0.084 5.00e-02 4.00e+02   1.24e-01 2.46e+01
        pdb=" N   PRO X 258 "   -0.214 5.00e-02 4.00e+02
        pdb=" CA  PRO X 258 "    0.064 5.00e-02 4.00e+02
        pdb=" CD  PRO X 258 "    0.067 5.00e-02 4.00e+02
  ... (remaining 1908 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 2448
        2.29 -     2.87: 26597
        2.87 -     3.45: 30408
        3.45 -     4.02: 43005
        4.02 -     4.60: 63202
  Nonbonded interactions: 165660
  Sorted by model distance:
  nonbonded pdb=" HE2 HIS H 477 "
            pdb=" O   LYS H 516 "
     model   vdw
     1.713 2.450
  nonbonded pdb="HE22 GLN H 234 "
            pdb=" O   SER X 235 "
     model   vdw
     1.733 2.450
  nonbonded pdb=" O   GLY R 124 "
            pdb="HH22 ARG X 390 "
     model   vdw
     1.737 2.450
  nonbonded pdb=" HE2 HIS X 477 "
            pdb=" O   LYS X 516 "
     model   vdw
     1.746 2.450
  nonbonded pdb=" HE  ARG X 522 "
            pdb=" OE1 GLN X 535 "
     model   vdw
     1.751 2.450
  ... (remaining 165655 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'H'
  selection = chain 'X'
}

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=0.00 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             5.110
  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:             0.100
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     13.680
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7016
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      :  0.007   0.077   6757  Z= 0.343
  Angle     :  1.411  34.775   9242  Z= 0.734
  Chirality :  0.068   0.572   1073
  Planarity :  0.009   0.124   1160
  Dihedral  : 16.551 110.256   2703
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.24 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  9.33 %
    Favored  : 90.39 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.06 (0.29), residues: 801
  helix: -1.61 (0.63), residues: 56
  sheet:  1.02 (0.27), residues: 357
  loop : -0.81 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG R 106 
 TYR   0.021   0.003   TYR R  80 
 PHE   0.021   0.003   PHE X 318 
 TRP   0.035   0.004   TRP R  13 
 HIS   0.013   0.003   HIS H 381 

Details of bonding type rmsd
  covalent geometry    : bond        0.00738 ( 6731)
  covalent geometry    : angle       1.30665 ( 9174)
  SS BOND              : bond        0.01230 (   10)
  SS BOND              : angle       4.43173 (   20)
  hydrogen bonds       : bond        0.10524 (  260)
  hydrogen bonds       : angle       6.95266 (  747)
  link_ALPHA1-3        : bond        0.00490 (    2)
  link_ALPHA1-3        : angle       1.51056 (    6)
  link_ALPHA1-4        : bond        0.00467 (    1)
  link_ALPHA1-4        : angle       1.27286 (    3)
  link_ALPHA1-6        : bond        0.00406 (    2)
  link_ALPHA1-6        : angle       1.57731 (    6)
  link_BETA1-4         : bond        0.00377 (    5)
  link_BETA1-4         : angle       2.48239 (   15)
  link_NAG-ASN         : bond        0.01119 (    6)
  link_NAG-ASN         : angle      11.11506 (   18)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 25
  average time/residue: 0.1475
  time to fit residues: 5.6551
Evaluate side-chains
  20 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
X 389 GLN
X 419 HIS
X 474 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.078589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.065339 restraints weight = 101939.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.067737 restraints weight = 41727.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.069163 restraints weight = 23405.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.069922 restraints weight = 16114.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.070459 restraints weight = 13023.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7020
moved from start:          0.1047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6757  Z= 0.147
  Angle     :  0.657   8.856   9242  Z= 0.328
  Chirality :  0.043   0.158   1073
  Planarity :  0.005   0.066   1160
  Dihedral  : 10.654  70.181   1193
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  9.05 %
    Favored  : 89.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.29), residues: 801
  helix: -1.61 (0.57), residues: 58
  sheet:  1.22 (0.26), residues: 376
  loop :  0.02 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG X 510 
 TYR   0.006   0.001   TYR H 307 
 PHE   0.008   0.001   PHE H 445 
 TRP   0.014   0.001   TRP X 513 
 HIS   0.004   0.001   HIS R 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6731)
  covalent geometry    : angle       0.61100 ( 9174)
  SS BOND              : bond        0.00677 (   10)
  SS BOND              : angle       1.32643 (   20)
  hydrogen bonds       : bond        0.03650 (  260)
  hydrogen bonds       : angle       5.54999 (  747)
  link_ALPHA1-3        : bond        0.00898 (    2)
  link_ALPHA1-3        : angle       2.87579 (    6)
  link_ALPHA1-4        : bond        0.00539 (    1)
  link_ALPHA1-4        : angle       1.34196 (    3)
  link_ALPHA1-6        : bond        0.00453 (    2)
  link_ALPHA1-6        : angle       2.35899 (    6)
  link_BETA1-4         : bond        0.00322 (    5)
  link_BETA1-4         : angle       2.38119 (   15)
  link_NAG-ASN         : bond        0.00543 (    6)
  link_NAG-ASN         : angle       4.46052 (   18)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 20
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: X  474 GLN cc_start: 0.6498 (OUTLIER) cc_final: 0.6271 (mm-40)
  outliers start: 9
  outliers final: 3
  residues processed: 28
  average time/residue: 0.1039
  time to fit residues: 4.8642
Evaluate side-chains
  23 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  263 ILE
Chi-restraints excluded: chain R residue  166 ASN
Chi-restraints excluded: chain X residue  474 GLN
Chi-restraints excluded: chain X residue  520 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 7 optimal weight:    8.9990
   chunk 42 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 40 optimal weight:    0.5980
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
H 381 HIS
** H 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.078483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.065508 restraints weight = 108801.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.067520 restraints weight = 50724.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.068785 restraints weight = 30946.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.069508 restraints weight = 22731.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.069850 restraints weight = 18914.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7123
moved from start:          0.1759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   6757  Z= 0.208
  Angle     :  0.662   8.649   9242  Z= 0.328
  Chirality :  0.042   0.223   1073
  Planarity :  0.005   0.051   1160
  Dihedral  :  8.264  49.739   1193
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  9.19 %
    Favored  : 89.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.29), residues: 801
  helix: -1.73 (0.59), residues: 58
  sheet:  1.43 (0.26), residues: 347
  loop :  0.18 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG X 457 
 TYR   0.009   0.001   TYR R 149 
 PHE   0.010   0.001   PHE H 445 
 TRP   0.012   0.002   TRP H 513 
 HIS   0.005   0.001   HIS X 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 6731)
  covalent geometry    : angle       0.61029 ( 9174)
  SS BOND              : bond        0.00416 (   10)
  SS BOND              : angle       2.36648 (   20)
  hydrogen bonds       : bond        0.03408 (  260)
  hydrogen bonds       : angle       5.17356 (  747)
  link_ALPHA1-3        : bond        0.01198 (    2)
  link_ALPHA1-3        : angle       2.26815 (    6)
  link_ALPHA1-4        : bond        0.00010 (    1)
  link_ALPHA1-4        : angle       1.82868 (    3)
  link_ALPHA1-6        : bond        0.00552 (    2)
  link_ALPHA1-6        : angle       2.38439 (    6)
  link_BETA1-4         : bond        0.00478 (    5)
  link_BETA1-4         : angle       2.35485 (   15)
  link_NAG-ASN         : bond        0.00658 (    6)
  link_NAG-ASN         : angle       4.48165 (   18)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 21
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 4
  residues processed: 27
  average time/residue: 0.1399
  time to fit residues: 5.7390
Evaluate side-chains
  23 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   68 CYS
Chi-restraints excluded: chain R residue  148 THR
Chi-restraints excluded: chain R residue  166 ASN
Chi-restraints excluded: chain X residue  520 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 14 optimal weight:    0.4980
   chunk 71 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0370
   chunk 45 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 73 optimal weight:    0.0020
   overall best weight:    0.4468

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

Flipped N/Q/H residues before XYZ refinement:
** H 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.076858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.063053 restraints weight = 100732.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.065437 restraints weight = 41842.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.066824 restraints weight = 23804.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.067662 restraints weight = 16764.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.068145 restraints weight = 13546.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7109
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6757  Z= 0.099
  Angle     :  0.564   8.201   9242  Z= 0.275
  Chirality :  0.042   0.157   1073
  Planarity :  0.004   0.044   1160
  Dihedral  :  6.791  47.256   1193
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  9.05 %
    Favored  : 90.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (0.29), residues: 801
  helix: -1.47 (0.61), residues: 58
  sheet:  1.56 (0.26), residues: 352
  loop :  0.38 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG X 457 
 TYR   0.004   0.001   TYR X 307 
 PHE   0.007   0.001   PHE X 501 
 TRP   0.013   0.001   TRP H 513 
 HIS   0.003   0.001   HIS H 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 6731)
  covalent geometry    : angle       0.51866 ( 9174)
  SS BOND              : bond        0.00392 (   10)
  SS BOND              : angle       1.57674 (   20)
  hydrogen bonds       : bond        0.02840 (  260)
  hydrogen bonds       : angle       4.82318 (  747)
  link_ALPHA1-3        : bond        0.01117 (    2)
  link_ALPHA1-3        : angle       2.38583 (    6)
  link_ALPHA1-4        : bond        0.00396 (    1)
  link_ALPHA1-4        : angle       1.59782 (    3)
  link_ALPHA1-6        : bond        0.00394 (    2)
  link_ALPHA1-6        : angle       2.04896 (    6)
  link_BETA1-4         : bond        0.00224 (    5)
  link_BETA1-4         : angle       1.86063 (   15)
  link_NAG-ASN         : bond        0.00504 (    6)
  link_NAG-ASN         : angle       4.12476 (   18)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 19
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 4
  residues processed: 23
  average time/residue: 0.1067
  time to fit residues: 4.2443
Evaluate side-chains
  20 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 16
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   68 CYS
Chi-restraints excluded: chain R residue  148 THR
Chi-restraints excluded: chain R residue  166 ASN
Chi-restraints excluded: chain X residue  520 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 8 optimal weight:    8.9990
   chunk 52 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   chunk 22 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
H 389 GLN
** R  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.074115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.059512 restraints weight = 93183.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.061887 restraints weight = 38166.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.063332 restraints weight = 21463.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.064148 restraints weight = 14821.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.064681 restraints weight = 11914.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6757  Z= 0.217
  Angle     :  0.630   7.744   9242  Z= 0.311
  Chirality :  0.040   0.136   1073
  Planarity :  0.004   0.045   1160
  Dihedral  :  6.470  51.048   1193
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  9.75 %
    Favored  : 89.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.29), residues: 801
  helix: -1.66 (0.60), residues: 58
  sheet:  1.28 (0.26), residues: 346
  loop :  0.25 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG X 457 
 TYR   0.011   0.002   TYR X 307 
 PHE   0.009   0.001   PHE H 445 
 TRP   0.011   0.002   TRP H 513 
 HIS   0.006   0.001   HIS X 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 6731)
  covalent geometry    : angle       0.58872 ( 9174)
  SS BOND              : bond        0.00476 (   10)
  SS BOND              : angle       1.87840 (   20)
  hydrogen bonds       : bond        0.03205 (  260)
  hydrogen bonds       : angle       4.93993 (  747)
  link_ALPHA1-3        : bond        0.01017 (    2)
  link_ALPHA1-3        : angle       2.14280 (    6)
  link_ALPHA1-4        : bond        0.00034 (    1)
  link_ALPHA1-4        : angle       1.89497 (    3)
  link_ALPHA1-6        : bond        0.00260 (    2)
  link_ALPHA1-6        : angle       1.72736 (    6)
  link_BETA1-4         : bond        0.00537 (    5)
  link_BETA1-4         : angle       2.09514 (   15)
  link_NAG-ASN         : bond        0.00695 (    6)
  link_NAG-ASN         : angle       4.05799 (   18)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 20
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  427 MET cc_start: 0.7893 (mpp) cc_final: 0.7567 (mpp)
  outliers start: 9
  outliers final: 4
  residues processed: 28
  average time/residue: 0.1005
  time to fit residues: 4.4405
Evaluate side-chains
  21 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 17
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   68 CYS
Chi-restraints excluded: chain R residue  148 THR
Chi-restraints excluded: chain R residue  166 ASN
Chi-restraints excluded: chain X residue  520 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 67 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 60 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 68 optimal weight:    0.5980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.075225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.062711 restraints weight = 88779.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.064044 restraints weight = 39240.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.064966 restraints weight = 23941.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.065124 restraints weight = 17626.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.065442 restraints weight = 17521.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6757  Z= 0.125
  Angle     :  0.562   7.706   9242  Z= 0.276
  Chirality :  0.040   0.146   1073
  Planarity :  0.004   0.043   1160
  Dihedral  :  5.943  48.653   1193
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 10.31 %
    Favored  : 88.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.90 (0.29), residues: 801
  helix: -1.36 (0.63), residues: 57
  sheet:  1.26 (0.26), residues: 348
  loop :  0.39 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG X 457 
 TYR   0.005   0.001   TYR X 307 
 PHE   0.007   0.001   PHE X 501 
 TRP   0.013   0.001   TRP H 513 
 HIS   0.003   0.001   HIS X 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6731)
  covalent geometry    : angle       0.51687 ( 9174)
  SS BOND              : bond        0.00272 (   10)
  SS BOND              : angle       2.13799 (   20)
  hydrogen bonds       : bond        0.02808 (  260)
  hydrogen bonds       : angle       4.74676 (  747)
  link_ALPHA1-3        : bond        0.01023 (    2)
  link_ALPHA1-3        : angle       1.95086 (    6)
  link_ALPHA1-4        : bond        0.00170 (    1)
  link_ALPHA1-4        : angle       1.65974 (    3)
  link_ALPHA1-6        : bond        0.00311 (    2)
  link_ALPHA1-6        : angle       1.63302 (    6)
  link_BETA1-4         : bond        0.00273 (    5)
  link_BETA1-4         : angle       1.72250 (   15)
  link_NAG-ASN         : bond        0.00505 (    6)
  link_NAG-ASN         : angle       3.95011 (   18)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 18
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  427 MET cc_start: 0.7852 (mpp) cc_final: 0.7547 (mpp)
  outliers start: 7
  outliers final: 5
  residues processed: 24
  average time/residue: 0.0799
  time to fit residues: 3.3958
Evaluate side-chains
  22 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 17
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   68 CYS
Chi-restraints excluded: chain R residue  148 THR
Chi-restraints excluded: chain R residue  166 ASN
Chi-restraints excluded: chain X residue  520 ILE
Chi-restraints excluded: chain X residue  529 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0980
   chunk 33 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 1 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 31 optimal weight:    0.2980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.074801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.061375 restraints weight = 94557.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.063462 restraints weight = 39187.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.064116 restraints weight = 23299.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.064305 restraints weight = 18530.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.064496 restraints weight = 17857.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.2832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6757  Z= 0.108
  Angle     :  0.548   9.957   9242  Z= 0.270
  Chirality :  0.040   0.151   1073
  Planarity :  0.004   0.042   1160
  Dihedral  :  5.572  47.629   1193
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 10.17 %
    Favored  : 89.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.29), residues: 801
  helix: -1.13 (0.65), residues: 57
  sheet:  1.34 (0.26), residues: 348
  loop :  0.50 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG X 390 
 TYR   0.012   0.001   TYR X 307 
 PHE   0.006   0.001   PHE X 501 
 TRP   0.013   0.001   TRP H 513 
 HIS   0.003   0.001   HIS X 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 6731)
  covalent geometry    : angle       0.49948 ( 9174)
  SS BOND              : bond        0.00251 (   10)
  SS BOND              : angle       2.71586 (   20)
  hydrogen bonds       : bond        0.02685 (  260)
  hydrogen bonds       : angle       4.61390 (  747)
  link_ALPHA1-3        : bond        0.00921 (    2)
  link_ALPHA1-3        : angle       1.78066 (    6)
  link_ALPHA1-4        : bond        0.00197 (    1)
  link_ALPHA1-4        : angle       1.56076 (    3)
  link_ALPHA1-6        : bond        0.00344 (    2)
  link_ALPHA1-6        : angle       1.57101 (    6)
  link_BETA1-4         : bond        0.00250 (    5)
  link_BETA1-4         : angle       1.62115 (   15)
  link_NAG-ASN         : bond        0.00465 (    6)
  link_NAG-ASN         : angle       3.82103 (   18)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 18
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 5
  residues processed: 22
  average time/residue: 0.0982
  time to fit residues: 3.7612
Evaluate side-chains
  21 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 16
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   68 CYS
Chi-restraints excluded: chain R residue  148 THR
Chi-restraints excluded: chain R residue  166 ASN
Chi-restraints excluded: chain X residue  520 ILE
Chi-restraints excluded: chain X residue  529 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 56 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 9 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** R  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.074214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.060652 restraints weight = 91627.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.063256 restraints weight = 38373.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.063554 restraints weight = 22249.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.063665 restraints weight = 17647.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.063859 restraints weight = 17214.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7266
moved from start:          0.3182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6757  Z= 0.137
  Angle     :  0.552   7.212   9242  Z= 0.271
  Chirality :  0.040   0.142   1073
  Planarity :  0.004   0.042   1160
  Dihedral  :  5.312  47.650   1193
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 10.31 %
    Favored  : 88.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.29), residues: 801
  helix: -1.19 (0.66), residues: 57
  sheet:  1.25 (0.26), residues: 343
  loop :  0.50 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG X 457 
 TYR   0.012   0.001   TYR X 307 
 PHE   0.007   0.001   PHE X 500 
 TRP   0.012   0.001   TRP H 513 
 HIS   0.004   0.001   HIS X 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6731)
  covalent geometry    : angle       0.51191 ( 9174)
  SS BOND              : bond        0.00583 (   10)
  SS BOND              : angle       2.16242 (   20)
  hydrogen bonds       : bond        0.02712 (  260)
  hydrogen bonds       : angle       4.61542 (  747)
  link_ALPHA1-3        : bond        0.00628 (    2)
  link_ALPHA1-3        : angle       1.49044 (    6)
  link_ALPHA1-4        : bond        0.00116 (    1)
  link_ALPHA1-4        : angle       1.71779 (    3)
  link_ALPHA1-6        : bond        0.00360 (    2)
  link_ALPHA1-6        : angle       1.44222 (    6)
  link_BETA1-4         : bond        0.00318 (    5)
  link_BETA1-4         : angle       1.65826 (   15)
  link_NAG-ASN         : bond        0.00536 (    6)
  link_NAG-ASN         : angle       3.70302 (   18)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 18
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  427 MET cc_start: 0.7793 (mpp) cc_final: 0.7518 (mpp)
  outliers start: 7
  outliers final: 4
  residues processed: 24
  average time/residue: 0.1122
  time to fit residues: 4.0627
Evaluate side-chains
  21 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 17
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  148 THR
Chi-restraints excluded: chain R residue  166 ASN
Chi-restraints excluded: chain X residue  520 ILE
Chi-restraints excluded: chain X residue  529 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 52 optimal weight:    0.0570
   chunk 61 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 72 optimal weight:    0.7980
   chunk 4 optimal weight:    8.9990
   chunk 54 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 56 optimal weight:    6.9990
   overall best weight:    0.6498

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.074433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.061145 restraints weight = 92075.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.063180 restraints weight = 37790.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.063898 restraints weight = 21860.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.064030 restraints weight = 16929.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.064349 restraints weight = 16747.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7218
moved from start:          0.3288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   6757  Z= 0.111
  Angle     :  0.536   9.078   9242  Z= 0.264
  Chirality :  0.040   0.154   1073
  Planarity :  0.004   0.041   1160
  Dihedral  :  5.133  46.519   1193
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 10.72 %
    Favored  : 88.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.30), residues: 801
  helix: -1.03 (0.67), residues: 57
  sheet:  1.27 (0.26), residues: 350
  loop :  0.56 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 106 
 TYR   0.011   0.001   TYR X 307 
 PHE   0.006   0.001   PHE X 501 
 TRP   0.013   0.001   TRP H 513 
 HIS   0.003   0.001   HIS R 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 6731)
  covalent geometry    : angle       0.49057 ( 9174)
  SS BOND              : bond        0.00240 (   10)
  SS BOND              : angle       2.60767 (   20)
  hydrogen bonds       : bond        0.02582 (  260)
  hydrogen bonds       : angle       4.56179 (  747)
  link_ALPHA1-3        : bond        0.00744 (    2)
  link_ALPHA1-3        : angle       1.53166 (    6)
  link_ALPHA1-4        : bond        0.00113 (    1)
  link_ALPHA1-4        : angle       1.58645 (    3)
  link_ALPHA1-6        : bond        0.00380 (    2)
  link_ALPHA1-6        : angle       1.48856 (    6)
  link_BETA1-4         : bond        0.00265 (    5)
  link_BETA1-4         : angle       1.54295 (   15)
  link_NAG-ASN         : bond        0.00467 (    6)
  link_NAG-ASN         : angle       3.67113 (   18)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 16
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  427 MET cc_start: 0.7753 (mpp) cc_final: 0.7491 (mpp)
  outliers start: 5
  outliers final: 4
  residues processed: 20
  average time/residue: 0.0840
  time to fit residues: 3.0690
Evaluate side-chains
  20 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 16
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  148 THR
Chi-restraints excluded: chain R residue  166 ASN
Chi-restraints excluded: chain X residue  520 ILE
Chi-restraints excluded: chain X residue  529 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 10 optimal weight:    0.4980
   chunk 55 optimal weight:    9.9990
   chunk 6 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 31 optimal weight:    0.4980
   chunk 4 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 32 optimal weight:    0.2980
   chunk 48 optimal weight:    6.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** R  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.074407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.059680 restraints weight = 92170.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.062085 restraints weight = 37671.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.063560 restraints weight = 21222.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.064390 restraints weight = 14738.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.064924 restraints weight = 11900.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7189
moved from start:          0.3499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6757  Z= 0.110
  Angle     :  0.522   7.223   9242  Z= 0.256
  Chirality :  0.040   0.159   1073
  Planarity :  0.004   0.042   1160
  Dihedral  :  4.851  45.117   1193
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 10.72 %
    Favored  : 88.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.30), residues: 801
  helix: -0.98 (0.67), residues: 57
  sheet:  1.36 (0.26), residues: 346
  loop :  0.57 (0.33), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 106 
 TYR   0.013   0.001   TYR X 307 
 PHE   0.006   0.001   PHE X 500 
 TRP   0.014   0.001   TRP H 513 
 HIS   0.002   0.001   HIS R  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 6731)
  covalent geometry    : angle       0.48202 ( 9174)
  SS BOND              : bond        0.00522 (   10)
  SS BOND              : angle       2.21539 (   20)
  hydrogen bonds       : bond        0.02527 (  260)
  hydrogen bonds       : angle       4.47470 (  747)
  link_ALPHA1-3        : bond        0.00702 (    2)
  link_ALPHA1-3        : angle       1.47001 (    6)
  link_ALPHA1-4        : bond        0.00108 (    1)
  link_ALPHA1-4        : angle       1.59104 (    3)
  link_ALPHA1-6        : bond        0.00389 (    2)
  link_ALPHA1-6        : angle       1.46144 (    6)
  link_BETA1-4         : bond        0.00267 (    5)
  link_BETA1-4         : angle       1.49120 (   15)
  link_NAG-ASN         : bond        0.00462 (    6)
  link_NAG-ASN         : angle       3.54398 (   18)

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

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

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1602 Ramachandran restraints generated.
    801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  427 MET cc_start: 0.7737 (mpp) cc_final: 0.7467 (mpp)
  outliers start: 4
  outliers final: 4
  residues processed: 22
  average time/residue: 0.0731
  time to fit residues: 2.8386
Evaluate side-chains
  20 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 16
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  148 THR
Chi-restraints excluded: chain R residue  166 ASN
Chi-restraints excluded: chain X residue  520 ILE
Chi-restraints excluded: chain X residue  529 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 77 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 40 optimal weight:    0.3980
   chunk 22 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** R  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.074252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.059602 restraints weight = 91869.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.061967 restraints weight = 38235.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.063421 restraints weight = 21753.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.064273 restraints weight = 15175.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.064690 restraints weight = 12224.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.3643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6757  Z= 0.117
  Angle     :  0.526   6.799   9242  Z= 0.259
  Chirality :  0.040   0.157   1073
  Planarity :  0.004   0.041   1160
  Dihedral  :  4.815  45.047   1193
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 10.86 %
    Favored  : 88.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.30), residues: 801
  helix: -0.97 (0.67), residues: 57
  sheet:  1.27 (0.26), residues: 350
  loop :  0.60 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 106 
 TYR   0.010   0.001   TYR X 307 
 PHE   0.006   0.001   PHE X 501 
 TRP   0.013   0.001   TRP H 513 
 HIS   0.003   0.001   HIS X 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 6731)
  covalent geometry    : angle       0.49071 ( 9174)
  SS BOND              : bond        0.00136 (   10)
  SS BOND              : angle       1.80544 (   20)
  hydrogen bonds       : bond        0.02533 (  260)
  hydrogen bonds       : angle       4.49362 (  747)
  link_ALPHA1-3        : bond        0.00652 (    2)
  link_ALPHA1-3        : angle       1.44067 (    6)
  link_ALPHA1-4        : bond        0.00059 (    1)
  link_ALPHA1-4        : angle       1.62205 (    3)
  link_ALPHA1-6        : bond        0.00376 (    2)
  link_ALPHA1-6        : angle       1.46160 (    6)
  link_BETA1-4         : bond        0.00277 (    5)
  link_BETA1-4         : angle       1.48951 (   15)
  link_NAG-ASN         : bond        0.00473 (    6)
  link_NAG-ASN         : angle       3.47974 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2143.09 seconds
wall clock time: 37 minutes 17.16 seconds (2237.16 seconds total)