Starting phenix.real_space_refine
on Fri Jul 25 03:25:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x7v_33049/07_2025/7x7v_33049.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x7v_33049/07_2025/7x7v_33049.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x7v_33049/07_2025/7x7v_33049.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x7v_33049/07_2025/7x7v_33049.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x7v_33049/07_2025/7x7v_33049.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x7v_33049/07_2025/7x7v_33049.cif"
  }
  resolution = 3.83
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      26      5.16       5
     C    4365      2.51       5
     N    1124      2.21       5
     O    1361      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6876
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "L"
      Number of atoms: 853
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 853
          Classifications: {'peptide': 111}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 946
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 117}
    Chain: "F"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 827
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103}
    Chain: "A"
      Number of atoms: 929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 929
          Classifications: {'peptide': 119}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "D"
      Number of atoms: 831
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 831
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 102}
    Chain: "C"
      Number of atoms: 921
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 921
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "E"
      Number of atoms: 1513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1513
          Classifications: {'peptide': 189}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 175}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 7.21, per 1000 atoms: 1.05
  Number of scatterers: 6876
  At special positions: 0
  Unit cell: (98.028, 118.256, 80.134, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      26     16.00
     O    1361      8.00
     N    1124      7.00
     C    4365      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  92 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  23 " - pdb=" SG  CYS F  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 323 " - pdb=" SG  CYS E 348 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 366 " - pdb=" SG  CYS E 419 " distance=1.98
    Simple disulfide: pdb=" SG  CYS E 467 " - pdb=" SG  CYS E 474 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG G   1 " - " NAG G   2 "
    NAG-ASN
      " NAG B   1 " - " ASN E 330 "
      " NAG G   1 " - " ASN E 357 "
  Time building additional restraints: 1.89
  Conformation dependent library (CDL) restraints added in 816.6 milliseconds
  

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1586

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 20 sheets defined
      4.5% alpha, 33.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'H' and resid 61 through 65
      removed outlier: 3.623A  pdb=" N   GLU H  65 " --> pdb=" O   LEU H  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 3.758A  pdb=" N   ASP A  90 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   SER A  91 " --> pdb=" O   SER A  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 87 through 91'
    Processing helix  chain 'A' and resid 101 through 105
      removed outlier: 3.888A  pdb=" N   GLY A 105 " --> pdb=" O   ASP A 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 65
      removed outlier: 4.086A  pdb=" N   LYS C  65 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 62 through 65'
    Processing helix  chain 'E' and resid 324 through 329
      removed outlier: 4.005A  pdb=" N   VAL E 328 " --> pdb=" O   PRO E 324 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 336 through 340
      removed outlier: 4.190A  pdb=" N   TRP E 340 " --> pdb=" O   VAL E 337 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 392 through 394
      No H-bonds generated for 'chain 'E' and resid 392 through 394'
    Processing helix  chain 'E' and resid 425 through 430
      removed outlier: 3.899A  pdb=" N   ALA E 430 " --> pdb=" O   ARG E 426 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.604A  pdb=" N   THR L  76 " --> pdb=" O   SER L  69 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12
      removed outlier: 7.220A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 109 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 52 through 53
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6
      removed outlier: 3.511A  pdb=" N   VAL H  18 " --> pdb=" O   LEU H  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 46 through 47
      removed outlier: 4.670A  pdb=" N   THR H  33 " --> pdb=" O   GLY H  99 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL H  37 " --> pdb=" O   TYR H  95 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   GLN H  39 " --> pdb=" O   VAL H  93 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 4 through 5
      removed outlier: 3.609A  pdb=" N   ARG F  24 " --> pdb=" O   THR F   5 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 10 through 13
      removed outlier: 3.657A  pdb=" N   GLU F 105 " --> pdb=" O   LEU F  11 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 44 through 48
      removed outlier: 6.824A  pdb=" N   TRP F  35 " --> pdb=" O   LEU F  47 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   THR F  97 " --> pdb=" O   GLN F  90 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 6
      removed outlier: 3.544A  pdb=" N   VAL A  18 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 3 through 6
      removed outlier: 3.657A  pdb=" N   THR A  78 " --> pdb=" O   ASP A  73 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 58 through 60
      removed outlier: 6.868A  pdb=" N   TRP A  36 " --> pdb=" O   ILE A  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 58 through 60
      removed outlier: 6.868A  pdb=" N   TRP A  36 " --> pdb=" O   ILE A  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 4 through 6
      removed outlier: 3.779A  pdb=" N   VAL D  19 " --> pdb=" O   ILE D  75 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ILE D  75 " --> pdb=" O   VAL D  19 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   SER D  74 " --> pdb=" O   SER D  63 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 11
    Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 54
      removed outlier: 6.367A  pdb=" N   TRP D  35 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
      removed outlier: 5.009A  pdb=" N   SER D  49 " --> pdb=" O   LEU D  33 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   LEU D  33 " --> pdb=" O   SER D  49 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLN D  38 " --> pdb=" O   THR D  85 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   THR D  85 " --> pdb=" O   GLN D  38 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 3 through 6
      removed outlier: 3.657A  pdb=" N   THR C  71 " --> pdb=" O   TYR C  80 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 58 through 60
      removed outlier: 3.500A  pdb=" N   THR C  59 " --> pdb=" O   TYR C  50 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   TRP C  36 " --> pdb=" O   ILE C  48 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   TYR C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   MET C  34 " --> pdb=" O   TYR C  50 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   CYS C  96 " --> pdb=" O   TRP C 112 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   TRP C 112 " --> pdb=" O   CYS C  96 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   LYS C  98 " --> pdb=" O   ALA C 110 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 58 through 60
      removed outlier: 3.500A  pdb=" N   THR C  59 " --> pdb=" O   TYR C  50 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   TRP C  36 " --> pdb=" O   ILE C  48 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   TYR C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   MET C  34 " --> pdb=" O   TYR C  50 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   TYR C  94 " --> pdb=" O   THR C 116 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   THR C 116 " --> pdb=" O   TYR C  94 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 341 through 345
      removed outlier: 3.804A  pdb=" N   GLU E 341 " --> pdb=" O   SER E 386 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   SER E 386 " --> pdb=" O   GLU E 341 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LYS E 343 " --> pdb=" O   ALA E 384 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ALA E 384 " --> pdb=" O   LYS E 343 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 439 through 441

    190 hydrogen bonds defined for protein.
    465 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.80

  Time building geometry restraints manager: 2.24 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1592
        1.33 -     1.45: 1828
        1.45 -     1.58: 3604
        1.58 -     1.70: 0
        1.70 -     1.82: 32
  Bond restraints: 7056
  Sorted by residual:
  bond pdb=" CA  CYS E 366 "
       pdb=" C   CYS E 366 "
    ideal  model  delta    sigma   weight residual
    1.522  1.463  0.059 1.22e-02 6.72e+03 2.30e+01
  bond pdb=" N   PRO E 507 "
       pdb=" CD  PRO E 507 "
    ideal  model  delta    sigma   weight residual
    1.473  1.530 -0.057 1.40e-02 5.10e+03 1.65e+01
  bond pdb=" CA  CYS E 366 "
       pdb=" CB  CYS E 366 "
    ideal  model  delta    sigma   weight residual
    1.533  1.455  0.078 2.29e-02 1.91e+03 1.16e+01
  bond pdb=" C   LYS E 365 "
       pdb=" O   LYS E 365 "
    ideal  model  delta    sigma   weight residual
    1.236  1.204  0.032 1.22e-02 6.72e+03 6.70e+00
  bond pdb=" N   CYS E 366 "
       pdb=" CA  CYS E 366 "
    ideal  model  delta    sigma   weight residual
    1.455  1.424  0.031 1.23e-02 6.61e+03 6.46e+00
  ... (remaining 7051 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.60: 9361
        2.60 -     5.20: 194
        5.20 -     7.81: 30
        7.81 -    10.41: 10
       10.41 -    13.01: 2
  Bond angle restraints: 9597
  Sorted by residual:
  angle pdb=" CA  PRO E 507 "
        pdb=" N   PRO E 507 "
        pdb=" CD  PRO E 507 "
      ideal   model   delta    sigma   weight residual
     112.00   98.99   13.01 1.40e+00 5.10e-01 8.63e+01
  angle pdb=" N   GLY E 418 "
        pdb=" CA  GLY E 418 "
        pdb=" C   GLY E 418 "
      ideal   model   delta    sigma   weight residual
     112.54  122.66  -10.12 1.28e+00 6.10e-01 6.25e+01
  angle pdb=" N   MET E 417 "
        pdb=" CA  MET E 417 "
        pdb=" C   MET E 417 "
      ideal   model   delta    sigma   weight residual
     112.92  104.95    7.97 1.23e+00 6.61e-01 4.20e+01
  angle pdb=" C   ILE L  98 "
        pdb=" N   PRO L  99 "
        pdb=" CA  PRO L  99 "
      ideal   model   delta    sigma   weight residual
     119.90  113.52    6.38 1.05e+00 9.07e-01 3.69e+01
  angle pdb=" N   ASP C  90 "
        pdb=" CA  ASP C  90 "
        pdb=" C   ASP C  90 "
      ideal   model   delta    sigma   weight residual
     113.30  105.24    8.06 1.34e+00 5.57e-01 3.62e+01
  ... (remaining 9592 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.99: 3661
       16.99 -    33.98: 404
       33.98 -    50.97: 76
       50.97 -    67.96: 11
       67.96 -    84.94: 3
  Dihedral angle restraints: 4155
    sinusoidal: 1639
      harmonic: 2516
  Sorted by residual:
  dihedral pdb=" CB  CYS E 366 "
           pdb=" SG  CYS E 366 "
           pdb=" SG  CYS E 419 "
           pdb=" CB  CYS E 419 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  137.56  -44.56     1      1.00e+01 1.00e-02 2.76e+01
  dihedral pdb=" CA  CYS E 467 "
           pdb=" C   CYS E 467 "
           pdb=" N   THR E 468 "
           pdb=" CA  THR E 468 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.30   25.70     0      5.00e+00 4.00e-02 2.64e+01
  dihedral pdb=" N   CYS E 366 "
           pdb=" C   CYS E 366 "
           pdb=" CA  CYS E 366 "
           pdb=" CB  CYS E 366 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.63  -12.83     0      2.50e+00 1.60e-01 2.63e+01
  ... (remaining 4152 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.151: 1010
       0.151 -    0.301: 25
       0.301 -    0.452: 1
       0.452 -    0.602: 0
       0.602 -    0.753: 1
  Chirality restraints: 1037
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.18   -0.22 2.00e-02 2.50e+03 1.17e+02
  chirality pdb=" C1  NAG G   2 "
            pdb=" O4  NAG G   1 "
            pdb=" C2  NAG G   2 "
            pdb=" O5  NAG G   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.27   -0.13 2.00e-02 2.50e+03 3.95e+01
  chirality pdb=" CA  CYS E 366 "
            pdb=" N   CYS E 366 "
            pdb=" C   CYS E 366 "
            pdb=" CB  CYS E 366 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.76    0.75 2.00e-01 2.50e+01 1.42e+01
  ... (remaining 1034 not shown)

  Planarity restraints: 1226
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG G   1 "   -0.193 2.00e-02 2.50e+03   1.60e-01 3.18e+02
        pdb=" C7  NAG G   1 "    0.052 2.00e-02 2.50e+03
        pdb=" C8  NAG G   1 "   -0.139 2.00e-02 2.50e+03
        pdb=" N2  NAG G   1 "    0.260 2.00e-02 2.50e+03
        pdb=" O7  NAG G   1 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B   1 "   -0.173 2.00e-02 2.50e+03   1.47e-01 2.70e+02
        pdb=" C7  NAG B   1 "    0.046 2.00e-02 2.50e+03
        pdb=" C8  NAG B   1 "   -0.125 2.00e-02 2.50e+03
        pdb=" N2  NAG B   1 "    0.245 2.00e-02 2.50e+03
        pdb=" O7  NAG B   1 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG G   2 "    0.092 2.00e-02 2.50e+03   7.60e-02 7.23e+01
        pdb=" C7  NAG G   2 "   -0.026 2.00e-02 2.50e+03
        pdb=" C8  NAG G   2 "    0.070 2.00e-02 2.50e+03
        pdb=" N2  NAG G   2 "   -0.121 2.00e-02 2.50e+03
        pdb=" O7  NAG G   2 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1223 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1968
        2.80 -     3.32: 5448
        3.32 -     3.85: 11089
        3.85 -     4.37: 11905
        4.37 -     4.90: 21706
  Nonbonded interactions: 52116
  Sorted by model distance:
  nonbonded pdb=" OG  SER E 336 "
            pdb=" O   LYS E 439 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   ILE F  29 "
            pdb=" OG1 THR F  92 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OG  SER E 380 "
            pdb=" O   LEU E 503 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OG  SER E 346 "
            pdb=" ND2 ASN E 381 "
     model   vdw
     2.302 3.120
  nonbonded pdb=" OH  TYR L  36 "
            pdb=" O   TYR E 436 "
     model   vdw
     2.311 3.040
  ... (remaining 52111 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 'B'
  selection = chain 'G'
}

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=0.67 max=1.00 mean=1.00
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:             30.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.090
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   56.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6888
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   0.078   7069  Z= 0.323
  Angle     :  0.989  13.009   9627  Z= 0.567
  Chirality :  0.064   0.753   1037
  Planarity :  0.011   0.160   1224
  Dihedral  : 13.942  84.945   2542
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.10 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  9.09 %
    Favored  : 90.50 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.88 (0.25), residues: 859
  helix: -5.12 (0.37), residues: 8
  sheet: -2.34 (0.25), residues: 363
  loop : -2.76 (0.23), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP E 423 
 HIS   0.006   0.001   HIS E 445 
 PHE   0.018   0.002   PHE E 334 
 TYR   0.021   0.002   TYR D  91 
 ARG   0.005   0.001   ARG F  53 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00382 (    2)
  link_NAG-ASN         : angle       2.24054 (    6)
  link_BETA1-4         : bond        0.00198 (    2)
  link_BETA1-4         : angle       1.04723 (    6)
  hydrogen bonds       : bond        0.29188 (  163)
  hydrogen bonds       : angle      10.55274 (  465)
  SS BOND              : bond        0.01805 (    9)
  SS BOND              : angle       3.73054 (   18)
  covalent geometry    : bond        0.00649 ( 7056)
  covalent geometry    : angle       0.97542 ( 9597)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 247
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   49 LYS cc_start: 0.7622 (tttt) cc_final: 0.7408 (tttm)
REVERT: L   51 LEU cc_start: 0.8456 (mp) cc_final: 0.8136 (mp)
REVERT: L   80 HIS cc_start: 0.8060 (t70) cc_final: 0.7779 (t70)
REVERT: H   19 LYS cc_start: 0.8290 (tttt) cc_final: 0.7554 (tttp)
REVERT: H   32 TYR cc_start: 0.7790 (m-80) cc_final: 0.7557 (m-10)
REVERT: H   46 GLU cc_start: 0.8203 (pt0) cc_final: 0.7695 (pt0)
REVERT: H  110 PHE cc_start: 0.7898 (m-80) cc_final: 0.7678 (m-10)
REVERT: H  113 GLN cc_start: 0.8745 (pt0) cc_final: 0.8345 (pm20)
REVERT: F   45 LYS cc_start: 0.7204 (ptmt) cc_final: 0.6782 (ptpp)
REVERT: F   80 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7791 (tp40)
REVERT: F   90 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7627 (tm-30)
REVERT: A    3 GLN cc_start: 0.8187 (pt0) cc_final: 0.7376 (pp30)
REVERT: A    5 GLN cc_start: 0.8265 (tp40) cc_final: 0.7670 (tp40)
REVERT: A   10 GLU cc_start: 0.6828 (mp0) cc_final: 0.6234 (mp0)
REVERT: A   19 LYS cc_start: 0.6978 (tppp) cc_final: 0.6473 (tptm)
REVERT: A   23 LYS cc_start: 0.6820 (tptt) cc_final: 0.6197 (ttpp)
REVERT: A   43 GLN cc_start: 0.7777 (mp10) cc_final: 0.7043 (mp10)
REVERT: A  113 THR cc_start: 0.7766 (t) cc_final: 0.6780 (t)
REVERT: D   79 GLN cc_start: 0.7315 (mp10) cc_final: 0.6456 (mp10)
REVERT: C    2 ILE cc_start: 0.8039 (mm) cc_final: 0.7816 (mm)
REVERT: C   23 LYS cc_start: 0.7499 (tmmt) cc_final: 0.7251 (tppp)
REVERT: C   43 LYS cc_start: 0.8973 (mmmt) cc_final: 0.8692 (mmmm)
REVERT: C  109 LEU cc_start: 0.8533 (mt) cc_final: 0.8333 (mt)
REVERT: C  114 GLN cc_start: 0.8912 (mt0) cc_final: 0.8621 (mt0)
REVERT: E  426 ARG cc_start: 0.8401 (tmm-80) cc_final: 0.7970 (ttt-90)
REVERT: E  447 LYS cc_start: 0.8723 (mppt) cc_final: 0.8041 (mtpt)
REVERT: E  505 ASN cc_start: 0.8627 (t0) cc_final: 0.8344 (t0)
  outliers start: 3
  outliers final: 2
  residues processed: 250
  average time/residue: 0.2884
  time to fit residues: 91.2874
Evaluate side-chains
  207 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 205
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain E residue  363 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 75 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** L  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  35 ASN
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
A  39 GLN
C  33 ASN
E 457 ASN
E 473 ASN
E 479 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.106998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.085397 restraints weight = 11917.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.087910 restraints weight = 7083.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.089589 restraints weight = 5082.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2940
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2939 r_free = 0.2939    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2939
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.1772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7069  Z= 0.171
  Angle     :  0.661   9.600   9627  Z= 0.343
  Chirality :  0.045   0.249   1037
  Planarity :  0.006   0.069   1224
  Dihedral  :  6.641  63.215   1049
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 16.69 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.18 (0.26), residues: 859
  helix: -5.12 (0.32), residues: 14
  sheet: -1.72 (0.26), residues: 340
  loop : -2.36 (0.25), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP E 423 
 HIS   0.003   0.001   HIS L  34 
 PHE   0.019   0.002   PHE E 416 
 TYR   0.015   0.001   TYR E 442 
 ARG   0.004   0.000   ARG C  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00213 (    2)
  link_NAG-ASN         : angle       1.58769 (    6)
  link_BETA1-4         : bond        0.00163 (    2)
  link_BETA1-4         : angle       0.95980 (    6)
  hydrogen bonds       : bond        0.04759 (  163)
  hydrogen bonds       : angle       6.94336 (  465)
  SS BOND              : bond        0.00476 (    9)
  SS BOND              : angle       1.14545 (   18)
  covalent geometry    : bond        0.00389 ( 7056)
  covalent geometry    : angle       0.65863 ( 9597)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 220
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 LYS cc_start: 0.8863 (tttt) cc_final: 0.8335 (tttp)
REVERT: H   32 TYR cc_start: 0.8762 (m-80) cc_final: 0.8510 (m-10)
REVERT: H   87 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8563 (p)
REVERT: F    4 MET cc_start: 0.8607 (mtp) cc_final: 0.8230 (mtp)
REVERT: F   24 ARG cc_start: 0.8130 (mtp-110) cc_final: 0.7704 (mtp-110)
REVERT: F   45 LYS cc_start: 0.8532 (ptmt) cc_final: 0.8149 (ptpp)
REVERT: F   78 LEU cc_start: 0.8892 (mm) cc_final: 0.8612 (mm)
REVERT: A   10 GLU cc_start: 0.7802 (mp0) cc_final: 0.7441 (mp0)
REVERT: A   23 LYS cc_start: 0.8793 (tptt) cc_final: 0.8246 (ttpp)
REVERT: D   79 GLN cc_start: 0.8369 (mp10) cc_final: 0.7862 (mp10)
REVERT: E  447 LYS cc_start: 0.8768 (mppt) cc_final: 0.8486 (mtpt)
  outliers start: 26
  outliers final: 16
  residues processed: 229
  average time/residue: 0.2228
  time to fit residues: 64.7063
Evaluate side-chains
  213 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 196
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain F residue   27 GLN
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain D residue  106 ILE
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain C residue   89 GLU
Chi-restraints excluded: chain E residue  405 ILE
Chi-restraints excluded: chain E residue  445 HIS
Chi-restraints excluded: chain E residue  449 ARG
Chi-restraints excluded: chain E residue  468 THR
Chi-restraints excluded: chain E residue  475 TYR
Chi-restraints excluded: chain E residue  489 ILE
Chi-restraints excluded: chain E residue  497 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 68 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 1 optimal weight:    7.9990
   chunk 20 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** L  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
F  90 GLN
D  30 ASN
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.109637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.088828 restraints weight = 11903.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.091417 restraints weight = 6898.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.093136 restraints weight = 4848.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2916
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2916
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.2309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7069  Z= 0.201
  Angle     :  0.652   9.957   9627  Z= 0.337
  Chirality :  0.044   0.229   1037
  Planarity :  0.005   0.056   1224
  Dihedral  :  6.361  58.449   1048
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 20.08 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.82 (0.27), residues: 859
  helix: -5.03 (0.35), residues: 14
  sheet: -1.43 (0.27), residues: 352
  loop : -2.15 (0.26), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP E 423 
 HIS   0.005   0.001   HIS L  94 
 PHE   0.017   0.001   PHE D  94 
 TYR   0.017   0.001   TYR F  49 
 ARG   0.006   0.001   ARG C  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00074 (    2)
  link_NAG-ASN         : angle       1.63989 (    6)
  link_BETA1-4         : bond        0.00145 (    2)
  link_BETA1-4         : angle       0.82145 (    6)
  hydrogen bonds       : bond        0.04154 (  163)
  hydrogen bonds       : angle       6.26366 (  465)
  SS BOND              : bond        0.00386 (    9)
  SS BOND              : angle       0.92507 (   18)
  covalent geometry    : bond        0.00465 ( 7056)
  covalent geometry    : angle       0.65003 ( 9597)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 191
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 LYS cc_start: 0.8885 (tttt) cc_final: 0.8515 (tttm)
REVERT: H   32 TYR cc_start: 0.8758 (m-80) cc_final: 0.8465 (m-10)
REVERT: F    4 MET cc_start: 0.8638 (mtp) cc_final: 0.8275 (mmm)
REVERT: F   24 ARG cc_start: 0.8099 (mtp-110) cc_final: 0.7802 (mtp-110)
REVERT: F   45 LYS cc_start: 0.8526 (ptmt) cc_final: 0.8159 (ptpp)
REVERT: F   78 LEU cc_start: 0.8878 (mm) cc_final: 0.8645 (mm)
REVERT: F  105 GLU cc_start: 0.5812 (tt0) cc_final: 0.5523 (tt0)
REVERT: A   10 GLU cc_start: 0.7999 (mp0) cc_final: 0.7647 (mp0)
REVERT: A   23 LYS cc_start: 0.8804 (tptt) cc_final: 0.8263 (ttpp)
REVERT: E  447 LYS cc_start: 0.8759 (mppt) cc_final: 0.8540 (mtpt)
  outliers start: 30
  outliers final: 19
  residues processed: 202
  average time/residue: 0.2737
  time to fit residues: 71.3852
Evaluate side-chains
  204 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 185
  time to evaluate  : 1.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue  110 ILE
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   44 SER
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue  121 SER
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain A residue   18 VAL
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain C residue   62 GLN
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain C residue   89 GLU
Chi-restraints excluded: chain E residue  404 VAL
Chi-restraints excluded: chain E residue  405 ILE
Chi-restraints excluded: chain E residue  443 LEU
Chi-restraints excluded: chain E residue  475 TYR
Chi-restraints excluded: chain E residue  497 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
** L  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  90 GLN
D  30 ASN
C  82 HIS
** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.103281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.081340 restraints weight = 12292.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.083991 restraints weight = 7004.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.085720 restraints weight = 4895.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7069  Z= 0.173
  Angle     :  0.623  10.164   9627  Z= 0.321
  Chirality :  0.044   0.214   1037
  Planarity :  0.005   0.056   1224
  Dihedral  :  6.161  55.339   1048
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 21.30 %
    Favored  : 74.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.52 (0.27), residues: 859
  helix: -5.06 (0.33), residues: 14
  sheet: -1.19 (0.27), residues: 356
  loop : -1.97 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E 423 
 HIS   0.004   0.001   HIS L  94 
 PHE   0.015   0.001   PHE D  94 
 TYR   0.017   0.001   TYR F  49 
 ARG   0.006   0.001   ARG L  65 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00038 (    2)
  link_NAG-ASN         : angle       1.56351 (    6)
  link_BETA1-4         : bond        0.00125 (    2)
  link_BETA1-4         : angle       0.78875 (    6)
  hydrogen bonds       : bond        0.03742 (  163)
  hydrogen bonds       : angle       5.88665 (  465)
  SS BOND              : bond        0.00293 (    9)
  SS BOND              : angle       0.77697 (   18)
  covalent geometry    : bond        0.00400 ( 7056)
  covalent geometry    : angle       0.62186 ( 9597)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 192
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   10 GLU cc_start: 0.7824 (pp20) cc_final: 0.7618 (pp20)
REVERT: H   19 LYS cc_start: 0.8953 (tttt) cc_final: 0.8477 (tttp)
REVERT: H   32 TYR cc_start: 0.8770 (m-80) cc_final: 0.8450 (m-10)
REVERT: H   87 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8522 (p)
REVERT: F    4 MET cc_start: 0.8603 (mtp) cc_final: 0.8247 (mmm)
REVERT: F   24 ARG cc_start: 0.8134 (mtp-110) cc_final: 0.7761 (mtp-110)
REVERT: F   45 LYS cc_start: 0.8525 (ptmt) cc_final: 0.8100 (ptpp)
REVERT: F   78 LEU cc_start: 0.8835 (mm) cc_final: 0.8570 (mm)
REVERT: F  105 GLU cc_start: 0.5844 (tt0) cc_final: 0.5479 (tt0)
REVERT: A   19 LYS cc_start: 0.8566 (tptt) cc_final: 0.8322 (tttp)
REVERT: A   23 LYS cc_start: 0.8786 (tttt) cc_final: 0.8284 (ttpp)
REVERT: C   38 ARG cc_start: 0.8532 (ttp80) cc_final: 0.8168 (ttm-80)
REVERT: C  109 LEU cc_start: 0.9135 (mt) cc_final: 0.8890 (mp)
REVERT: E  423 TRP cc_start: 0.8995 (OUTLIER) cc_final: 0.8534 (p-90)
REVERT: E  447 LYS cc_start: 0.8759 (mppt) cc_final: 0.8552 (mtpt)
  outliers start: 32
  outliers final: 17
  residues processed: 209
  average time/residue: 0.2381
  time to fit residues: 62.5306
Evaluate side-chains
  202 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 183
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue  106 THR
Chi-restraints excluded: chain L residue  110 ILE
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   44 SER
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain C residue   62 GLN
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain C residue   89 GLU
Chi-restraints excluded: chain E residue  358 SER
Chi-restraints excluded: chain E residue  404 VAL
Chi-restraints excluded: chain E residue  423 TRP
Chi-restraints excluded: chain E residue  445 HIS
Chi-restraints excluded: chain E residue  475 TYR
Chi-restraints excluded: chain E residue  497 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 71 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  34 HIS
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  90 GLN
D  30 ASN
C  82 HIS
** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.099733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.078498 restraints weight = 12416.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.080808 restraints weight = 7493.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.082358 restraints weight = 5413.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.048   7069  Z= 0.327
  Angle     :  0.715   9.123   9627  Z= 0.375
  Chirality :  0.046   0.303   1037
  Planarity :  0.005   0.055   1224
  Dihedral  :  6.363  54.753   1048
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  5.97 %
    Allowed  : 22.12 %
    Favored  : 71.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.73 (0.27), residues: 859
  helix: -5.01 (0.36), residues: 14
  sheet: -1.41 (0.25), residues: 376
  loop : -2.04 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP E 423 
 HIS   0.007   0.002   HIS L  94 
 PHE   0.024   0.002   PHE D  94 
 TYR   0.024   0.002   TYR F  49 
 ARG   0.010   0.001   ARG L  65 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00345 (    2)
  link_NAG-ASN         : angle       2.30607 (    6)
  link_BETA1-4         : bond        0.00269 (    2)
  link_BETA1-4         : angle       1.12605 (    6)
  hydrogen bonds       : bond        0.04162 (  163)
  hydrogen bonds       : angle       5.97587 (  465)
  SS BOND              : bond        0.00461 (    9)
  SS BOND              : angle       0.72845 (   18)
  covalent geometry    : bond        0.00757 ( 7056)
  covalent geometry    : angle       0.71277 ( 9597)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 185
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   21 ILE cc_start: 0.9042 (mt) cc_final: 0.8823 (mt)
REVERT: H   10 GLU cc_start: 0.7917 (pp20) cc_final: 0.7688 (pp20)
REVERT: H   19 LYS cc_start: 0.8996 (tttt) cc_final: 0.8431 (tttp)
REVERT: H   32 TYR cc_start: 0.8813 (m-80) cc_final: 0.8440 (m-10)
REVERT: H   87 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8484 (p)
REVERT: F    4 MET cc_start: 0.8758 (mtp) cc_final: 0.8346 (mmm)
REVERT: F   24 ARG cc_start: 0.8135 (mtp-110) cc_final: 0.7867 (mtp-110)
REVERT: F   78 LEU cc_start: 0.8859 (mm) cc_final: 0.8605 (mm)
REVERT: F   90 GLN cc_start: 0.8879 (tm130) cc_final: 0.8564 (tm-30)
REVERT: F  105 GLU cc_start: 0.6056 (tt0) cc_final: 0.5723 (tt0)
REVERT: A   23 LYS cc_start: 0.8816 (tttt) cc_final: 0.8258 (ttpp)
REVERT: A   34 MET cc_start: 0.8763 (tpp) cc_final: 0.8234 (ttm)
REVERT: C  109 LEU cc_start: 0.9229 (mt) cc_final: 0.8998 (mp)
REVERT: E  423 TRP cc_start: 0.9121 (OUTLIER) cc_final: 0.8564 (p-90)
REVERT: E  447 LYS cc_start: 0.8808 (mppt) cc_final: 0.8536 (mtpt)
  outliers start: 44
  outliers final: 35
  residues processed: 206
  average time/residue: 0.2265
  time to fit residues: 59.4292
Evaluate side-chains
  214 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 177
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   74 ASP
Chi-restraints excluded: chain L residue   98 ILE
Chi-restraints excluded: chain L residue  106 THR
Chi-restraints excluded: chain L residue  110 ILE
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   77 ASN
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain F residue   73 LEU
Chi-restraints excluded: chain F residue   97 THR
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   18 VAL
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain D residue   49 SER
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   63 SER
Chi-restraints excluded: chain C residue   62 GLN
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain C residue   89 GLU
Chi-restraints excluded: chain C residue  114 GLN
Chi-restraints excluded: chain E residue  388 VAL
Chi-restraints excluded: chain E residue  394 VAL
Chi-restraints excluded: chain E residue  404 VAL
Chi-restraints excluded: chain E residue  405 ILE
Chi-restraints excluded: chain E residue  423 TRP
Chi-restraints excluded: chain E residue  449 ARG
Chi-restraints excluded: chain E residue  467 CYS
Chi-restraints excluded: chain E residue  475 TYR
Chi-restraints excluded: chain E residue  497 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 57 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 75 optimal weight:    0.5980
   chunk 66 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0070
   chunk 28 optimal weight:    0.5980
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.4798

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
** L  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   6 GLN
C  82 HIS
** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.105405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.084389 restraints weight = 12091.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.086841 restraints weight = 7165.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.088481 restraints weight = 5111.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.2997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7069  Z= 0.132
  Angle     :  0.618   9.633   9627  Z= 0.318
  Chirality :  0.044   0.300   1037
  Planarity :  0.005   0.057   1224
  Dihedral  :  6.061  53.066   1048
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 24.97 %
    Favored  : 70.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.38 (0.28), residues: 859
  helix: -4.68 (0.49), residues: 20
  sheet: -1.09 (0.26), residues: 363
  loop : -1.83 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 423 
 HIS   0.002   0.001   HIS L  94 
 PHE   0.014   0.001   PHE E 460 
 TYR   0.016   0.001   TYR F  49 
 ARG   0.011   0.001   ARG L  65 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00070 (    2)
  link_NAG-ASN         : angle       1.37284 (    6)
  link_BETA1-4         : bond        0.00285 (    2)
  link_BETA1-4         : angle       0.77878 (    6)
  hydrogen bonds       : bond        0.03472 (  163)
  hydrogen bonds       : angle       5.58569 (  465)
  SS BOND              : bond        0.00317 (    9)
  SS BOND              : angle       0.51703 (   18)
  covalent geometry    : bond        0.00302 ( 7056)
  covalent geometry    : angle       0.61727 ( 9597)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 196
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 LYS cc_start: 0.8966 (tttt) cc_final: 0.8401 (tttp)
REVERT: H   87 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8487 (p)
REVERT: F    4 MET cc_start: 0.8588 (mtp) cc_final: 0.8094 (mmm)
REVERT: F   24 ARG cc_start: 0.8140 (mtp-110) cc_final: 0.7671 (mtp-110)
REVERT: F   46 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8134 (tt)
REVERT: F   78 LEU cc_start: 0.8831 (mm) cc_final: 0.8565 (mm)
REVERT: F   90 GLN cc_start: 0.8792 (tm130) cc_final: 0.8501 (tm-30)
REVERT: F  105 GLU cc_start: 0.6077 (tt0) cc_final: 0.5781 (tt0)
REVERT: A   23 LYS cc_start: 0.8779 (tttt) cc_final: 0.8267 (ttpp)
REVERT: A   34 MET cc_start: 0.8599 (tpp) cc_final: 0.8184 (ttm)
REVERT: C   38 ARG cc_start: 0.8466 (ttp80) cc_final: 0.8188 (ttm-80)
REVERT: E  423 TRP cc_start: 0.9101 (OUTLIER) cc_final: 0.8494 (p-90)
REVERT: E  447 LYS cc_start: 0.8733 (mppt) cc_final: 0.8502 (mtpt)
  outliers start: 31
  outliers final: 23
  residues processed: 214
  average time/residue: 0.2313
  time to fit residues: 62.4788
Evaluate side-chains
  213 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 187
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   98 ILE
Chi-restraints excluded: chain L residue  106 THR
Chi-restraints excluded: chain L residue  110 ILE
Chi-restraints excluded: chain H residue   44 SER
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   46 LEU
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain F residue   73 LEU
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   30 ASN
Chi-restraints excluded: chain D residue   49 SER
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   63 SER
Chi-restraints excluded: chain C residue   62 GLN
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain C residue   89 GLU
Chi-restraints excluded: chain E residue  404 VAL
Chi-restraints excluded: chain E residue  423 TRP
Chi-restraints excluded: chain E residue  445 HIS
Chi-restraints excluded: chain E residue  467 CYS
Chi-restraints excluded: chain E residue  475 TYR
Chi-restraints excluded: chain E residue  497 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 69 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
** L  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  31 ASN
C  82 HIS
** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.103355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.081158 restraints weight = 12035.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.083707 restraints weight = 7034.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.085433 restraints weight = 4999.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7069  Z= 0.179
  Angle     :  0.648   9.624   9627  Z= 0.332
  Chirality :  0.044   0.295   1037
  Planarity :  0.005   0.071   1224
  Dihedral  :  5.978  50.651   1048
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 26.19 %
    Favored  : 69.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.23 (0.28), residues: 859
  helix: -4.94 (0.39), residues: 14
  sheet: -1.02 (0.26), residues: 364
  loop : -1.74 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP E 423 
 HIS   0.004   0.001   HIS L  94 
 PHE   0.015   0.001   PHE A  64 
 TYR   0.017   0.001   TYR A  32 
 ARG   0.015   0.001   ARG L  65 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00131 (    2)
  link_NAG-ASN         : angle       1.74979 (    6)
  link_BETA1-4         : bond        0.00207 (    2)
  link_BETA1-4         : angle       0.94447 (    6)
  hydrogen bonds       : bond        0.03459 (  163)
  hydrogen bonds       : angle       5.55655 (  465)
  SS BOND              : bond        0.00490 (    9)
  SS BOND              : angle       0.90424 (   18)
  covalent geometry    : bond        0.00417 ( 7056)
  covalent geometry    : angle       0.64561 ( 9597)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 192
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   21 ILE cc_start: 0.8949 (mt) cc_final: 0.8748 (mt)
REVERT: H   19 LYS cc_start: 0.8944 (tttt) cc_final: 0.8367 (tttp)
REVERT: H   32 TYR cc_start: 0.8619 (m-80) cc_final: 0.8322 (m-10)
REVERT: H   67 LYS cc_start: 0.9064 (ptpp) cc_final: 0.8661 (ttmm)
REVERT: H   87 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8486 (p)
REVERT: F    4 MET cc_start: 0.8661 (mtp) cc_final: 0.8126 (mmm)
REVERT: F   24 ARG cc_start: 0.8217 (mtp-110) cc_final: 0.7710 (mtp-110)
REVERT: F   65 SER cc_start: 0.8846 (t) cc_final: 0.8399 (m)
REVERT: F   78 LEU cc_start: 0.8846 (mm) cc_final: 0.8573 (mm)
REVERT: F   90 GLN cc_start: 0.8895 (tm130) cc_final: 0.8532 (tm-30)
REVERT: F  105 GLU cc_start: 0.6268 (tt0) cc_final: 0.5955 (tt0)
REVERT: A   23 LYS cc_start: 0.8782 (tttt) cc_final: 0.8230 (ttpp)
REVERT: A   34 MET cc_start: 0.8702 (tpp) cc_final: 0.8237 (ttm)
REVERT: C   38 ARG cc_start: 0.8493 (ttp80) cc_final: 0.8111 (ttm-80)
REVERT: C  117 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8400 (tt)
REVERT: E  393 ASP cc_start: 0.8868 (p0) cc_final: 0.8426 (p0)
REVERT: E  423 TRP cc_start: 0.9091 (OUTLIER) cc_final: 0.8491 (p-90)
REVERT: E  447 LYS cc_start: 0.8800 (mppt) cc_final: 0.8486 (mtpt)
  outliers start: 32
  outliers final: 24
  residues processed: 211
  average time/residue: 0.2201
  time to fit residues: 59.0673
Evaluate side-chains
  215 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 188
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   98 ILE
Chi-restraints excluded: chain L residue  106 THR
Chi-restraints excluded: chain L residue  110 ILE
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   46 LEU
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain F residue   73 LEU
Chi-restraints excluded: chain F residue   97 THR
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain D residue   49 SER
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   63 SER
Chi-restraints excluded: chain C residue   62 GLN
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain C residue   89 GLU
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain E residue  404 VAL
Chi-restraints excluded: chain E residue  423 TRP
Chi-restraints excluded: chain E residue  445 HIS
Chi-restraints excluded: chain E residue  467 CYS
Chi-restraints excluded: chain E residue  475 TYR
Chi-restraints excluded: chain E residue  497 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 8 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 35 optimal weight:    0.5980
   chunk 38 optimal weight:    0.4980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
** L  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  41 HIS
C  82 HIS
** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.102528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.080293 restraints weight = 12220.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.082843 restraints weight = 7118.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.084548 restraints weight = 5050.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   7069  Z= 0.229
  Angle     :  0.675   9.206   9627  Z= 0.350
  Chirality :  0.045   0.295   1037
  Planarity :  0.005   0.071   1224
  Dihedral  :  6.053  49.906   1048
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 25.92 %
    Favored  : 69.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.29 (0.28), residues: 859
  helix: -4.94 (0.39), residues: 14
  sheet: -1.08 (0.26), residues: 370
  loop : -1.76 (0.28), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP E 423 
 HIS   0.006   0.001   HIS C  41 
 PHE   0.018   0.002   PHE D  94 
 TYR   0.019   0.001   TYR F  49 
 ARG   0.016   0.001   ARG L  65 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00241 (    2)
  link_NAG-ASN         : angle       2.17842 (    6)
  link_BETA1-4         : bond        0.00292 (    2)
  link_BETA1-4         : angle       1.19353 (    6)
  hydrogen bonds       : bond        0.03667 (  163)
  hydrogen bonds       : angle       5.61362 (  465)
  SS BOND              : bond        0.00333 (    9)
  SS BOND              : angle       0.81067 (   18)
  covalent geometry    : bond        0.00531 ( 7056)
  covalent geometry    : angle       0.67209 ( 9597)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 189
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 LYS cc_start: 0.8963 (tttt) cc_final: 0.8376 (tttp)
REVERT: H   87 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8456 (p)
REVERT: F    4 MET cc_start: 0.8698 (mtp) cc_final: 0.8151 (mmm)
REVERT: F   24 ARG cc_start: 0.8224 (mtp-110) cc_final: 0.7812 (mtp-110)
REVERT: F   65 SER cc_start: 0.8830 (t) cc_final: 0.8367 (m)
REVERT: F   78 LEU cc_start: 0.8843 (mm) cc_final: 0.8578 (mm)
REVERT: F   90 GLN cc_start: 0.8942 (tm130) cc_final: 0.8272 (tm130)
REVERT: F  105 GLU cc_start: 0.6276 (tt0) cc_final: 0.5995 (tt0)
REVERT: A   23 LYS cc_start: 0.8832 (tttt) cc_final: 0.8234 (ttpp)
REVERT: A   34 MET cc_start: 0.8755 (tpp) cc_final: 0.8347 (ttm)
REVERT: A   82 GLN cc_start: 0.9003 (mm110) cc_final: 0.8757 (mm-40)
REVERT: C   38 ARG cc_start: 0.8544 (ttp80) cc_final: 0.8124 (ttm-80)
REVERT: C  117 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8444 (tt)
REVERT: E  423 TRP cc_start: 0.9123 (OUTLIER) cc_final: 0.8500 (p-90)
REVERT: E  447 LYS cc_start: 0.8818 (mppt) cc_final: 0.8466 (mtpt)
  outliers start: 36
  outliers final: 29
  residues processed: 209
  average time/residue: 0.2223
  time to fit residues: 59.2319
Evaluate side-chains
  216 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 184
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   74 ASP
Chi-restraints excluded: chain L residue   98 ILE
Chi-restraints excluded: chain L residue  106 THR
Chi-restraints excluded: chain L residue  110 ILE
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   46 LEU
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain F residue   73 LEU
Chi-restraints excluded: chain F residue   97 THR
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain D residue   49 SER
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   63 SER
Chi-restraints excluded: chain C residue   62 GLN
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain C residue   89 GLU
Chi-restraints excluded: chain C residue  114 GLN
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain E residue  404 VAL
Chi-restraints excluded: chain E residue  423 TRP
Chi-restraints excluded: chain E residue  467 CYS
Chi-restraints excluded: chain E residue  475 TYR
Chi-restraints excluded: chain E residue  497 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0970
   chunk 47 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
** L  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 111 GLN
D  31 ASN
C  82 HIS
E 381 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.105191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.083056 restraints weight = 12149.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.085672 restraints weight = 7028.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.087402 restraints weight = 4954.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.3290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7069  Z= 0.150
  Angle     :  0.641  10.192   9627  Z= 0.328
  Chirality :  0.044   0.300   1037
  Planarity :  0.005   0.086   1224
  Dihedral  :  5.897  52.376   1048
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 26.59 %
    Favored  : 68.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.28), residues: 859
  helix: -4.83 (0.35), residues: 20
  sheet: -0.90 (0.27), residues: 368
  loop : -1.70 (0.28), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E 423 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.017   0.001   PHE A  64 
 TYR   0.016   0.001   TYR H  32 
 ARG   0.017   0.001   ARG L  65 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00045 (    2)
  link_NAG-ASN         : angle       1.74802 (    6)
  link_BETA1-4         : bond        0.00324 (    2)
  link_BETA1-4         : angle       0.93824 (    6)
  hydrogen bonds       : bond        0.03351 (  163)
  hydrogen bonds       : angle       5.42619 (  465)
  SS BOND              : bond        0.00329 (    9)
  SS BOND              : angle       0.67886 (   18)
  covalent geometry    : bond        0.00352 ( 7056)
  covalent geometry    : angle       0.63951 ( 9597)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 191
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 LYS cc_start: 0.8941 (tttt) cc_final: 0.8358 (tttp)
REVERT: H   78 THR cc_start: 0.8938 (m) cc_final: 0.8471 (m)
REVERT: H   87 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8520 (p)
REVERT: F    4 MET cc_start: 0.8614 (mtp) cc_final: 0.8156 (mmm)
REVERT: F   24 ARG cc_start: 0.8220 (mtp-110) cc_final: 0.7781 (mtp-110)
REVERT: F   65 SER cc_start: 0.8699 (t) cc_final: 0.8298 (m)
REVERT: F   90 GLN cc_start: 0.8849 (tm130) cc_final: 0.8488 (tm-30)
REVERT: F  105 GLU cc_start: 0.6231 (tt0) cc_final: 0.5978 (tt0)
REVERT: A   23 LYS cc_start: 0.8829 (tttt) cc_final: 0.8268 (ttpp)
REVERT: A   34 MET cc_start: 0.8651 (tpp) cc_final: 0.8204 (ttm)
REVERT: A   82 GLN cc_start: 0.9014 (mm110) cc_final: 0.8734 (mm-40)
REVERT: C   38 ARG cc_start: 0.8455 (ttp80) cc_final: 0.8142 (ttm-80)
REVERT: C   43 LYS cc_start: 0.8264 (mppt) cc_final: 0.7850 (pttt)
REVERT: C  117 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8393 (tt)
REVERT: E  423 TRP cc_start: 0.9102 (OUTLIER) cc_final: 0.8469 (p-90)
REVERT: E  447 LYS cc_start: 0.8778 (mppt) cc_final: 0.8503 (mtpt)
  outliers start: 39
  outliers final: 26
  residues processed: 213
  average time/residue: 0.2183
  time to fit residues: 59.1746
Evaluate side-chains
  220 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 191
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   74 ASP
Chi-restraints excluded: chain L residue   76 THR
Chi-restraints excluded: chain L residue   98 ILE
Chi-restraints excluded: chain L residue  110 ILE
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain F residue   73 LEU
Chi-restraints excluded: chain F residue   97 THR
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   49 SER
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   63 SER
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain C residue   89 GLU
Chi-restraints excluded: chain C residue  114 GLN
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain E residue  404 VAL
Chi-restraints excluded: chain E residue  423 TRP
Chi-restraints excluded: chain E residue  467 CYS
Chi-restraints excluded: chain E residue  475 TYR
Chi-restraints excluded: chain E residue  497 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 74 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 52 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 6 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
** L  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  31 ASN
C  82 HIS
** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.104200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.082093 restraints weight = 12275.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.084669 restraints weight = 7069.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.086388 restraints weight = 4987.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.3334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7069  Z= 0.160
  Angle     :  0.645  10.045   9627  Z= 0.330
  Chirality :  0.044   0.295   1037
  Planarity :  0.005   0.075   1224
  Dihedral  :  5.818  51.432   1048
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 27.14 %
    Favored  : 68.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.28), residues: 859
  helix: -4.83 (0.33), residues: 20
  sheet: -0.85 (0.27), residues: 368
  loop : -1.67 (0.28), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E 423 
 HIS   0.003   0.001   HIS L  94 
 PHE   0.016   0.001   PHE E 460 
 TYR   0.015   0.001   TYR F  49 
 ARG   0.016   0.001   ARG L  65 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00088 (    2)
  link_NAG-ASN         : angle       1.80080 (    6)
  link_BETA1-4         : bond        0.00299 (    2)
  link_BETA1-4         : angle       1.00425 (    6)
  hydrogen bonds       : bond        0.03340 (  163)
  hydrogen bonds       : angle       5.36946 (  465)
  SS BOND              : bond        0.00323 (    9)
  SS BOND              : angle       0.67228 (   18)
  covalent geometry    : bond        0.00374 ( 7056)
  covalent geometry    : angle       0.64343 ( 9597)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 194
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 LYS cc_start: 0.8947 (tttt) cc_final: 0.8374 (tttp)
REVERT: H   78 THR cc_start: 0.8936 (m) cc_final: 0.8465 (m)
REVERT: H   84 ARG cc_start: 0.8537 (ptt-90) cc_final: 0.8307 (ptt-90)
REVERT: H   87 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8514 (p)
REVERT: F    4 MET cc_start: 0.8638 (mtp) cc_final: 0.8167 (mmm)
REVERT: F   24 ARG cc_start: 0.8235 (mtp-110) cc_final: 0.7794 (mtp-110)
REVERT: F   65 SER cc_start: 0.8690 (t) cc_final: 0.8278 (m)
REVERT: F   90 GLN cc_start: 0.8861 (tm130) cc_final: 0.8493 (tm-30)
REVERT: F  105 GLU cc_start: 0.6213 (tt0) cc_final: 0.5965 (tt0)
REVERT: A   23 LYS cc_start: 0.8816 (tttt) cc_final: 0.8239 (ttpp)
REVERT: A   34 MET cc_start: 0.8683 (tpp) cc_final: 0.8464 (ttm)
REVERT: A   82 GLN cc_start: 0.9030 (mm110) cc_final: 0.8758 (mm-40)
REVERT: C   38 ARG cc_start: 0.8455 (ttp80) cc_final: 0.8134 (ttm-80)
REVERT: C   43 LYS cc_start: 0.8319 (mppt) cc_final: 0.7929 (pttt)
REVERT: C  117 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8383 (tt)
REVERT: E  393 ASP cc_start: 0.8847 (p0) cc_final: 0.8451 (p0)
REVERT: E  423 TRP cc_start: 0.9099 (OUTLIER) cc_final: 0.8454 (p-90)
REVERT: E  447 LYS cc_start: 0.8787 (mppt) cc_final: 0.8500 (mtpt)
  outliers start: 34
  outliers final: 28
  residues processed: 213
  average time/residue: 0.2165
  time to fit residues: 59.1825
Evaluate side-chains
  218 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 187
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   41 GLN
Chi-restraints excluded: chain L residue   74 ASP
Chi-restraints excluded: chain L residue   76 THR
Chi-restraints excluded: chain L residue   98 ILE
Chi-restraints excluded: chain L residue  110 ILE
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain F residue    8 THR
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain F residue   73 LEU
Chi-restraints excluded: chain F residue   97 THR
Chi-restraints excluded: chain F residue  106 ILE
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   31 ASN
Chi-restraints excluded: chain D residue   49 SER
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue   63 SER
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain C residue   89 GLU
Chi-restraints excluded: chain C residue  114 GLN
Chi-restraints excluded: chain C residue  117 LEU
Chi-restraints excluded: chain E residue  404 VAL
Chi-restraints excluded: chain E residue  423 TRP
Chi-restraints excluded: chain E residue  467 CYS
Chi-restraints excluded: chain E residue  475 TYR
Chi-restraints excluded: chain E residue  497 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0570
   chunk 61 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 73 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.6500

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
** L  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 111 GLN
D  31 ASN
C  82 HIS
** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.105723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.083789 restraints weight = 12124.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.086395 restraints weight = 6949.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.088166 restraints weight = 4896.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.3397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7069  Z= 0.153
  Angle     :  0.646   9.912   9627  Z= 0.330
  Chirality :  0.044   0.291   1037
  Planarity :  0.006   0.110   1224
  Dihedral  :  5.812  51.703   1048
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 27.27 %
    Favored  : 68.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.08 (0.28), residues: 859
  helix: -4.84 (0.33), residues: 20
  sheet: -0.85 (0.27), residues: 369
  loop : -1.65 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP D  92 
 HIS   0.003   0.001   HIS D  28 
 PHE   0.016   0.001   PHE E 460 
 TYR   0.014   0.001   TYR F  49 
 ARG   0.022   0.001   ARG L  65 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00068 (    2)
  link_NAG-ASN         : angle       1.76724 (    6)
  link_BETA1-4         : bond        0.00284 (    2)
  link_BETA1-4         : angle       0.96735 (    6)
  hydrogen bonds       : bond        0.03312 (  163)
  hydrogen bonds       : angle       5.37131 (  465)
  SS BOND              : bond        0.00316 (    9)
  SS BOND              : angle       0.64920 (   18)
  covalent geometry    : bond        0.00357 ( 7056)
  covalent geometry    : angle       0.64405 ( 9597)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3891.41 seconds
wall clock time: 69 minutes 1.84 seconds (4141.84 seconds total)