Starting phenix.real_space_refine
on Tue Mar  3 16:19:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x7v_33049/03_2026/7x7v_33049.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x7v_33049/03_2026/7x7v_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x7v_33049/03_2026/7x7v_33049.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x7v_33049/03_2026/7x7v_33049.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x7v_33049/03_2026/7x7v_33049.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x7v_33049/03_2026/7x7v_33049.map"
  }
  resolution = 3.83
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.55, per 1000 atoms: 0.23
  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: 0.57
  Conformation dependent library (CDL) restraints added in 236.3 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: 0.25
  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: 1.01

  Time building geometry restraints manager: 0.78 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:             17.450
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.450
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.330
-------------------------------------------------------------------------------
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 : 5.29
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.005   0.001   ARG F  53 
 TYR   0.021   0.002   TYR D  91 
 PHE   0.018   0.002   PHE E 334 
 TRP   0.033   0.002   TRP E 423 
 HIS   0.006   0.001   HIS E 445 

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

*********************** 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  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   49 LYS cc_start: 0.7621 (tttt) cc_final: 0.7407 (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   79 GLU cc_start: 0.7393 (tt0) cc_final: 0.7136 (tt0)
REVERT: F   80 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7837 (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: 0.7767 (t) cc_final: 0.6780 (t)
REVERT: D   79 GLN cc_start: 0.7314 (mp10) cc_final: 0.6445 (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: 0.7252 (tppp)
REVERT: C   43 LYS cc_start: 0.8972 (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: 0.8724 (mppt) cc_final: 0.8042 (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: 0.0976
  time to fit residues: 31.1764
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  : 0.169 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.0870
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0770
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0980
   overall best weight:    0.3316

-------------------------------------------------------------------------------
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 473 ASN
E 479 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.115444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.095559 restraints weight = 11596.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.098014 restraints weight = 6976.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.099673 restraints weight = 4985.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.100730 restraints weight = 3986.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.101357 restraints weight = 3451.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3085
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3085 r_free = 0.3085    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3083
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7069  Z= 0.124
  Angle     :  0.639   9.723   9627  Z= 0.328
  Chirality :  0.045   0.264   1037
  Planarity :  0.006   0.069   1224
  Dihedral  :  6.538  62.325   1049
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 16.55 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.12 (0.26), residues: 859
  helix: -5.14 (0.30), residues: 14
  sheet: -1.65 (0.27), residues: 340
  loop : -2.34 (0.25), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  38 
 TYR   0.016   0.001   TYR E 442 
 PHE   0.018   0.001   PHE E 416 
 TRP   0.013   0.001   TRP E 423 
 HIS   0.003   0.001   HIS L  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 7056)
  covalent geometry    : angle       0.63697 ( 9597)
  SS BOND              : bond        0.00468 (    9)
  SS BOND              : angle       1.08744 (   18)
  hydrogen bonds       : bond        0.04401 (  163)
  hydrogen bonds       : angle       6.80814 (  465)
  link_BETA1-4         : bond        0.00085 (    2)
  link_BETA1-4         : angle       0.92936 (    6)
  link_NAG-ASN         : bond        0.00280 (    2)
  link_NAG-ASN         : angle       1.33680 (    6)

*********************** 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
  247 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 223
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 LYS cc_start: 0.8826 (tttt) cc_final: 0.8360 (tttp)
REVERT: H   32 TYR cc_start: 0.8678 (m-80) cc_final: 0.8372 (m-10)
REVERT: H   87 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8585 (p)
REVERT: F    4 MET cc_start: 0.8432 (mtp) cc_final: 0.7903 (mtp)
REVERT: F   24 ARG cc_start: 0.8034 (mtp-110) cc_final: 0.7670 (mtp-110)
REVERT: F   45 LYS cc_start: 0.8516 (ptmt) cc_final: 0.8174 (ptpp)
REVERT: F   70 ASP cc_start: 0.8689 (m-30) cc_final: 0.8141 (m-30)
REVERT: F   78 LEU cc_start: 0.8843 (mm) cc_final: 0.8530 (mm)
REVERT: A   23 LYS cc_start: 0.8779 (tptt) cc_final: 0.8259 (ttpp)
REVERT: A   43 GLN cc_start: 0.8346 (mp10) cc_final: 0.7909 (mp10)
REVERT: A   82 GLN cc_start: 0.7998 (tt0) cc_final: 0.7691 (tt0)
REVERT: E  351 ASP cc_start: 0.8370 (p0) cc_final: 0.8062 (t0)
REVERT: E  447 LYS cc_start: 0.8662 (mppt) cc_final: 0.8404 (mtpt)
  outliers start: 24
  outliers final: 11
  residues processed: 232
  average time/residue: 0.0893
  time to fit residues: 26.5779
Evaluate side-chains
  207 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 195
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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  468 THR
Chi-restraints excluded: chain E residue  475 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 8 optimal weight:    0.4980
   chunk 2 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
D  30 ASN
D  79 GLN
C   6 GLN
** 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 = 0.3175 r_free = 0.3175 target = 0.105768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.084385 restraints weight = 12086.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.086917 restraints weight = 7116.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.088523 restraints weight = 5066.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.089619 restraints weight = 4090.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.090273 restraints weight = 3549.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2983
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2983 r_free = 0.2983    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2983 r_free = 0.2983    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2983
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7069  Z= 0.173
  Angle     :  0.638   9.803   9627  Z= 0.330
  Chirality :  0.044   0.229   1037
  Planarity :  0.005   0.057   1224
  Dihedral  :  6.215  57.171   1048
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 19.27 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.68 (0.27), residues: 859
  helix: -5.03 (0.36), residues: 14
  sheet: -1.33 (0.27), residues: 352
  loop : -2.05 (0.26), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  38 
 TYR   0.016   0.001   TYR C  60 
 PHE   0.015   0.001   PHE D  94 
 TRP   0.017   0.001   TRP E 423 
 HIS   0.004   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 7056)
  covalent geometry    : angle       0.63561 ( 9597)
  SS BOND              : bond        0.00864 (    9)
  SS BOND              : angle       1.16659 (   18)
  hydrogen bonds       : bond        0.03974 (  163)
  hydrogen bonds       : angle       6.15638 (  465)
  link_BETA1-4         : bond        0.00196 (    2)
  link_BETA1-4         : angle       0.86520 (    6)
  link_NAG-ASN         : bond        0.00084 (    2)
  link_NAG-ASN         : angle       1.50918 (    6)

*********************** 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
  230 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 200
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 LYS cc_start: 0.8886 (tttt) cc_final: 0.8304 (tttp)
REVERT: H   32 TYR cc_start: 0.8738 (m-80) cc_final: 0.8451 (m-10)
REVERT: H   71 THR cc_start: 0.7919 (m) cc_final: 0.7562 (p)
REVERT: H   87 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8552 (p)
REVERT: F    4 MET cc_start: 0.8566 (mtp) cc_final: 0.8205 (mmm)
REVERT: F   45 LYS cc_start: 0.8508 (ptmt) cc_final: 0.8087 (ptpp)
REVERT: F   65 SER cc_start: 0.8713 (t) cc_final: 0.8366 (m)
REVERT: F   78 LEU cc_start: 0.8830 (mm) cc_final: 0.8605 (mm)
REVERT: F   90 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8131 (tm-30)
REVERT: A   23 LYS cc_start: 0.8787 (tttt) cc_final: 0.8260 (ttpp)
REVERT: E  447 LYS cc_start: 0.8735 (mppt) cc_final: 0.8530 (mtpt)
  outliers start: 30
  outliers final: 17
  residues processed: 211
  average time/residue: 0.0915
  time to fit residues: 24.7192
Evaluate side-chains
  200 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 182
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   13 VAL
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   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  358 SER
Chi-restraints excluded: chain E residue  392 ASP
Chi-restraints excluded: chain E residue  404 VAL
Chi-restraints excluded: chain E residue  405 ILE
Chi-restraints excluded: chain E residue  445 HIS
Chi-restraints excluded: chain E residue  475 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 10 optimal weight:    0.4980
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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**
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  30 ASN
C  82 HIS
E 381 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.103810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.082371 restraints weight = 12223.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.084839 restraints weight = 7215.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.086456 restraints weight = 5156.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.087544 restraints weight = 4148.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.088165 restraints weight = 3599.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.2572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   7069  Z= 0.210
  Angle     :  0.644   8.695   9627  Z= 0.334
  Chirality :  0.044   0.212   1037
  Planarity :  0.005   0.062   1224
  Dihedral  :  6.146  54.527   1048
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 21.30 %
    Favored  : 74.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.54 (0.27), residues: 859
  helix: -4.92 (0.41), residues: 14
  sheet: -1.29 (0.26), residues: 369
  loop : -1.90 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  38 
 TYR   0.018   0.001   TYR F  49 
 PHE   0.018   0.001   PHE D  94 
 TRP   0.018   0.001   TRP E 423 
 HIS   0.005   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 7056)
  covalent geometry    : angle       0.64197 ( 9597)
  SS BOND              : bond        0.00292 (    9)
  SS BOND              : angle       0.92784 (   18)
  hydrogen bonds       : bond        0.03882 (  163)
  hydrogen bonds       : angle       5.94332 (  465)
  link_BETA1-4         : bond        0.00265 (    2)
  link_BETA1-4         : angle       0.94208 (    6)
  link_NAG-ASN         : bond        0.00066 (    2)
  link_NAG-ASN         : angle       1.68198 (    6)

*********************** 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
  218 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 184
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 LYS cc_start: 0.8953 (tttt) cc_final: 0.8330 (tttp)
REVERT: H   32 TYR cc_start: 0.8768 (m-80) cc_final: 0.8451 (m-10)
REVERT: H   71 THR cc_start: 0.8052 (m) cc_final: 0.7707 (p)
REVERT: H   87 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8547 (p)
REVERT: F    4 MET cc_start: 0.8626 (mtp) cc_final: 0.8189 (mmm)
REVERT: F   24 ARG cc_start: 0.8222 (mtp-110) cc_final: 0.8021 (ttt90)
REVERT: F   45 LYS cc_start: 0.8527 (ptmt) cc_final: 0.8126 (ptpp)
REVERT: F   65 SER cc_start: 0.8755 (t) cc_final: 0.8364 (m)
REVERT: F   78 LEU cc_start: 0.8848 (mm) cc_final: 0.8575 (mm)
REVERT: F   90 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8293 (tm-30)
REVERT: F  105 GLU cc_start: 0.5882 (tt0) cc_final: 0.5531 (tt0)
REVERT: A   19 LYS cc_start: 0.8535 (tptt) cc_final: 0.8144 (tttp)
REVERT: A   23 LYS cc_start: 0.8768 (tttt) cc_final: 0.8266 (ttpp)
REVERT: A   82 GLN cc_start: 0.8732 (tp40) cc_final: 0.8393 (mm110)
REVERT: C   38 ARG cc_start: 0.8572 (ttp80) cc_final: 0.8097 (ttm-80)
REVERT: C  109 LEU cc_start: 0.9176 (mt) cc_final: 0.8954 (mp)
REVERT: E  447 LYS cc_start: 0.8752 (mppt) cc_final: 0.8549 (mtpt)
  outliers start: 34
  outliers final: 20
  residues processed: 201
  average time/residue: 0.0991
  time to fit residues: 25.2026
Evaluate side-chains
  204 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 183
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
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 A residue   17 SER
Chi-restraints excluded: chain A residue   81 ILE
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 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  405 ILE
Chi-restraints excluded: chain E residue  475 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 53 optimal weight:    0.1980
   chunk 76 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 11 optimal weight:    0.1980
   chunk 68 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
H  39 GLN
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3169 r_free = 0.3169 target = 0.105200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.083848 restraints weight = 12174.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.086390 restraints weight = 7097.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.088064 restraints weight = 5018.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.089012 restraints weight = 4015.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.089812 restraints weight = 3503.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7069  Z= 0.134
  Angle     :  0.600   8.644   9627  Z= 0.309
  Chirality :  0.044   0.302   1037
  Planarity :  0.005   0.052   1224
  Dihedral  :  5.936  52.649   1048
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 23.88 %
    Favored  : 73.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.27 (0.28), residues: 859
  helix: -4.93 (0.40), residues: 14
  sheet: -0.98 (0.28), residues: 351
  loop : -1.83 (0.27), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG L  65 
 TYR   0.014   0.001   TYR F  49 
 PHE   0.014   0.001   PHE A  64 
 TRP   0.013   0.001   TRP E 423 
 HIS   0.002   0.001   HIS L  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7056)
  covalent geometry    : angle       0.59823 ( 9597)
  SS BOND              : bond        0.00323 (    9)
  SS BOND              : angle       1.01536 (   18)
  hydrogen bonds       : bond        0.03431 (  163)
  hydrogen bonds       : angle       5.50985 (  465)
  link_BETA1-4         : bond        0.00277 (    2)
  link_BETA1-4         : angle       0.79745 (    6)
  link_NAG-ASN         : bond        0.00073 (    2)
  link_NAG-ASN         : angle       1.36259 (    6)

*********************** 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
  219 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 196
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 LYS cc_start: 0.8917 (tttt) cc_final: 0.8351 (tttp)
REVERT: H   32 TYR cc_start: 0.8741 (m-80) cc_final: 0.8421 (m-10)
REVERT: H   71 THR cc_start: 0.7985 (m) cc_final: 0.7631 (p)
REVERT: H   87 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8474 (p)
REVERT: F    4 MET cc_start: 0.8529 (mtp) cc_final: 0.8248 (mmm)
REVERT: F   24 ARG cc_start: 0.8197 (mtp-110) cc_final: 0.7784 (mtp-110)
REVERT: F   45 LYS cc_start: 0.8505 (ptmt) cc_final: 0.8066 (ptpp)
REVERT: F   46 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8042 (tt)
REVERT: F   61 ARG cc_start: 0.8447 (ptp90) cc_final: 0.8117 (mtm-85)
REVERT: F   65 SER cc_start: 0.8706 (t) cc_final: 0.8382 (m)
REVERT: F   78 LEU cc_start: 0.8811 (mm) cc_final: 0.8551 (mm)
REVERT: F  105 GLU cc_start: 0.6091 (tt0) cc_final: 0.5723 (tt0)
REVERT: A   19 LYS cc_start: 0.8552 (tptt) cc_final: 0.8293 (tttp)
REVERT: A   23 LYS cc_start: 0.8761 (tttt) cc_final: 0.8302 (ttpp)
REVERT: A   34 MET cc_start: 0.8730 (tpp) cc_final: 0.8119 (ttm)
REVERT: C   38 ARG cc_start: 0.8497 (ttp80) cc_final: 0.8072 (ttm-80)
REVERT: C  109 LEU cc_start: 0.9169 (mt) cc_final: 0.8936 (mp)
REVERT: C  114 GLN cc_start: 0.8449 (pm20) cc_final: 0.8234 (pm20)
  outliers start: 23
  outliers final: 13
  residues processed: 206
  average time/residue: 0.0994
  time to fit residues: 25.9572
Evaluate side-chains
  194 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 179
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain F residue   46 LEU
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain D residue   58 VAL
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  445 HIS
Chi-restraints excluded: chain E residue  475 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 49 optimal weight:    0.3980
   chunk 51 optimal weight:    2.9990
   chunk 78 optimal weight:    0.4980
   chunk 48 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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**
H   5 GLN
H  39 GLN
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  90 GLN
D  30 ASN
C  82 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.105457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.083074 restraints weight = 12104.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.085692 restraints weight = 6965.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.087435 restraints weight = 4923.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.088524 restraints weight = 3932.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.089201 restraints weight = 3414.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.3013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7069  Z= 0.147
  Angle     :  0.621   8.547   9627  Z= 0.317
  Chirality :  0.043   0.277   1037
  Planarity :  0.005   0.057   1224
  Dihedral  :  5.815  51.585   1048
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.20 (0.28), residues: 859
  helix: -4.80 (0.50), residues: 14
  sheet: -0.98 (0.26), residues: 368
  loop : -1.74 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  65 
 TYR   0.014   0.001   TYR F  49 
 PHE   0.013   0.001   PHE A  64 
 TRP   0.014   0.001   TRP A 109 
 HIS   0.003   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 7056)
  covalent geometry    : angle       0.61897 ( 9597)
  SS BOND              : bond        0.00306 (    9)
  SS BOND              : angle       0.97165 (   18)
  hydrogen bonds       : bond        0.03308 (  163)
  hydrogen bonds       : angle       5.36379 (  465)
  link_BETA1-4         : bond        0.00310 (    2)
  link_BETA1-4         : angle       0.93091 (    6)
  link_NAG-ASN         : bond        0.00054 (    2)
  link_NAG-ASN         : angle       1.45179 (    6)

*********************** 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
  215 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 184
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   58 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6754 (pp)
REVERT: L   65 ARG cc_start: 0.9126 (mtm180) cc_final: 0.8588 (ptt-90)
REVERT: H   19 LYS cc_start: 0.8947 (tttt) cc_final: 0.8364 (tttp)
REVERT: H   32 TYR cc_start: 0.8759 (m-80) cc_final: 0.8428 (m-10)
REVERT: H   67 LYS cc_start: 0.9022 (ptpp) cc_final: 0.8632 (ttmm)
REVERT: H   71 THR cc_start: 0.8004 (m) cc_final: 0.7649 (p)
REVERT: H   87 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8459 (p)
REVERT: F    4 MET cc_start: 0.8584 (mtp) cc_final: 0.8286 (mmm)
REVERT: F   24 ARG cc_start: 0.8267 (mtp-110) cc_final: 0.7853 (mtp-110)
REVERT: F   65 SER cc_start: 0.8748 (t) cc_final: 0.8344 (m)
REVERT: F   78 LEU cc_start: 0.8794 (mm) cc_final: 0.8515 (mm)
REVERT: F  105 GLU cc_start: 0.6077 (tt0) cc_final: 0.5728 (tt0)
REVERT: A   23 LYS cc_start: 0.8718 (tttt) cc_final: 0.8195 (ttpp)
REVERT: A   34 MET cc_start: 0.8784 (tpp) cc_final: 0.8518 (tpp)
REVERT: C   38 ARG cc_start: 0.8508 (ttp80) cc_final: 0.8024 (ttm-80)
REVERT: C  117 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8456 (tt)
REVERT: E  423 TRP cc_start: 0.9018 (OUTLIER) cc_final: 0.8488 (p-90)
  outliers start: 31
  outliers final: 20
  residues processed: 202
  average time/residue: 0.0876
  time to fit residues: 22.7122
Evaluate side-chains
  207 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 183
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   41 GLN
Chi-restraints excluded: chain L residue   58 LEU
Chi-restraints excluded: chain L residue   98 ILE
Chi-restraints excluded: chain H residue    5 GLN
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 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 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  447 LYS
Chi-restraints excluded: chain E residue  475 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 80 optimal weight:    0.2980
   chunk 36 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0010
   chunk 35 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.6188

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
H   5 GLN
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  90 GLN
C  82 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.106232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.084031 restraints weight = 12028.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.086650 restraints weight = 6875.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.088402 restraints weight = 4841.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.089421 restraints weight = 3859.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.090215 restraints weight = 3359.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.3138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7069  Z= 0.145
  Angle     :  0.626   8.965   9627  Z= 0.318
  Chirality :  0.043   0.276   1037
  Planarity :  0.005   0.050   1224
  Dihedral  :  5.742  51.774   1048
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 24.56 %
    Favored  : 70.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.16 (0.28), residues: 859
  helix: -4.80 (0.50), residues: 14
  sheet: -0.99 (0.26), residues: 367
  loop : -1.68 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 426 
 TYR   0.014   0.001   TYR F  49 
 PHE   0.013   0.001   PHE A  64 
 TRP   0.034   0.001   TRP A 109 
 HIS   0.003   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 7056)
  covalent geometry    : angle       0.62458 ( 9597)
  SS BOND              : bond        0.00285 (    9)
  SS BOND              : angle       0.89362 (   18)
  hydrogen bonds       : bond        0.03289 (  163)
  hydrogen bonds       : angle       5.29524 (  465)
  link_BETA1-4         : bond        0.00274 (    2)
  link_BETA1-4         : angle       0.89746 (    6)
  link_NAG-ASN         : bond        0.00040 (    2)
  link_NAG-ASN         : angle       1.45671 (    6)

*********************** 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
  227 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 191
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   65 ARG cc_start: 0.9137 (mtm180) cc_final: 0.8666 (ptt-90)
REVERT: H   19 LYS cc_start: 0.8934 (tttt) cc_final: 0.8524 (tttm)
REVERT: H   67 LYS cc_start: 0.9014 (ptpp) cc_final: 0.8631 (ttmm)
REVERT: H   71 THR cc_start: 0.8015 (m) cc_final: 0.7665 (p)
REVERT: H   87 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8451 (p)
REVERT: F    4 MET cc_start: 0.8580 (mtp) cc_final: 0.8288 (mmm)
REVERT: F   24 ARG cc_start: 0.8263 (mtp-110) cc_final: 0.7836 (mtp-110)
REVERT: F   65 SER cc_start: 0.8736 (t) cc_final: 0.8339 (m)
REVERT: F   78 LEU cc_start: 0.8779 (mm) cc_final: 0.8478 (mm)
REVERT: F  105 GLU cc_start: 0.6112 (tt0) cc_final: 0.5796 (tt0)
REVERT: A   19 LYS cc_start: 0.8478 (tttp) cc_final: 0.7985 (tptt)
REVERT: A   23 LYS cc_start: 0.8711 (tttt) cc_final: 0.8198 (ttpp)
REVERT: A   34 MET cc_start: 0.8776 (tpp) cc_final: 0.8507 (tpp)
REVERT: A   82 GLN cc_start: 0.9021 (mm110) cc_final: 0.8373 (mm110)
REVERT: C   38 ARG cc_start: 0.8463 (ttp80) cc_final: 0.8009 (ttm-80)
REVERT: C  117 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8456 (tt)
REVERT: E  423 TRP cc_start: 0.9035 (OUTLIER) cc_final: 0.8450 (p-90)
  outliers start: 36
  outliers final: 23
  residues processed: 211
  average time/residue: 0.0909
  time to fit residues: 24.5233
Evaluate side-chains
  209 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 183
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   41 GLN
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   97 THR
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   81 ILE
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 C residue    5 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  358 SER
Chi-restraints excluded: chain E residue  404 VAL
Chi-restraints excluded: chain E residue  423 TRP
Chi-restraints excluded: chain E residue  447 LYS
Chi-restraints excluded: chain E residue  475 TYR
Chi-restraints excluded: chain E residue  489 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 55 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0970
   chunk 16 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
H   5 GLN
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  90 GLN
D  31 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.106417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.084259 restraints weight = 12056.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.086882 restraints weight = 6915.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.088616 restraints weight = 4880.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.089636 restraints weight = 3898.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.090462 restraints weight = 3393.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.3262

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= 0.161
  Angle     :  0.633   9.487   9627  Z= 0.322
  Chirality :  0.044   0.278   1037
  Planarity :  0.005   0.050   1224
  Dihedral  :  5.693  51.307   1048
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 24.83 %
    Favored  : 70.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.12 (0.28), residues: 859
  helix: -4.85 (0.46), residues: 14
  sheet: -0.97 (0.27), residues: 363
  loop : -1.65 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 449 
 TYR   0.014   0.001   TYR F  49 
 PHE   0.016   0.001   PHE A  64 
 TRP   0.054   0.002   TRP A 109 
 HIS   0.003   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 7056)
  covalent geometry    : angle       0.63078 ( 9597)
  SS BOND              : bond        0.00290 (    9)
  SS BOND              : angle       0.84295 (   18)
  hydrogen bonds       : bond        0.03302 (  163)
  hydrogen bonds       : angle       5.30217 (  465)
  link_BETA1-4         : bond        0.00320 (    2)
  link_BETA1-4         : angle       0.90469 (    6)
  link_NAG-ASN         : bond        0.00062 (    2)
  link_NAG-ASN         : angle       1.59888 (    6)

*********************** 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
  220 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 187
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   65 ARG cc_start: 0.9114 (mtm180) cc_final: 0.8679 (ptt-90)
REVERT: H   19 LYS cc_start: 0.8934 (tttt) cc_final: 0.8533 (tttm)
REVERT: H   67 LYS cc_start: 0.8996 (ptpp) cc_final: 0.8641 (ttmm)
REVERT: H   71 THR cc_start: 0.8060 (m) cc_final: 0.7716 (p)
REVERT: H   87 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8497 (p)
REVERT: F    4 MET cc_start: 0.8523 (mtp) cc_final: 0.8208 (mmm)
REVERT: F   24 ARG cc_start: 0.8244 (mtp-110) cc_final: 0.7790 (ttt90)
REVERT: F   46 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8012 (tt)
REVERT: F   65 SER cc_start: 0.8694 (t) cc_final: 0.8288 (m)
REVERT: F   90 GLN cc_start: 0.8579 (tm130) cc_final: 0.8354 (tm-30)
REVERT: F  105 GLU cc_start: 0.6257 (tt0) cc_final: 0.5975 (tt0)
REVERT: A   19 LYS cc_start: 0.8493 (tttp) cc_final: 0.7952 (tptt)
REVERT: A   23 LYS cc_start: 0.8746 (tttt) cc_final: 0.8250 (ttpp)
REVERT: A   82 GLN cc_start: 0.8987 (mm110) cc_final: 0.8339 (mm110)
REVERT: C   38 ARG cc_start: 0.8476 (ttp80) cc_final: 0.8067 (ttm-80)
REVERT: C  117 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8481 (tt)
REVERT: E  423 TRP cc_start: 0.9063 (OUTLIER) cc_final: 0.8380 (p-90)
  outliers start: 33
  outliers final: 24
  residues processed: 204
  average time/residue: 0.0959
  time to fit residues: 25.0197
Evaluate side-chains
  215 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 187
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   41 GLN
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   46 LEU
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain F residue   97 THR
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   81 ILE
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 C residue    5 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  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  447 LYS
Chi-restraints excluded: chain E residue  475 TYR
Chi-restraints excluded: chain E residue  489 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0070
   chunk 15 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 1 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 111 GLN
C  82 HIS
C 114 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.106428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.084147 restraints weight = 12030.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.086818 restraints weight = 6863.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.088609 restraints weight = 4801.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.089618 restraints weight = 3813.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.090359 restraints weight = 3316.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.3364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7069  Z= 0.140
  Angle     :  0.629   8.563   9627  Z= 0.320
  Chirality :  0.044   0.280   1037
  Planarity :  0.005   0.051   1224
  Dihedral  :  5.629  52.076   1048
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 25.37 %
    Favored  : 70.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.07 (0.28), residues: 859
  helix: -5.09 (0.29), residues: 20
  sheet: -0.87 (0.27), residues: 364
  loop : -1.60 (0.28), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 426 
 TYR   0.014   0.001   TYR F  49 
 PHE   0.016   0.001   PHE E 460 
 TRP   0.060   0.002   TRP A 109 
 HIS   0.002   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 7056)
  covalent geometry    : angle       0.62763 ( 9597)
  SS BOND              : bond        0.00303 (    9)
  SS BOND              : angle       0.79113 (   18)
  hydrogen bonds       : bond        0.03244 (  163)
  hydrogen bonds       : angle       5.27310 (  465)
  link_BETA1-4         : bond        0.00298 (    2)
  link_BETA1-4         : angle       0.88344 (    6)
  link_NAG-ASN         : bond        0.00048 (    2)
  link_NAG-ASN         : angle       1.51365 (    6)

*********************** 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
  215 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 183
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   65 ARG cc_start: 0.9120 (mtm180) cc_final: 0.8685 (ptt-90)
REVERT: H   19 LYS cc_start: 0.8939 (tttt) cc_final: 0.8530 (tttm)
REVERT: H   67 LYS cc_start: 0.8995 (ptpp) cc_final: 0.8687 (ttmm)
REVERT: H   71 THR cc_start: 0.8083 (m) cc_final: 0.7723 (p)
REVERT: H   87 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8454 (p)
REVERT: F    4 MET cc_start: 0.8482 (mtp) cc_final: 0.8175 (mmm)
REVERT: F   24 ARG cc_start: 0.8197 (mtp-110) cc_final: 0.7805 (ttt90)
REVERT: F   46 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7938 (tt)
REVERT: F   65 SER cc_start: 0.8686 (t) cc_final: 0.8285 (m)
REVERT: F  105 GLU cc_start: 0.6239 (tt0) cc_final: 0.5980 (tt0)
REVERT: A   23 LYS cc_start: 0.8736 (tttt) cc_final: 0.8241 (ttpp)
REVERT: A   34 MET cc_start: 0.8717 (tpp) cc_final: 0.8108 (ttm)
REVERT: A   58 THR cc_start: 0.9307 (p) cc_final: 0.9085 (t)
REVERT: A  108 TYR cc_start: 0.8728 (m-80) cc_final: 0.8509 (m-80)
REVERT: C   34 MET cc_start: 0.8880 (tpp) cc_final: 0.8633 (tpp)
REVERT: C   38 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8079 (ttm-80)
REVERT: C  117 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8440 (tt)
REVERT: E  423 TRP cc_start: 0.9046 (OUTLIER) cc_final: 0.8360 (p-90)
  outliers start: 32
  outliers final: 23
  residues processed: 201
  average time/residue: 0.0875
  time to fit residues: 22.8278
Evaluate side-chains
  202 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 175
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   41 GLN
Chi-restraints excluded: chain L residue   74 ASP
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   46 LEU
Chi-restraints excluded: chain F residue   48 ILE
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   19 VAL
Chi-restraints excluded: chain D residue   58 VAL
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  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  447 LYS
Chi-restraints excluded: chain E residue  475 TYR
Chi-restraints excluded: chain E residue  489 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 13 optimal weight:    0.2980
   chunk 45 optimal weight:    0.3980
   chunk 5 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
H  39 GLN
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  90 GLN
A 111 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.121681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.099417 restraints weight = 11987.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.102503 restraints weight = 6602.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.104552 restraints weight = 4565.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.105904 restraints weight = 3602.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.106803 restraints weight = 3076.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.3398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7069  Z= 0.213
  Angle     :  0.678  10.216   9627  Z= 0.348
  Chirality :  0.045   0.281   1037
  Planarity :  0.005   0.050   1224
  Dihedral  :  5.722  50.246   1048
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 25.51 %
    Favored  : 70.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.16 (0.28), residues: 859
  helix: -5.13 (0.27), residues: 20
  sheet: -0.92 (0.27), residues: 365
  loop : -1.67 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 426 
 TYR   0.017   0.001   TYR F  49 
 PHE   0.017   0.001   PHE D  94 
 TRP   0.069   0.002   TRP A 109 
 HIS   0.004   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 7056)
  covalent geometry    : angle       0.67605 ( 9597)
  SS BOND              : bond        0.00309 (    9)
  SS BOND              : angle       0.87608 (   18)
  hydrogen bonds       : bond        0.03479 (  163)
  hydrogen bonds       : angle       5.39083 (  465)
  link_BETA1-4         : bond        0.00238 (    2)
  link_BETA1-4         : angle       0.98423 (    6)
  link_NAG-ASN         : bond        0.00109 (    2)
  link_NAG-ASN         : angle       1.82008 (    6)

********************** 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
  208 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 176
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   65 ARG cc_start: 0.9072 (mtm180) cc_final: 0.8657 (ptt-90)
REVERT: H   19 LYS cc_start: 0.8942 (tttt) cc_final: 0.8409 (tttp)
REVERT: H   67 LYS cc_start: 0.8992 (ptpp) cc_final: 0.8693 (ttmm)
REVERT: H   87 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8523 (p)
REVERT: F    4 MET cc_start: 0.8525 (mtp) cc_final: 0.8205 (mmm)
REVERT: F   24 ARG cc_start: 0.8148 (mtp-110) cc_final: 0.7787 (ttt90)
REVERT: F   46 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8078 (tt)
REVERT: F   65 SER cc_start: 0.8683 (t) cc_final: 0.8265 (m)
REVERT: F   78 LEU cc_start: 0.8779 (mm) cc_final: 0.8520 (mm)
REVERT: F  105 GLU cc_start: 0.6234 (tt0) cc_final: 0.5971 (tt0)
REVERT: A   23 LYS cc_start: 0.8801 (tttt) cc_final: 0.8276 (ttpp)
REVERT: A   34 MET cc_start: 0.8735 (tpp) cc_final: 0.8118 (ttm)
REVERT: A   82 GLN cc_start: 0.9088 (mm110) cc_final: 0.8869 (mm110)
REVERT: C   38 ARG cc_start: 0.8488 (ttp80) cc_final: 0.8126 (ttm-80)
REVERT: C  117 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8437 (tt)
REVERT: E  423 TRP cc_start: 0.9093 (OUTLIER) cc_final: 0.8375 (p-90)
  outliers start: 32
  outliers final: 21
  residues processed: 192
  average time/residue: 0.0937
  time to fit residues: 23.0940
Evaluate side-chains
  201 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 176
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   74 ASP
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   46 LEU
Chi-restraints excluded: chain F residue   48 ILE
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   19 VAL
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  106 ILE
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  358 SER
Chi-restraints excluded: chain E residue  404 VAL
Chi-restraints excluded: chain E residue  423 TRP
Chi-restraints excluded: chain E residue  447 LYS
Chi-restraints excluded: chain E residue  475 TYR
Chi-restraints excluded: chain E residue  489 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
H  39 GLN
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  90 GLN
A 111 GLN
D  31 ASN
** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.122078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.099746 restraints weight = 12054.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.102910 restraints weight = 6645.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.104989 restraints weight = 4568.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.106284 restraints weight = 3595.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.107206 restraints weight = 3081.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.3454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7069  Z= 0.183
  Angle     :  0.667   8.929   9627  Z= 0.341
  Chirality :  0.045   0.287   1037
  Planarity :  0.005   0.050   1224
  Dihedral  :  5.732  51.267   1048
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 25.64 %
    Favored  : 70.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.14 (0.28), residues: 859
  helix: -5.16 (0.25), residues: 20
  sheet: -0.93 (0.27), residues: 364
  loop : -1.63 (0.28), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 426 
 TYR   0.018   0.001   TYR H  32 
 PHE   0.014   0.001   PHE D  94 
 TRP   0.059   0.002   TRP A 109 
 HIS   0.003   0.001   HIS L  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 7056)
  covalent geometry    : angle       0.66464 ( 9597)
  SS BOND              : bond        0.00295 (    9)
  SS BOND              : angle       0.82238 (   18)
  hydrogen bonds       : bond        0.03407 (  163)
  hydrogen bonds       : angle       5.36978 (  465)
  link_BETA1-4         : bond        0.00272 (    2)
  link_BETA1-4         : angle       1.01088 (    6)
  link_NAG-ASN         : bond        0.00100 (    2)
  link_NAG-ASN         : angle       1.83478 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1557.47 seconds
wall clock time: 27 minutes 33.92 seconds (1653.92 seconds total)