Starting phenix.real_space_refine
on Thu Jul  2 05:41:15 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7x7v_33049/07_2026/7x7v_33049.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x7v_33049/07_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 {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7x7v_33049/07_2026/7x7v_33049.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7x7v_33049/07_2026/7x7v_33049.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x7v_33049/07_2026/7x7v_33049.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x7v_33049/07_2026/7x7v_33049.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x7v_33049/07_2026/7x7v_33049.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x7v_33049/07_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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 chiralities: 2
  Time building chain proxies: 1.54, per 1000 atoms: 0.22
  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: 0.63
  Conformation dependent library (CDL) restraints added in 554.2 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: 0.21
  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: 1.09

  Time building geometry restraints manager: 0.86 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: 3584
       16.99 -    33.98: 399
       33.98 -    50.97: 76
       50.97 -    67.96: 9
       67.96 -    84.94: 3
  Dihedral angle restraints: 4071
    sinusoidal: 1555
      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 4068 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:             21.740
  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:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.780
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7057
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  : 14.025  84.945   2458
  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/Z
  covalent geometry    : bond        0.00649 /  0.32 ( 7056)
  covalent geometry    : angle       0.97542 /  0.56 ( 9597)
  SS BOND              : bond        0.01805 /  0.95 (    9)
  SS BOND              : angle       3.73054 /  1.98 (   18)
  hydrogen bonds       : bond        0.29188 / 19.03 (  163)
  hydrogen bonds       : angle      10.55274 /  7.24 (  465)
  link_BETA1-4         : bond        0.00198 /  0.10 (    2)
  link_BETA1-4         : angle       1.04723 /  0.49 (    6)
  link_NAG-ASN         : bond        0.00382 /  0.19 (    2)
  link_NAG-ASN         : angle       2.24054 /  1.79 (    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  : 0.160 
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: 0.0949
  time to fit residues: 30.0545
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  : 0.170 
-------------------------------------------------------------------------------
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...
** 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 = 0.3305 r_free = 0.3305 target = 0.115194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.094617 restraints weight = 11612.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.097278 restraints weight = 6599.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.099045 restraints weight = 4609.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.100226 restraints weight = 3645.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.100914 restraints weight = 3121.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3020
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3020 r_free = 0.3020    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3019 r_free = 0.3019    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (9 function evaluations)
r_final: 0.3019
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7069  Z= 0.127
  Angle     :  0.642   9.856   9627  Z= 0.330
  Chirality :  0.045   0.254   1037
  Planarity :  0.006   0.069   1224
  Dihedral  :  6.345  62.458    965
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 16.82 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.14 (0.26), residues: 859
  helix: -5.15 (0.30), residues: 14
  sheet: -1.66 (0.27), residues: 340
  loop : -2.36 (0.24), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  38 
 TYR   0.015   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/Z
  covalent geometry    : bond        0.00280 /  0.13 ( 7056)
  covalent geometry    : angle       0.64004 /  0.33 ( 9597)
  SS BOND              : bond        0.00406 /  0.23 (    9)
  SS BOND              : angle       1.01352 /  0.66 (   18)
  hydrogen bonds       : bond        0.04628 /  2.95 (  163)
  hydrogen bonds       : angle       6.88625 /  4.69 (  465)
  link_BETA1-4         : bond        0.00349 /  0.18 (    2)
  link_BETA1-4         : angle       0.82978 /  0.62 (    6)
  link_NAG-ASN         : bond        0.00232 /  0.11 (    2)
  link_NAG-ASN         : angle       1.33018 /  0.62 (    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
  248 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 223
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 LYS cc_start: 0.8862 (tttt) cc_final: 0.8364 (tttp)
REVERT: H   32 TYR cc_start: 0.8699 (m-80) cc_final: 0.8384 (m-10)
REVERT: H   87 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8570 (p)
REVERT: F    4 MET cc_start: 0.8479 (mtp) cc_final: 0.7875 (mtp)
REVERT: F   24 ARG cc_start: 0.8105 (mtp-110) cc_final: 0.7714 (mtp-110)
REVERT: F   45 LYS cc_start: 0.8521 (ptmt) cc_final: 0.8132 (ptpp)
REVERT: F   70 ASP cc_start: 0.8761 (m-30) cc_final: 0.8222 (m-30)
REVERT: F   78 LEU cc_start: 0.8858 (mm) cc_final: 0.8538 (mm)
REVERT: A   23 LYS cc_start: 0.8776 (tptt) cc_final: 0.8208 (ttpp)
REVERT: A   43 GLN cc_start: 0.8380 (mp10) cc_final: 0.7889 (mp10)
REVERT: D   36 TYR cc_start: 0.9278 (m-80) cc_final: 0.9055 (m-80)
REVERT: D   79 GLN cc_start: 0.8371 (mp10) cc_final: 0.7830 (mp-120)
REVERT: E  351 ASP cc_start: 0.8431 (p0) cc_final: 0.8064 (t0)
REVERT: E  447 LYS cc_start: 0.8699 (mppt) cc_final: 0.8406 (mtpt)
  outliers start: 25
  outliers final: 13
  residues processed: 231
  average time/residue: 0.0792
  time to fit residues: 23.6296
Evaluate side-chains
  209 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 195
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain F residue   27 GLN
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain D residue  106 ILE
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain C residue   89 GLU
Chi-restraints excluded: chain E residue  405 ILE
Chi-restraints excluded: chain E residue  445 HIS
Chi-restraints excluded: chain E residue  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:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0970
   chunk 82 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.2182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
D  30 ASN
C   6 GLN
** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.104856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.083323 restraints weight = 12136.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.085812 restraints weight = 7220.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.087470 restraints weight = 5170.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.088538 restraints weight = 4167.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.089101 restraints weight = 3619.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2916
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2915 r_free = 0.2915    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2915
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   7069  Z= 0.240
  Angle     :  0.680   9.681   9627  Z= 0.354
  Chirality :  0.045   0.231   1037
  Planarity :  0.005   0.058   1224
  Dihedral  :  6.191  60.438    964
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 19.40 %
    Favored  : 75.98 %
  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: -2.78 (0.27), residues: 859
  helix: -5.02 (0.36), residues: 14
  sheet: -1.44 (0.27), residues: 350
  loop : -2.08 (0.26), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  38 
 TYR   0.018   0.002   TYR F  49 
 PHE   0.020   0.002   PHE D  94 
 TRP   0.021   0.002   TRP E 423 
 HIS   0.006   0.001   HIS L  94 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00553 /  0.24 ( 7056)
  covalent geometry    : angle       0.67715 /  0.35 ( 9597)
  SS BOND              : bond        0.00495 /  0.30 (    9)
  SS BOND              : angle       1.17056 /  0.63 (   18)
  hydrogen bonds       : bond        0.04232 /  2.78 (  163)
  hydrogen bonds       : angle       6.26895 /  4.28 (  465)
  link_BETA1-4         : bond        0.00240 /  0.13 (    2)
  link_BETA1-4         : angle       0.91658 /  0.62 (    6)
  link_NAG-ASN         : bond        0.00085 /  0.04 (    2)
  link_NAG-ASN         : angle       1.73512 /  0.82 (    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: 34
    poor density    : 196
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 LYS cc_start: 0.8898 (tttt) cc_final: 0.8449 (tttp)
REVERT: H   32 TYR cc_start: 0.8761 (m-80) cc_final: 0.8452 (m-10)
REVERT: F    4 MET cc_start: 0.8604 (mtp) cc_final: 0.8209 (mmm)
REVERT: F   24 ARG cc_start: 0.8038 (mtp-110) cc_final: 0.7702 (mtp-110)
REVERT: F   45 LYS cc_start: 0.8532 (ptmt) cc_final: 0.8146 (ptpp)
REVERT: F   65 SER cc_start: 0.8751 (t) cc_final: 0.8376 (m)
REVERT: F   78 LEU cc_start: 0.8869 (mm) cc_final: 0.8642 (mm)
REVERT: F   90 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8217 (tm-30)
REVERT: F  105 GLU cc_start: 0.5869 (tt0) cc_final: 0.5569 (tt0)
REVERT: A   23 LYS cc_start: 0.8798 (tttt) cc_final: 0.8269 (ttpp)
REVERT: A   43 GLN cc_start: 0.8360 (mp10) cc_final: 0.7818 (mp10)
REVERT: E  447 LYS cc_start: 0.8757 (mppt) cc_final: 0.8541 (mtpt)
  outliers start: 34
  outliers final: 20
  residues processed: 206
  average time/residue: 0.0928
  time to fit residues: 24.4129
Evaluate side-chains
  207 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 187
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
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   62 LEU
Chi-restraints excluded: chain H residue   77 ASN
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain A residue   18 VAL
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain C residue   62 GLN
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue   81 ILE
Chi-restraints excluded: chain C residue   89 GLU
Chi-restraints excluded: chain E residue  404 VAL
Chi-restraints excluded: chain E residue  405 ILE
Chi-restraints excluded: chain E residue  443 LEU
Chi-restraints excluded: chain E residue  475 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 79 optimal weight:    0.0770
   chunk 31 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.5938

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3161 r_free = 0.3161 target = 0.104679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.082884 restraints weight = 12142.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.085518 restraints weight = 6898.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.087275 restraints weight = 4824.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.088343 restraints weight = 3827.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.089118 restraints weight = 3313.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7069  Z= 0.140
  Angle     :  0.609   8.855   9627  Z= 0.313
  Chirality :  0.043   0.215   1037
  Planarity :  0.005   0.061   1224
  Dihedral  :  5.896  57.460    964
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 22.12 %
    Favored  : 74.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.45 (0.28), residues: 859
  helix: -5.01 (0.36), residues: 14
  sheet: -1.14 (0.27), residues: 357
  loop : -1.91 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  38 
 TYR   0.015   0.001   TYR F  49 
 PHE   0.014   0.001   PHE A  64 
 TRP   0.014   0.001   TRP E 423 
 HIS   0.003   0.001   HIS L  94 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.14 ( 7056)
  covalent geometry    : angle       0.60798 /  0.31 ( 9597)
  SS BOND              : bond        0.00297 /  0.17 (    9)
  SS BOND              : angle       0.81808 /  0.47 (   18)
  hydrogen bonds       : bond        0.03674 /  2.42 (  163)
  hydrogen bonds       : angle       5.87355 /  4.01 (  465)
  link_BETA1-4         : bond        0.00402 /  0.20 (    2)
  link_BETA1-4         : angle       0.77960 /  0.55 (    6)
  link_NAG-ASN         : bond        0.00075 /  0.04 (    2)
  link_NAG-ASN         : angle       1.38346 /  0.69 (    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: 26
    poor density    : 192
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   10 GLU cc_start: 0.7735 (pm20) cc_final: 0.7485 (pm20)
REVERT: H   19 LYS cc_start: 0.8897 (tttt) cc_final: 0.8531 (tttm)
REVERT: H   32 TYR cc_start: 0.8746 (m-80) cc_final: 0.8439 (m-10)
REVERT: H   71 THR cc_start: 0.8052 (m) cc_final: 0.7681 (p)
REVERT: H   87 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8535 (p)
REVERT: F    4 MET cc_start: 0.8589 (mtp) cc_final: 0.8226 (mmm)
REVERT: F   24 ARG cc_start: 0.8105 (mtp-110) cc_final: 0.7561 (mtp-110)
REVERT: F   45 LYS cc_start: 0.8508 (ptmt) cc_final: 0.8088 (ptpp)
REVERT: F   65 SER cc_start: 0.8737 (t) cc_final: 0.8390 (m)
REVERT: F   78 LEU cc_start: 0.8823 (mm) cc_final: 0.8543 (mm)
REVERT: F  105 GLU cc_start: 0.5795 (tt0) cc_final: 0.5469 (tt0)
REVERT: A   23 LYS cc_start: 0.8759 (tttt) cc_final: 0.8257 (ttpp)
REVERT: A   43 GLN cc_start: 0.8271 (mp10) cc_final: 0.7873 (mp10)
REVERT: C   38 ARG cc_start: 0.8494 (ttp80) cc_final: 0.7983 (ttm-80)
  outliers start: 26
  outliers final: 16
  residues processed: 209
  average time/residue: 0.0949
  time to fit residues: 25.1726
Evaluate side-chains
  202 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 185
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
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 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 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  404 VAL
Chi-restraints excluded: chain E residue  445 HIS
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:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0000
   chunk 25 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   chunk 79 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0050
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.5198

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L   6 GLN
L  27 GLN
H  39 GLN
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  90 GLN
D  30 ASN
C  82 HIS
** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.106329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.085191 restraints weight = 12072.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.087647 restraints weight = 6980.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.089310 restraints weight = 4962.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.090429 restraints weight = 3973.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.090996 restraints weight = 3434.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.2851

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= 0.128
  Angle     :  0.586   8.589   9627  Z= 0.301
  Chirality :  0.043   0.301   1037
  Planarity :  0.005   0.059   1224
  Dihedral  :  5.574  52.900    964
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 22.93 %
    Favored  : 72.73 %
  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: -2.29 (0.28), residues: 859
  helix: -4.61 (0.52), residues: 20
  sheet: -0.99 (0.27), residues: 357
  loop : -1.80 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG L  65 
 TYR   0.014   0.001   TYR F  49 
 PHE   0.013   0.001   PHE A  64 
 TRP   0.013   0.001   TRP E 423 
 HIS   0.003   0.001   HIS L  94 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.13 ( 7056)
  covalent geometry    : angle       0.58529 /  0.30 ( 9597)
  SS BOND              : bond        0.00559 /  0.42 (    9)
  SS BOND              : angle       0.75042 /  0.45 (   18)
  hydrogen bonds       : bond        0.03371 /  2.22 (  163)
  hydrogen bonds       : angle       5.50166 /  3.75 (  465)
  link_BETA1-4         : bond        0.00343 /  0.17 (    2)
  link_BETA1-4         : angle       0.73370 /  0.51 (    6)
  link_NAG-ASN         : bond        0.00091 /  0.05 (    2)
  link_NAG-ASN         : angle       1.31809 /  0.68 (    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
  228 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 196
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 LYS cc_start: 0.8909 (tttt) cc_final: 0.8518 (tttm)
REVERT: H   71 THR cc_start: 0.8028 (m) cc_final: 0.7673 (p)
REVERT: H   87 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8488 (p)
REVERT: F    4 MET cc_start: 0.8625 (mtp) cc_final: 0.8314 (mmm)
REVERT: F   24 ARG cc_start: 0.8070 (mtp-110) cc_final: 0.7543 (mtp-110)
REVERT: F   45 LYS cc_start: 0.8480 (ptmt) cc_final: 0.8062 (ptpp)
REVERT: F   65 SER cc_start: 0.8685 (t) cc_final: 0.8376 (m)
REVERT: F   78 LEU cc_start: 0.8797 (mm) cc_final: 0.8528 (mm)
REVERT: F   90 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8207 (tm-30)
REVERT: F  105 GLU cc_start: 0.5910 (tt0) cc_final: 0.5552 (tt0)
REVERT: A   23 LYS cc_start: 0.8747 (tttt) cc_final: 0.8299 (ttpp)
REVERT: A   43 GLN cc_start: 0.8263 (mp10) cc_final: 0.7847 (mp10)
REVERT: C   38 ARG cc_start: 0.8417 (ttp80) cc_final: 0.8122 (ttm-80)
  outliers start: 32
  outliers final: 21
  residues processed: 209
  average time/residue: 0.0984
  time to fit residues: 26.0193
Evaluate side-chains
  207 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 184
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   13 VAL
Chi-restraints excluded: chain L residue   74 ASP
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 F residue    8 THR
Chi-restraints excluded: chain F residue   48 ILE
Chi-restraints excluded: chain F residue   90 GLN
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   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 E residue  404 VAL
Chi-restraints excluded: chain E residue  445 HIS
Chi-restraints excluded: chain E residue  447 LYS
Chi-restraints excluded: chain E residue  467 CYS
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:    3.9990
   chunk 49 optimal weight:    0.3980
   chunk 51 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 48 optimal weight:    0.3980
   chunk 22 optimal weight:    0.8980
   chunk 43 optimal weight:    0.4980
   chunk 40 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0670
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.4518

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.106836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.084732 restraints weight = 12052.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.087365 restraints weight = 6893.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.089091 restraints weight = 4850.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.090254 restraints weight = 3871.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.090910 restraints weight = 3348.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.3042

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= 0.124
  Angle     :  0.596   8.693   9627  Z= 0.305
  Chirality :  0.043   0.272   1037
  Planarity :  0.005   0.056   1224
  Dihedral  :  5.442  51.652    964
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 23.34 %
    Favored  : 72.46 %
  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: -2.22 (0.28), residues: 859
  helix: -4.65 (0.48), residues: 20
  sheet: -0.93 (0.27), residues: 360
  loop : -1.76 (0.27), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  65 
 TYR   0.012   0.001   TYR F  49 
 PHE   0.015   0.001   PHE A  64 
 TRP   0.013   0.001   TRP A 109 
 HIS   0.002   0.001   HIS L  34 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.12 ( 7056)
  covalent geometry    : angle       0.59531 /  0.30 ( 9597)
  SS BOND              : bond        0.00340 /  0.20 (    9)
  SS BOND              : angle       0.71579 /  0.42 (   18)
  hydrogen bonds       : bond        0.03277 /  2.14 (  163)
  hydrogen bonds       : angle       5.30632 /  3.60 (  465)
  link_BETA1-4         : bond        0.00244 /  0.13 (    2)
  link_BETA1-4         : angle       0.65817 /  0.44 (    6)
  link_NAG-ASN         : bond        0.00092 /  0.05 (    2)
  link_NAG-ASN         : angle       1.28100 /  0.67 (    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
  213 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 182
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   65 ARG cc_start: 0.9061 (mtm180) cc_final: 0.8548 (ptt-90)
REVERT: H   19 LYS cc_start: 0.8943 (tttt) cc_final: 0.8531 (tttm)
REVERT: H   32 TYR cc_start: 0.8563 (m-80) cc_final: 0.8315 (m-10)
REVERT: H   67 LYS cc_start: 0.8982 (ptpp) cc_final: 0.8632 (ttmm)
REVERT: H   71 THR cc_start: 0.8027 (m) cc_final: 0.7637 (p)
REVERT: H   87 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8477 (p)
REVERT: F    4 MET cc_start: 0.8600 (mtp) cc_final: 0.8267 (mmm)
REVERT: F   24 ARG cc_start: 0.8098 (mtp-110) cc_final: 0.7671 (mtp-110)
REVERT: F   65 SER cc_start: 0.8703 (t) cc_final: 0.8353 (m)
REVERT: F   78 LEU cc_start: 0.8748 (mm) cc_final: 0.8481 (mm)
REVERT: F  105 GLU cc_start: 0.6115 (tt0) cc_final: 0.5789 (tt0)
REVERT: A   23 LYS cc_start: 0.8715 (tttt) cc_final: 0.8224 (ttpp)
REVERT: A   34 MET cc_start: 0.8771 (tpp) cc_final: 0.8451 (tpp)
REVERT: A   43 GLN cc_start: 0.8391 (mp10) cc_final: 0.7773 (mp10)
REVERT: C   38 ARG cc_start: 0.8401 (ttp80) cc_final: 0.8030 (ttm-80)
REVERT: C  117 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8462 (tt)
REVERT: E  423 TRP cc_start: 0.8985 (OUTLIER) cc_final: 0.8431 (p-90)
  outliers start: 31
  outliers final: 23
  residues processed: 200
  average time/residue: 0.0915
  time to fit residues: 23.4817
Evaluate side-chains
  207 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 181
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
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   98 ILE
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 F residue   97 THR
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   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  405 ILE
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  467 CYS
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:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 71 optimal weight:    0.5980
   chunk 13 optimal weight:    0.3980
   chunk 35 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3174 r_free = 0.3174 target = 0.105512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.083287 restraints weight = 12118.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.085949 restraints weight = 6980.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.087668 restraints weight = 4914.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.088689 restraints weight = 3930.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.089461 restraints weight = 3422.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8633
moved from start:          0.3147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7069  Z= 0.156
  Angle     :  0.613   8.788   9627  Z= 0.312
  Chirality :  0.043   0.275   1037
  Planarity :  0.005   0.051   1224
  Dihedral  :  5.374  49.831    964
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 23.88 %
    Favored  : 71.37 %
  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: -2.18 (0.28), residues: 859
  helix: -4.97 (0.38), residues: 14
  sheet: -0.99 (0.26), residues: 364
  loop : -1.70 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 449 
 TYR   0.014   0.001   TYR E 436 
 PHE   0.015   0.001   PHE A  64 
 TRP   0.037   0.001   TRP A 109 
 HIS   0.003   0.001   HIS L  94 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00363 /  0.16 ( 7056)
  covalent geometry    : angle       0.61241 /  0.31 ( 9597)
  SS BOND              : bond        0.00316 /  0.19 (    9)
  SS BOND              : angle       0.59064 /  0.37 (   18)
  hydrogen bonds       : bond        0.03218 /  2.12 (  163)
  hydrogen bonds       : angle       5.23983 /  3.57 (  465)
  link_BETA1-4         : bond        0.00246 /  0.13 (    2)
  link_BETA1-4         : angle       0.82472 /  0.54 (    6)
  link_NAG-ASN         : bond        0.00021 /  0.01 (    2)
  link_NAG-ASN         : angle       1.46399 /  0.75 (    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
  222 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 187
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   65 ARG cc_start: 0.9126 (mtm180) cc_final: 0.8672 (ptt-90)
REVERT: H   10 GLU cc_start: 0.7880 (pp20) cc_final: 0.7663 (pp20)
REVERT: H   19 LYS cc_start: 0.8953 (tttt) cc_final: 0.8452 (tttp)
REVERT: H   67 LYS cc_start: 0.9008 (ptpp) cc_final: 0.8631 (ttmm)
REVERT: H   71 THR cc_start: 0.8077 (m) cc_final: 0.7716 (p)
REVERT: H   87 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8464 (p)
REVERT: F    4 MET cc_start: 0.8609 (mtp) cc_final: 0.8257 (mmm)
REVERT: F   24 ARG cc_start: 0.8100 (mtp-110) cc_final: 0.7643 (mtp-110)
REVERT: F   65 SER cc_start: 0.8725 (t) cc_final: 0.8337 (m)
REVERT: F   78 LEU cc_start: 0.8723 (mm) cc_final: 0.8475 (mm)
REVERT: F   80 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8256 (mm110)
REVERT: F  105 GLU cc_start: 0.6261 (tt0) cc_final: 0.5953 (tt0)
REVERT: A   23 LYS cc_start: 0.8715 (tttt) cc_final: 0.8227 (ttpp)
REVERT: A   43 GLN cc_start: 0.8407 (mp10) cc_final: 0.8197 (mp10)
REVERT: C   38 ARG cc_start: 0.8425 (ttp80) cc_final: 0.8059 (ttm-80)
REVERT: C   90 ASP cc_start: 0.8562 (m-30) cc_final: 0.8334 (t0)
REVERT: C  117 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8460 (tt)
REVERT: E  405 ILE cc_start: 0.8874 (mm) cc_final: 0.8668 (tt)
REVERT: E  423 TRP cc_start: 0.9036 (OUTLIER) cc_final: 0.8459 (p-90)
  outliers start: 35
  outliers final: 26
  residues processed: 206
  average time/residue: 0.0914
  time to fit residues: 24.3830
Evaluate side-chains
  211 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 182
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
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   98 ILE
Chi-restraints excluded: chain L residue  110 ILE
Chi-restraints excluded: chain H residue    5 GLN
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 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   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  358 SER
Chi-restraints excluded: chain E residue  394 VAL
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  467 CYS
Chi-restraints excluded: chain E residue  475 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 55 optimal weight:    0.1980
   chunk 52 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0070
   chunk 41 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   overall best weight:    0.5398

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.106263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.084082 restraints weight = 12094.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.086773 restraints weight = 6949.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.088510 restraints weight = 4876.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.089654 restraints weight = 3889.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.090084 restraints weight = 3359.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
moved from start:          0.3241

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= 0.132
  Angle     :  0.604   8.440   9627  Z= 0.308
  Chirality :  0.043   0.277   1037
  Planarity :  0.005   0.050   1224
  Dihedral  :  5.291  49.702    964
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 24.15 %
    Favored  : 71.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.11 (0.28), residues: 859
  helix: -4.99 (0.38), residues: 14
  sheet: -0.90 (0.26), residues: 363
  loop : -1.68 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 426 
 TYR   0.013   0.001   TYR E 436 
 PHE   0.015   0.001   PHE A  64 
 TRP   0.020   0.001   TRP A 109 
 HIS   0.003   0.001   HIS L  34 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.13 ( 7056)
  covalent geometry    : angle       0.60280 /  0.31 ( 9597)
  SS BOND              : bond        0.00308 /  0.18 (    9)
  SS BOND              : angle       0.53098 /  0.34 (   18)
  hydrogen bonds       : bond        0.03174 /  2.09 (  163)
  hydrogen bonds       : angle       5.16223 /  3.51 (  465)
  link_BETA1-4         : bond        0.00282 /  0.14 (    2)
  link_BETA1-4         : angle       0.74960 /  0.50 (    6)
  link_NAG-ASN         : bond        0.00021 /  0.01 (    2)
  link_NAG-ASN         : angle       1.42949 /  0.76 (    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
  212 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 183
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   65 ARG cc_start: 0.9132 (mtm180) cc_final: 0.8673 (ptt-90)
REVERT: H   10 GLU cc_start: 0.7891 (pp20) cc_final: 0.7622 (pp20)
REVERT: H   19 LYS cc_start: 0.8953 (tttt) cc_final: 0.8536 (tttm)
REVERT: H   67 LYS cc_start: 0.8991 (ptpp) cc_final: 0.8634 (ttmm)
REVERT: H   71 THR cc_start: 0.8081 (m) cc_final: 0.7709 (p)
REVERT: H   87 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8457 (p)
REVERT: F    4 MET cc_start: 0.8563 (mtp) cc_final: 0.8267 (mmm)
REVERT: F   24 ARG cc_start: 0.8064 (mtp-110) cc_final: 0.7788 (mtp-110)
REVERT: F   65 SER cc_start: 0.8691 (t) cc_final: 0.8310 (m)
REVERT: F   78 LEU cc_start: 0.8716 (mm) cc_final: 0.8469 (mm)
REVERT: F   80 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8221 (mm110)
REVERT: F   90 GLN cc_start: 0.8731 (tm130) cc_final: 0.8176 (tm-30)
REVERT: F  105 GLU cc_start: 0.6263 (tt0) cc_final: 0.5930 (tt0)
REVERT: A   23 LYS cc_start: 0.8718 (tttt) cc_final: 0.8235 (ttpp)
REVERT: A   34 MET cc_start: 0.8747 (tpp) cc_final: 0.8117 (ttm)
REVERT: C   38 ARG cc_start: 0.8394 (ttp80) cc_final: 0.8066 (ttm-80)
REVERT: C   90 ASP cc_start: 0.8553 (m-30) cc_final: 0.8325 (t0)
REVERT: C  117 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8438 (tt)
REVERT: E  423 TRP cc_start: 0.9040 (OUTLIER) cc_final: 0.8388 (p-90)
  outliers start: 29
  outliers final: 21
  residues processed: 198
  average time/residue: 0.0920
  time to fit residues: 23.5523
Evaluate side-chains
  208 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 184
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
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    5 GLN
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  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  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  467 CYS
Chi-restraints excluded: chain E residue  475 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 82 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0010
   chunk 70 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.5986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L   6 GLN
H   5 GLN
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  82 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.106301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.084189 restraints weight = 12041.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.086897 restraints weight = 6889.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.088647 restraints weight = 4824.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.089794 restraints weight = 3841.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.090451 restraints weight = 3318.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.3263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7069  Z= 0.141
  Angle     :  0.612   8.373   9627  Z= 0.313
  Chirality :  0.043   0.277   1037
  Planarity :  0.005   0.050   1224
  Dihedral  :  5.253  49.145    964
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 24.29 %
    Favored  : 71.37 %
  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: -4.98 (0.38), residues: 14
  sheet: -0.87 (0.27), residues: 362
  loop : -1.67 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 426 
 TYR   0.014   0.001   TYR E 436 
 PHE   0.014   0.001   PHE E 460 
 TRP   0.055   0.002   TRP A 109 
 HIS   0.003   0.001   HIS L  34 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.14 ( 7056)
  covalent geometry    : angle       0.61082 /  0.31 ( 9597)
  SS BOND              : bond        0.00310 /  0.19 (    9)
  SS BOND              : angle       0.54467 /  0.35 (   18)
  hydrogen bonds       : bond        0.03252 /  2.16 (  163)
  hydrogen bonds       : angle       5.16461 /  3.51 (  465)
  link_BETA1-4         : bond        0.00231 /  0.11 (    2)
  link_BETA1-4         : angle       0.78827 /  0.53 (    6)
  link_NAG-ASN         : bond        0.00016 /  0.01 (    2)
  link_NAG-ASN         : angle       1.45195 /  0.77 (    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
  219 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 187
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   65 ARG cc_start: 0.9115 (mtm180) cc_final: 0.8520 (ptt-90)
REVERT: H   10 GLU cc_start: 0.7925 (pp20) cc_final: 0.7619 (pp20)
REVERT: H   19 LYS cc_start: 0.8959 (tttt) cc_final: 0.8311 (tttp)
REVERT: H   67 LYS cc_start: 0.8992 (ptpp) cc_final: 0.8669 (ttmm)
REVERT: H   71 THR cc_start: 0.8083 (m) cc_final: 0.7704 (p)
REVERT: H   87 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8465 (p)
REVERT: F    4 MET cc_start: 0.8518 (mtp) cc_final: 0.8218 (mmm)
REVERT: F   46 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7937 (tt)
REVERT: F   65 SER cc_start: 0.8695 (t) cc_final: 0.8289 (m)
REVERT: F   78 LEU cc_start: 0.8712 (mm) cc_final: 0.8465 (mm)
REVERT: F   80 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8261 (mm110)
REVERT: F  105 GLU cc_start: 0.6257 (tt0) cc_final: 0.5964 (tt0)
REVERT: A   10 GLU cc_start: 0.8028 (mp0) cc_final: 0.7728 (mp0)
REVERT: A   23 LYS cc_start: 0.8705 (tttt) cc_final: 0.8212 (ttpp)
REVERT: A   34 MET cc_start: 0.8738 (tpp) cc_final: 0.8108 (ttm)
REVERT: C   38 ARG cc_start: 0.8401 (ttp80) cc_final: 0.8068 (ttm-80)
REVERT: C   90 ASP cc_start: 0.8567 (m-30) cc_final: 0.8319 (t0)
REVERT: C  117 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8458 (tt)
REVERT: E  423 TRP cc_start: 0.9034 (OUTLIER) cc_final: 0.8314 (p-90)
  outliers start: 32
  outliers final: 22
  residues processed: 203
  average time/residue: 0.0880
  time to fit residues: 23.1897
Evaluate side-chains
  205 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 179
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
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  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   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  467 CYS
Chi-restraints excluded: chain E residue  475 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 45 optimal weight:    0.2980
   chunk 5 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L   6 GLN
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  90 GLN
A 111 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.106106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.084063 restraints weight = 12059.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.086742 restraints weight = 6942.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.088481 restraints weight = 4882.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.089504 restraints weight = 3896.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.090345 restraints weight = 3388.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8628
moved from start:          0.3372

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= 0.154
  Angle     :  0.634   9.267   9627  Z= 0.325
  Chirality :  0.044   0.278   1037
  Planarity :  0.005   0.050   1224
  Dihedral  :  5.297  48.576    964
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 24.69 %
    Favored  : 71.37 %
  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: -2.05 (0.28), residues: 859
  helix: -4.90 (0.43), residues: 14
  sheet: -0.86 (0.27), residues: 358
  loop : -1.64 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 426 
 TYR   0.016   0.001   TYR H  32 
 PHE   0.015   0.001   PHE E 460 
 TRP   0.065   0.002   TRP A 109 
 HIS   0.003   0.001   HIS L  34 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.15 ( 7056)
  covalent geometry    : angle       0.63334 /  0.32 ( 9597)
  SS BOND              : bond        0.00304 /  0.18 (    9)
  SS BOND              : angle       0.56182 /  0.34 (   18)
  hydrogen bonds       : bond        0.03333 /  2.19 (  163)
  hydrogen bonds       : angle       5.24379 /  3.57 (  465)
  link_BETA1-4         : bond        0.00281 /  0.14 (    2)
  link_BETA1-4         : angle       0.80098 /  0.52 (    6)
  link_NAG-ASN         : bond        0.00011 /  0.01 (    2)
  link_NAG-ASN         : angle       1.56761 /  0.85 (    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
  212 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 183
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   65 ARG cc_start: 0.9073 (mtm180) cc_final: 0.8508 (ptt-90)
REVERT: H   10 GLU cc_start: 0.7971 (pp20) cc_final: 0.7639 (pp20)
REVERT: H   19 LYS cc_start: 0.8955 (tttt) cc_final: 0.8318 (tttp)
REVERT: H   67 LYS cc_start: 0.8976 (ptpp) cc_final: 0.8680 (ttmm)
REVERT: H   87 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8488 (p)
REVERT: F    4 MET cc_start: 0.8523 (mtp) cc_final: 0.8200 (mmm)
REVERT: F   24 ARG cc_start: 0.8106 (mtp-110) cc_final: 0.7739 (mtp-110)
REVERT: F   46 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7971 (tt)
REVERT: F   65 SER cc_start: 0.8690 (t) cc_final: 0.8303 (m)
REVERT: F   78 LEU cc_start: 0.8720 (mm) cc_final: 0.8478 (mm)
REVERT: F   80 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8235 (mm110)
REVERT: F  105 GLU cc_start: 0.6228 (tt0) cc_final: 0.5977 (tt0)
REVERT: A   10 GLU cc_start: 0.8011 (mp0) cc_final: 0.7769 (mp0)
REVERT: A   23 LYS cc_start: 0.8734 (tttt) cc_final: 0.8262 (ttpp)
REVERT: A   34 MET cc_start: 0.8720 (tpp) cc_final: 0.8029 (ttm)
REVERT: A   82 GLN cc_start: 0.9031 (mm110) cc_final: 0.8422 (mm-40)
REVERT: C   38 ARG cc_start: 0.8405 (ttp80) cc_final: 0.8097 (ttm-80)
REVERT: C  117 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8482 (tt)
REVERT: E  423 TRP cc_start: 0.9053 (OUTLIER) cc_final: 0.8368 (p-90)
  outliers start: 29
  outliers final: 23
  residues processed: 198
  average time/residue: 0.0880
  time to fit residues: 22.4339
Evaluate side-chains
  208 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 181
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
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   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   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  467 CYS
Chi-restraints excluded: chain E residue  475 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 66 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 69 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0770
   chunk 43 optimal weight:    1.9990
   chunk 10 optimal weight:    0.3980
   chunk 17 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.5138

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L   6 GLN
H  39 GLN
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  90 GLN
A 111 GLN
D  31 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.108777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.087389 restraints weight = 12024.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.089934 restraints weight = 6986.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.091633 restraints weight = 4978.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.092630 restraints weight = 3993.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.093426 restraints weight = 3479.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.3471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7069  Z= 0.135
  Angle     :  0.630   9.591   9627  Z= 0.323
  Chirality :  0.043   0.280   1037
  Planarity :  0.005   0.051   1224
  Dihedral  :  5.186  48.761    964
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 25.10 %
    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: -1.99 (0.28), residues: 859
  helix: -5.11 (0.28), residues: 20
  sheet: -0.78 (0.27), residues: 357
  loop : -1.57 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  98 
 TYR   0.017   0.001   TYR H  32 
 PHE   0.014   0.001   PHE E 460 
 TRP   0.053   0.002   TRP A 109 
 HIS   0.002   0.001   HIS L  34 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.13 ( 7056)
  covalent geometry    : angle       0.62958 /  0.32 ( 9597)
  SS BOND              : bond        0.00322 /  0.18 (    9)
  SS BOND              : angle       0.57527 /  0.35 (   18)
  hydrogen bonds       : bond        0.03204 /  2.09 (  163)
  hydrogen bonds       : angle       5.15174 /  3.52 (  465)
  link_BETA1-4         : bond        0.00351 /  0.18 (    2)
  link_BETA1-4         : angle       0.77063 /  0.48 (    6)
  link_NAG-ASN         : bond        0.00051 /  0.03 (    2)
  link_NAG-ASN         : angle       1.47637 /  0.82 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1566.80 seconds
wall clock time: 27 minutes 47.55 seconds (1667.55 seconds total)