Starting phenix.real_space_refine
on Wed Apr 30 03:20:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tve_41639/04_2025/8tve_41639.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tve_41639/04_2025/8tve_41639.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tve_41639/04_2025/8tve_41639.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tve_41639/04_2025/8tve_41639.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tve_41639/04_2025/8tve_41639.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tve_41639/04_2025/8tve_41639.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.016
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      48      5.16       5
     C    5799      2.51       5
     N    1536      2.21       5
     O    1707      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9090
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3002
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 409, 3002
          Classifications: {'peptide': 409}
          Incomplete info: {'truncation_to_alanine': 64}
          Link IDs: {'PTRANS': 15, 'TRANS': 393}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 159
          Unresolved non-hydrogen angles: 202
          Unresolved non-hydrogen dihedrals: 116
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 13}
          Unresolved non-hydrogen planarities: 73
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 8.44, per 1000 atoms: 0.93
  Number of scatterers: 9090
  At special positions: 0
  Unit cell: (84.96, 85.845, 171.69, 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      48     16.00
     O    1707      8.00
     N    1536      7.00
     C    5799      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  66 " - pdb=" SG  CYS A 187 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A 326 " - pdb=" SG  CYS A 335 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 350 " - pdb=" SG  CYS A 358 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 382 " - pdb=" SG  CYS A 387 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 389 " - pdb=" SG  CYS A 412 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  66 " - pdb=" SG  CYS C 187 " distance=2.06
    Simple disulfide: pdb=" SG  CYS B  66 " - pdb=" SG  CYS B 187 " distance=2.06
    Simple disulfide: pdb=" SG  CYS C 326 " - pdb=" SG  CYS C 335 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 326 " - pdb=" SG  CYS B 335 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 350 " - pdb=" SG  CYS C 358 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 350 " - pdb=" SG  CYS B 358 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 382 " - pdb=" SG  CYS C 387 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 382 " - pdb=" SG  CYS B 387 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 389 " - pdb=" SG  CYS C 412 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 389 " - pdb=" SG  CYS B 412 " 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
    NAG-ASN
      " NAG A 601 " - " ASN A  65 "
      " NAG A 602 " - " ASN A 459 "
      " NAG B 601 " - " ASN B  65 "
      " NAG B 602 " - " ASN B 459 "
      " NAG C 601 " - " ASN C  65 "
      " NAG C 602 " - " ASN C 459 "
  Time building additional restraints: 2.17
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2310

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 18 sheets defined
      42.8% alpha, 17.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 32
      removed outlier: 4.997A  pdb=" N   LYS A  30 " --> pdb=" O   ASP A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 92
      Proline residue:  A  84  - end of helix
    Processing helix  chain 'A' and resid 141 through 178
    Processing helix  chain 'A' and resid 178 through 207
    Processing helix  chain 'A' and resid 209 through 215
    Processing helix  chain 'A' and resid 222 through 230
    Processing helix  chain 'A' and resid 233 through 242
    Processing helix  chain 'A' and resid 244 through 254
    Processing helix  chain 'A' and resid 344 through 353
      removed outlier: 4.237A  pdb=" N   CYS A 350 " --> pdb=" O   GLU A 346 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LEU A 351 " --> pdb=" O   LEU A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 476
    Processing helix  chain 'B' and resid 24 through 32
      removed outlier: 4.997A  pdb=" N   LYS B  30 " --> pdb=" O   ASP B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 92
      Proline residue:  B  84  - end of helix
    Processing helix  chain 'B' and resid 141 through 178
    Processing helix  chain 'B' and resid 178 through 207
    Processing helix  chain 'B' and resid 209 through 215
    Processing helix  chain 'B' and resid 222 through 230
    Processing helix  chain 'B' and resid 233 through 242
    Processing helix  chain 'B' and resid 244 through 254
    Processing helix  chain 'B' and resid 344 through 353
      removed outlier: 4.237A  pdb=" N   CYS B 350 " --> pdb=" O   GLU B 346 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LEU B 351 " --> pdb=" O   LEU B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 476
    Processing helix  chain 'C' and resid 24 through 32
      removed outlier: 4.997A  pdb=" N   LYS C  30 " --> pdb=" O   ASP C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 92
      Proline residue:  C  84  - end of helix
    Processing helix  chain 'C' and resid 141 through 178
    Processing helix  chain 'C' and resid 178 through 207
    Processing helix  chain 'C' and resid 209 through 215
    Processing helix  chain 'C' and resid 222 through 230
    Processing helix  chain 'C' and resid 233 through 242
    Processing helix  chain 'C' and resid 244 through 254
    Processing helix  chain 'C' and resid 344 through 353
      removed outlier: 4.237A  pdb=" N   CYS C 350 " --> pdb=" O   GLU C 346 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   LEU C 351 " --> pdb=" O   LEU C 347 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 452 through 476
    Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 38
      removed outlier: 5.344A  pdb=" N   GLU A 290 " --> pdb=" O   GLY A  36 " (cutoff:3.500A)
      removed outlier: 4.829A  pdb=" N   THR A  38 " --> pdb=" O   VAL A 288 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   VAL A 288 " --> pdb=" O   THR A  38 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   PHE A 310 " --> pdb=" O   ILE A 321 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ILE A 321 " --> pdb=" O   PHE A 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 281 through 282
    Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 220
      removed outlier: 7.012A  pdb=" N   ALA A 272 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   VAL A 264 " --> pdb=" O   TYR A 270 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   TYR A 270 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
      removed outlier: 8.957A  pdb=" N   GLY B 431 " --> pdb=" O   THR A  49 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   LEU A  51 " --> pdb=" O   GLY B 431 " (cutoff:3.500A)
      removed outlier: 7.965A  pdb=" N   TYR B 433 " --> pdb=" O   LEU A  51 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   VAL A  53 " --> pdb=" O   TYR B 433 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 298
    Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 374
      removed outlier: 4.031A  pdb=" N   VAL A 378 " --> pdb=" O   LEU A 407 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 394 through 395
      removed outlier: 3.526A  pdb=" N   THR A 394 " --> pdb=" O   CYS A 389 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 433
      removed outlier: 6.900A  pdb=" N   TYR C 270 " --> pdb=" O   VAL C 264 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   VAL C 264 " --> pdb=" O   TYR C 270 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   ALA C 272 " --> pdb=" O   ILE C 262 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 33 through 38
      removed outlier: 5.345A  pdb=" N   GLU B 290 " --> pdb=" O   GLY B  36 " (cutoff:3.500A)
      removed outlier: 4.828A  pdb=" N   THR B  38 " --> pdb=" O   VAL B 288 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   VAL B 288 " --> pdb=" O   THR B  38 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   PHE B 310 " --> pdb=" O   ILE B 321 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ILE B 321 " --> pdb=" O   PHE B 310 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 281 through 282
    Processing sheet with id=AB1, first strand: chain 'B' and resid 219 through 220
      removed outlier: 7.012A  pdb=" N   ALA B 272 " --> pdb=" O   ILE B 262 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   VAL B 264 " --> pdb=" O   TYR B 270 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   TYR B 270 " --> pdb=" O   VAL B 264 " (cutoff:3.500A)
      removed outlier: 8.957A  pdb=" N   GLY C 431 " --> pdb=" O   THR B  49 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   LEU B  51 " --> pdb=" O   GLY C 431 " (cutoff:3.500A)
      removed outlier: 7.965A  pdb=" N   TYR C 433 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   VAL B  53 " --> pdb=" O   TYR C 433 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 296 through 298
    Processing sheet with id=AB3, first strand: chain 'B' and resid 371 through 374
      removed outlier: 4.032A  pdb=" N   VAL B 378 " --> pdb=" O   LEU B 407 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 394 through 395
      removed outlier: 3.525A  pdb=" N   THR B 394 " --> pdb=" O   CYS B 389 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 33 through 38
      removed outlier: 5.344A  pdb=" N   GLU C 290 " --> pdb=" O   GLY C  36 " (cutoff:3.500A)
      removed outlier: 4.829A  pdb=" N   THR C  38 " --> pdb=" O   VAL C 288 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   VAL C 288 " --> pdb=" O   THR C  38 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   PHE C 310 " --> pdb=" O   ILE C 321 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ILE C 321 " --> pdb=" O   PHE C 310 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 281 through 282
    Processing sheet with id=AB7, first strand: chain 'C' and resid 296 through 298
    Processing sheet with id=AB8, first strand: chain 'C' and resid 371 through 374
      removed outlier: 4.031A  pdb=" N   VAL C 378 " --> pdb=" O   LEU C 407 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 394 through 395
      removed outlier: 3.525A  pdb=" N   THR C 394 " --> pdb=" O   CYS C 389 " (cutoff:3.500A)

    547 hydrogen bonds defined for protein.
    1530 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: 3.15

  Time building geometry restraints manager: 2.61 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: 2310
        1.33 -     1.46: 2146
        1.46 -     1.59: 4691
        1.59 -     1.71: 3
        1.71 -     1.84: 66
  Bond restraints: 9216
  Sorted by residual:
  bond pdb=" CB  LEU A  23 "
       pdb=" CG  LEU A  23 "
    ideal  model  delta    sigma   weight residual
    1.530  1.602 -0.072 2.00e-02 2.50e+03 1.28e+01
  bond pdb=" CB  LEU B  23 "
       pdb=" CG  LEU B  23 "
    ideal  model  delta    sigma   weight residual
    1.530  1.601 -0.071 2.00e-02 2.50e+03 1.28e+01
  bond pdb=" CB  LEU C  23 "
       pdb=" CG  LEU C  23 "
    ideal  model  delta    sigma   weight residual
    1.530  1.601 -0.071 2.00e-02 2.50e+03 1.26e+01
  bond pdb=" NE  ARG C 171 "
       pdb=" CZ  ARG C 171 "
    ideal  model  delta    sigma   weight residual
    1.326  1.362 -0.036 1.10e-02 8.26e+03 1.07e+01
  bond pdb=" NE  ARG A 171 "
       pdb=" CZ  ARG A 171 "
    ideal  model  delta    sigma   weight residual
    1.326  1.362 -0.036 1.10e-02 8.26e+03 1.05e+01
  ... (remaining 9211 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 11244
        2.28 -     4.56: 1059
        4.56 -     6.85: 225
        6.85 -     9.13: 33
        9.13 -    11.41: 12
  Bond angle restraints: 12573
  Sorted by residual:
  angle pdb=" N   ASN C 464 "
        pdb=" CA  ASN C 464 "
        pdb=" C   ASN C 464 "
      ideal   model   delta    sigma   weight residual
     111.36  101.68    9.68 1.09e+00 8.42e-01 7.89e+01
  angle pdb=" N   ASN B 464 "
        pdb=" CA  ASN B 464 "
        pdb=" C   ASN B 464 "
      ideal   model   delta    sigma   weight residual
     111.36  101.68    9.68 1.09e+00 8.42e-01 7.88e+01
  angle pdb=" N   ASN A 464 "
        pdb=" CA  ASN A 464 "
        pdb=" C   ASN A 464 "
      ideal   model   delta    sigma   weight residual
     111.36  101.69    9.67 1.09e+00 8.42e-01 7.88e+01
  angle pdb=" N   MET C 142 "
        pdb=" CA  MET C 142 "
        pdb=" C   MET C 142 "
      ideal   model   delta    sigma   weight residual
     111.28  101.66    9.62 1.09e+00 8.42e-01 7.79e+01
  angle pdb=" N   MET A 142 "
        pdb=" CA  MET A 142 "
        pdb=" C   MET A 142 "
      ideal   model   delta    sigma   weight residual
     111.28  101.67    9.61 1.09e+00 8.42e-01 7.77e+01
  ... (remaining 12568 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.38: 5451
       16.38 -    32.75: 183
       32.75 -    49.13: 33
       49.13 -    65.50: 21
       65.50 -    81.88: 12
  Dihedral angle restraints: 5700
    sinusoidal: 2118
      harmonic: 3582
  Sorted by residual:
  dihedral pdb=" CB  CYS B 389 "
           pdb=" SG  CYS B 389 "
           pdb=" SG  CYS B 412 "
           pdb=" CB  CYS B 412 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -167.88   81.88     1      1.00e+01 1.00e-02 8.24e+01
  dihedral pdb=" CB  CYS C 389 "
           pdb=" SG  CYS C 389 "
           pdb=" SG  CYS C 412 "
           pdb=" CB  CYS C 412 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -167.87   81.87     1      1.00e+01 1.00e-02 8.24e+01
  dihedral pdb=" CB  CYS A 389 "
           pdb=" SG  CYS A 389 "
           pdb=" SG  CYS A 412 "
           pdb=" CB  CYS A 412 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -167.87   81.87     1      1.00e+01 1.00e-02 8.24e+01
  ... (remaining 5697 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 940
       0.070 -    0.139: 466
       0.139 -    0.208: 118
       0.208 -    0.278: 30
       0.278 -    0.347: 9
  Chirality restraints: 1563
  Sorted by residual:
  chirality pdb=" C2  NAG B 602 "
            pdb=" C1  NAG B 602 "
            pdb=" C3  NAG B 602 "
            pdb=" N2  NAG B 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.84    0.35 2.00e-01 2.50e+01 3.01e+00
  chirality pdb=" C2  NAG A 602 "
            pdb=" C1  NAG A 602 "
            pdb=" C3  NAG A 602 "
            pdb=" N2  NAG A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.84    0.35 2.00e-01 2.50e+01 3.00e+00
  chirality pdb=" C2  NAG C 602 "
            pdb=" C1  NAG C 602 "
            pdb=" C3  NAG C 602 "
            pdb=" N2  NAG C 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.84    0.35 2.00e-01 2.50e+01 2.99e+00
  ... (remaining 1560 not shown)

  Planarity restraints: 1620
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B  65 "    0.028 2.00e-02 2.50e+03   2.98e-02 1.11e+01
        pdb=" CG  ASN B  65 "   -0.009 2.00e-02 2.50e+03
        pdb=" OD1 ASN B  65 "   -0.008 2.00e-02 2.50e+03
        pdb=" ND2 ASN B  65 "   -0.047 2.00e-02 2.50e+03
        pdb=" C1  NAG B 601 "    0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A  65 "    0.028 2.00e-02 2.50e+03   2.97e-02 1.11e+01
        pdb=" CG  ASN A  65 "   -0.009 2.00e-02 2.50e+03
        pdb=" OD1 ASN A  65 "   -0.008 2.00e-02 2.50e+03
        pdb=" ND2 ASN A  65 "   -0.047 2.00e-02 2.50e+03
        pdb=" C1  NAG A 601 "    0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C  65 "   -0.027 2.00e-02 2.50e+03   2.97e-02 1.10e+01
        pdb=" CG  ASN C  65 "    0.009 2.00e-02 2.50e+03
        pdb=" OD1 ASN C  65 "    0.008 2.00e-02 2.50e+03
        pdb=" ND2 ASN C  65 "    0.047 2.00e-02 2.50e+03
        pdb=" C1  NAG C 601 "   -0.036 2.00e-02 2.50e+03
  ... (remaining 1617 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.93: 3860
        2.93 -     3.42: 8456
        3.42 -     3.91: 14542
        3.91 -     4.41: 15317
        4.41 -     4.90: 25936
  Nonbonded interactions: 68111
  Sorted by model distance:
  nonbonded pdb=" N   THR B 392 "
            pdb=" N   ASP B 393 "
     model   vdw
     2.433 2.560
  nonbonded pdb=" N   THR C 392 "
            pdb=" N   ASP C 393 "
     model   vdw
     2.433 2.560
  nonbonded pdb=" N   THR A 392 "
            pdb=" N   ASP A 393 "
     model   vdw
     2.433 2.560
  nonbonded pdb=" N   SER B 356 "
            pdb=" O   SER B 356 "
     model   vdw
     2.513 2.496
  nonbonded pdb=" N   SER C 356 "
            pdb=" O   SER C 356 "
     model   vdw
     2.513 2.496
  ... (remaining 68106 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             124.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     26.880
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.040
  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:3.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  154.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
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      :  0.013   0.072   9237  Z= 0.713
  Angle     :  1.541  11.571  12621  Z= 1.078
  Chirality :  0.087   0.347   1563
  Planarity :  0.005   0.020   1614
  Dihedral  :  9.806  79.964   3345
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  0.33 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.21), residues: 1209
  helix:  0.53 (0.20), residues: 504
  sheet:  0.73 (0.40), residues: 159
  loop : -0.14 (0.23), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.005   TRP A 303 
 HIS   0.002   0.001   HIS C 253 
 PHE   0.016   0.004   PHE B 230 
 TYR   0.027   0.005   TYR B 202 
 ARG   0.004   0.001   ARG C 314 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.06274 (    6)
  link_NAG-ASN         : angle       2.01855 (   18)
  hydrogen bonds       : bond        0.20863 (  547)
  hydrogen bonds       : angle       7.56919 ( 1530)
  SS BOND              : bond        0.01491 (   15)
  SS BOND              : angle       5.16874 (   30)
  covalent geometry    : bond        0.01280 ( 9216)
  covalent geometry    : angle       1.52164 (12573)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 156
  time to evaluate  : 0.894 
Fit side-chains
REVERT: B  217 VAL cc_start: 0.9116 (t) cc_final: 0.8912 (m)
REVERT: B  404 VAL cc_start: 0.8501 (t) cc_final: 0.8275 (t)
REVERT: B  473 GLU cc_start: 0.7893 (tt0) cc_final: 0.7653 (tt0)
REVERT: C  463 GLN cc_start: 0.7851 (mm110) cc_final: 0.7644 (mm110)
  outliers start: 3
  outliers final: 0
  residues processed: 159
  average time/residue: 0.2916
  time to fit residues: 62.0119
Evaluate side-chains
  85 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    0.5980
   chunk 90 optimal weight:    0.5980
   chunk 50 optimal weight:    0.1980
   chunk 31 optimal weight:    0.0170
   chunk 61 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 94 optimal weight:    0.3980
   chunk 36 optimal weight:    0.8980
   chunk 57 optimal weight:    0.6980
   chunk 70 optimal weight:    0.3980
   chunk 108 optimal weight:    0.9990
   overall best weight:    0.3218

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

Flipped N/Q/H residues before XYZ refinement:
A  95 ASN
A 352 GLN
B  95 ASN
B 352 GLN
C  95 ASN
C 352 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.148303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.125487 restraints weight = 11214.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.125965 restraints weight = 11881.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.127383 restraints weight = 9583.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9237  Z= 0.152
  Angle     :  0.593   6.329  12621  Z= 0.327
  Chirality :  0.045   0.138   1563
  Planarity :  0.004   0.029   1614
  Dihedral  :  4.843  18.982   1431
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  :  7.09 %
    Favored  : 90.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.23), residues: 1209
  helix:  2.65 (0.23), residues: 510
  sheet:  0.59 (0.39), residues: 150
  loop : -0.30 (0.22), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C 303 
 HIS   0.000   0.000   HIS C 253 
 PHE   0.011   0.002   PHE C 209 
 TYR   0.020   0.002   TYR C 427 
 ARG   0.003   0.001   ARG A 232 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00287 (    6)
  link_NAG-ASN         : angle       1.49274 (   18)
  hydrogen bonds       : bond        0.05709 (  547)
  hydrogen bonds       : angle       4.84453 ( 1530)
  SS BOND              : bond        0.00179 (   15)
  SS BOND              : angle       1.54719 (   30)
  covalent geometry    : bond        0.00329 ( 9216)
  covalent geometry    : angle       0.58675 (12573)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 1.096 
Fit side-chains
REVERT: B  217 VAL cc_start: 0.9052 (t) cc_final: 0.8786 (m)
REVERT: B  447 ASP cc_start: 0.8095 (m-30) cc_final: 0.7861 (m-30)
REVERT: C  427 TYR cc_start: 0.8327 (t80) cc_final: 0.8067 (t80)
  outliers start: 20
  outliers final: 9
  residues processed: 105
  average time/residue: 0.1756
  time to fit residues: 27.8046
Evaluate side-chains
  73 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  357 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 17 optimal weight:    0.1980
   chunk 21 optimal weight:    0.1980
   chunk 119 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 103 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 279 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.141868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.119900 restraints weight = 11478.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.121417 restraints weight = 10498.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.121995 restraints weight = 9098.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.3187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9237  Z= 0.189
  Angle     :  0.589   6.603  12621  Z= 0.322
  Chirality :  0.046   0.145   1563
  Planarity :  0.004   0.035   1614
  Dihedral  :  4.436  17.759   1431
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  :  7.86 %
    Favored  : 88.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.23), residues: 1209
  helix:  2.75 (0.23), residues: 513
  sheet:  0.58 (0.41), residues: 150
  loop : -0.48 (0.22), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 303 
 HIS   0.003   0.001   HIS B 253 
 PHE   0.009   0.002   PHE A 310 
 TYR   0.017   0.002   TYR C 427 
 ARG   0.002   0.000   ARG A 360 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00221 (    6)
  link_NAG-ASN         : angle       1.69705 (   18)
  hydrogen bonds       : bond        0.04965 (  547)
  hydrogen bonds       : angle       4.48767 ( 1530)
  SS BOND              : bond        0.00187 (   15)
  SS BOND              : angle       0.89768 (   30)
  covalent geometry    : bond        0.00467 ( 9216)
  covalent geometry    : angle       0.58456 (12573)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 74
  time to evaluate  : 1.163 
Fit side-chains
   revert: symmetry clash
REVERT: A  233 ASN cc_start: 0.8641 (t0) cc_final: 0.8418 (t0)
REVERT: C  233 ASN cc_start: 0.8771 (t0) cc_final: 0.8466 (t0)
REVERT: C  427 TYR cc_start: 0.8282 (t80) cc_final: 0.7759 (t80)
  outliers start: 35
  outliers final: 22
  residues processed: 106
  average time/residue: 0.2245
  time to fit residues: 34.2017
Evaluate side-chains
  86 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 64
  time to evaluate  : 1.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain B residue  363 VAL
Chi-restraints excluded: chain B residue  432 GLU
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain C residue  190 ILE
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  357 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 114 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 116 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 113 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 83 optimal weight:    0.3980
   chunk 90 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 279 ASN
** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.139598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.119323 restraints weight = 11441.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.118491 restraints weight = 12704.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.118991 restraints weight = 12532.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.3613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   9237  Z= 0.210
  Angle     :  0.594   8.012  12621  Z= 0.320
  Chirality :  0.047   0.156   1563
  Planarity :  0.004   0.041   1614
  Dihedral  :  4.481  17.803   1431
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  :  8.75 %
    Favored  : 87.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.23), residues: 1209
  helix:  2.59 (0.23), residues: 513
  sheet:  0.52 (0.43), residues: 144
  loop : -0.67 (0.22), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 303 
 HIS   0.004   0.001   HIS B 253 
 PHE   0.009   0.002   PHE A 310 
 TYR   0.022   0.002   TYR B 427 
 ARG   0.002   0.000   ARG C 258 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00126 (    6)
  link_NAG-ASN         : angle       1.67135 (   18)
  hydrogen bonds       : bond        0.04838 (  547)
  hydrogen bonds       : angle       4.46457 ( 1530)
  SS BOND              : bond        0.00249 (   15)
  SS BOND              : angle       0.87464 (   30)
  covalent geometry    : bond        0.00532 ( 9216)
  covalent geometry    : angle       0.58997 (12573)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 74
  time to evaluate  : 1.060 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7183 (tt)
REVERT: A  233 ASN cc_start: 0.8741 (t0) cc_final: 0.8535 (t0)
REVERT: B  233 ASN cc_start: 0.8776 (t0) cc_final: 0.8473 (t0)
REVERT: C  184 GLN cc_start: 0.7811 (tm-30) cc_final: 0.7472 (tm-30)
REVERT: C  233 ASN cc_start: 0.8903 (t0) cc_final: 0.8632 (t0)
  outliers start: 37
  outliers final: 24
  residues processed: 106
  average time/residue: 0.1821
  time to fit residues: 28.9025
Evaluate side-chains
  95 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 70
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  279 ASN
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  348 ILE
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain B residue  432 GLU
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain C residue  190 ILE
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  348 ILE
Chi-restraints excluded: chain C residue  357 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 107 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 108 optimal weight:    1.9990
   chunk 45 optimal weight:    0.2980
   chunk 94 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9990
   chunk 29 optimal weight:    0.3980
   chunk 114 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 279 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.139748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.118539 restraints weight = 11507.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.119324 restraints weight = 10268.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.119615 restraints weight = 9243.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.3808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   9237  Z= 0.179
  Angle     :  0.564   8.277  12621  Z= 0.299
  Chirality :  0.045   0.164   1563
  Planarity :  0.004   0.043   1614
  Dihedral  :  4.383  17.693   1431
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 10.41 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.24), residues: 1209
  helix:  2.75 (0.24), residues: 513
  sheet:  0.46 (0.45), residues: 144
  loop : -0.77 (0.22), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP C 303 
 HIS   0.002   0.001   HIS A 253 
 PHE   0.012   0.002   PHE A 277 
 TYR   0.018   0.002   TYR A 427 
 ARG   0.002   0.000   ARG B 220 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00108 (    6)
  link_NAG-ASN         : angle       1.59573 (   18)
  hydrogen bonds       : bond        0.04590 (  547)
  hydrogen bonds       : angle       4.32364 ( 1530)
  SS BOND              : bond        0.00190 (   15)
  SS BOND              : angle       0.62948 (   30)
  covalent geometry    : bond        0.00450 ( 9216)
  covalent geometry    : angle       0.56137 (12573)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 79
  time to evaluate  : 1.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  233 ASN cc_start: 0.8729 (t0) cc_final: 0.8526 (t0)
REVERT: A  279 ASN cc_start: 0.9073 (OUTLIER) cc_final: 0.8817 (m-40)
REVERT: B  233 ASN cc_start: 0.8757 (t0) cc_final: 0.8517 (t0)
REVERT: C  184 GLN cc_start: 0.7754 (tm-30) cc_final: 0.7383 (tm-30)
REVERT: C  233 ASN cc_start: 0.8887 (t0) cc_final: 0.8619 (t0)
REVERT: C  446 ILE cc_start: 0.8387 (mm) cc_final: 0.8009 (mt)
  outliers start: 40
  outliers final: 28
  residues processed: 110
  average time/residue: 0.2007
  time to fit residues: 32.4556
Evaluate side-chains
  98 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 69
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  279 ASN
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain C residue  169 THR
Chi-restraints excluded: chain C residue  190 ILE
Chi-restraints excluded: chain C residue  205 ILE
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  357 LYS
Chi-restraints excluded: chain C residue  463 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 116 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0870
   chunk 50 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 83 optimal weight:    0.7980
   chunk 64 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.138908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.118423 restraints weight = 11467.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.117474 restraints weight = 11834.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.117810 restraints weight = 11998.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.4032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   9237  Z= 0.190
  Angle     :  0.580  10.123  12621  Z= 0.305
  Chirality :  0.045   0.161   1563
  Planarity :  0.004   0.044   1614
  Dihedral  :  4.358  17.524   1431
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 11.30 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.24), residues: 1209
  helix:  2.73 (0.23), residues: 513
  sheet:  0.28 (0.46), residues: 144
  loop : -0.95 (0.23), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 303 
 HIS   0.002   0.001   HIS A 253 
 PHE   0.008   0.001   PHE B 277 
 TYR   0.019   0.002   TYR B 427 
 ARG   0.002   0.001   ARG A 220 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00122 (    6)
  link_NAG-ASN         : angle       1.66530 (   18)
  hydrogen bonds       : bond        0.04559 (  547)
  hydrogen bonds       : angle       4.34424 ( 1530)
  SS BOND              : bond        0.00199 (   15)
  SS BOND              : angle       0.61560 (   30)
  covalent geometry    : bond        0.00486 ( 9216)
  covalent geometry    : angle       0.57683 (12573)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 69
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  233 ASN cc_start: 0.8798 (t0) cc_final: 0.8561 (t0)
REVERT: C  233 ASN cc_start: 0.8922 (t0) cc_final: 0.8671 (t0)
REVERT: C  446 ILE cc_start: 0.8409 (mm) cc_final: 0.8012 (mt)
  outliers start: 44
  outliers final: 33
  residues processed: 105
  average time/residue: 0.1787
  time to fit residues: 28.1744
Evaluate side-chains
  96 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 63
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  279 ASN
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  153 VAL
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  348 ILE
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain C residue  169 THR
Chi-restraints excluded: chain C residue  190 ILE
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  348 ILE
Chi-restraints excluded: chain C residue  357 LYS
Chi-restraints excluded: chain C residue  463 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 86 optimal weight:    0.2980
   chunk 6 optimal weight:    0.6980
   chunk 70 optimal weight:    0.2980
   chunk 63 optimal weight:    0.2980
   chunk 87 optimal weight:    0.7980
   chunk 98 optimal weight:    0.5980
   chunk 89 optimal weight:    1.9990
   chunk 113 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.4380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.140720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.120001 restraints weight = 11606.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.119779 restraints weight = 11109.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.119832 restraints weight = 11220.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.4154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9237  Z= 0.142
  Angle     :  0.550  11.016  12621  Z= 0.287
  Chirality :  0.044   0.224   1563
  Planarity :  0.004   0.044   1614
  Dihedral  :  4.258  17.393   1431
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 12.74 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.24), residues: 1209
  helix:  2.93 (0.24), residues: 513
  sheet:  0.32 (0.47), residues: 144
  loop : -0.92 (0.23), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 303 
 HIS   0.001   0.000   HIS B 253 
 PHE   0.010   0.001   PHE A 277 
 TYR   0.020   0.002   TYR B 427 
 ARG   0.002   0.000   ARG C 220 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00402 (    6)
  link_NAG-ASN         : angle       1.49653 (   18)
  hydrogen bonds       : bond        0.04218 (  547)
  hydrogen bonds       : angle       4.17665 ( 1530)
  SS BOND              : bond        0.00217 (   15)
  SS BOND              : angle       1.64784 (   30)
  covalent geometry    : bond        0.00345 ( 9216)
  covalent geometry    : angle       0.54268 (12573)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 70
  time to evaluate  : 1.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  233 ASN cc_start: 0.8905 (t0) cc_final: 0.8659 (t0)
REVERT: C  446 ILE cc_start: 0.8425 (mm) cc_final: 0.8034 (mt)
  outliers start: 34
  outliers final: 28
  residues processed: 100
  average time/residue: 0.1708
  time to fit residues: 26.2363
Evaluate side-chains
  90 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 62
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  348 ILE
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain C residue   66 CYS
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  169 THR
Chi-restraints excluded: chain C residue  190 ILE
Chi-restraints excluded: chain C residue  205 ILE
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  348 ILE
Chi-restraints excluded: chain C residue  357 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 84 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 99 optimal weight:    0.0470
   chunk 93 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0030
   chunk 113 optimal weight:    3.9990
   chunk 76 optimal weight:    0.0570
   overall best weight:    0.2806

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.144301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.135716 restraints weight = 11772.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.124605 restraints weight = 17486.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.123007 restraints weight = 18819.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.4324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9237  Z= 0.113
  Angle     :  0.527   9.231  12621  Z= 0.272
  Chirality :  0.043   0.138   1563
  Planarity :  0.004   0.043   1614
  Dihedral  :  4.108  17.154   1431
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 13.84 %
    Favored  : 83.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.25), residues: 1209
  helix:  3.10 (0.24), residues: 516
  sheet:  0.42 (0.48), residues: 144
  loop : -0.89 (0.23), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 303 
 HIS   0.001   0.000   HIS A  24 
 PHE   0.009   0.001   PHE C 230 
 TYR   0.013   0.001   TYR A 379 
 ARG   0.001   0.000   ARG C 220 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00214 (    6)
  link_NAG-ASN         : angle       1.44077 (   18)
  hydrogen bonds       : bond        0.03639 (  547)
  hydrogen bonds       : angle       3.92963 ( 1530)
  SS BOND              : bond        0.00170 (   15)
  SS BOND              : angle       1.49615 (   30)
  covalent geometry    : bond        0.00261 ( 9216)
  covalent geometry    : angle       0.51977 (12573)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 74
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  185 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6858 (tt)
REVERT: C  233 ASN cc_start: 0.8889 (t0) cc_final: 0.8687 (t0)
REVERT: C  446 ILE cc_start: 0.8387 (mm) cc_final: 0.8010 (mt)
  outliers start: 28
  outliers final: 23
  residues processed: 99
  average time/residue: 0.2096
  time to fit residues: 32.8812
Evaluate side-chains
  86 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 62
  time to evaluate  : 1.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain C residue   66 CYS
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  205 ILE
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  357 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 91 optimal weight:    0.8980
   chunk 75 optimal weight:    0.4980
   chunk 116 optimal weight:    0.0670
   chunk 69 optimal weight:    0.0170
   chunk 28 optimal weight:    0.7980
   chunk 41 optimal weight:    0.4980
   chunk 103 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.3556

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.143700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.134839 restraints weight = 11639.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.122539 restraints weight = 20812.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.120812 restraints weight = 19975.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.4413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9237  Z= 0.123
  Angle     :  0.532   8.634  12621  Z= 0.275
  Chirality :  0.044   0.145   1563
  Planarity :  0.004   0.044   1614
  Dihedral  :  4.085  17.131   1431
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 15.28 %
    Favored  : 81.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.25), residues: 1209
  helix:  3.11 (0.24), residues: 516
  sheet:  0.61 (0.48), residues: 144
  loop : -0.89 (0.23), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 303 
 HIS   0.000   0.000   HIS A 253 
 PHE   0.008   0.001   PHE A 277 
 TYR   0.025   0.001   TYR A 427 
 ARG   0.001   0.000   ARG C 232 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00165 (    6)
  link_NAG-ASN         : angle       1.47689 (   18)
  hydrogen bonds       : bond        0.03643 (  547)
  hydrogen bonds       : angle       3.93561 ( 1530)
  SS BOND              : bond        0.00188 (   15)
  SS BOND              : angle       1.31001 (   30)
  covalent geometry    : bond        0.00296 ( 9216)
  covalent geometry    : angle       0.52647 (12573)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 65
  time to evaluate  : 0.963 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  185 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6971 (tt)
REVERT: C  233 ASN cc_start: 0.8969 (t0) cc_final: 0.8740 (t0)
REVERT: C  446 ILE cc_start: 0.8357 (mm) cc_final: 0.7976 (mt)
  outliers start: 28
  outliers final: 24
  residues processed: 89
  average time/residue: 0.1591
  time to fit residues: 22.2898
Evaluate side-chains
  86 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 61
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  144 ASN
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain C residue   66 CYS
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  205 ILE
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  357 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 45 optimal weight:    0.3980
   chunk 95 optimal weight:    0.5980
   chunk 80 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0670
   chunk 17 optimal weight:    0.0370
   chunk 42 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.3996

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

Flipped N/Q/H residues before XYZ refinement:
B 279 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.143115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.134999 restraints weight = 11718.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.123259 restraints weight = 20802.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.119188 restraints weight = 26156.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.4467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9237  Z= 0.132
  Angle     :  0.563  10.420  12621  Z= 0.289
  Chirality :  0.044   0.224   1563
  Planarity :  0.004   0.045   1614
  Dihedral  :  4.119  17.044   1431
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 15.61 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.25), residues: 1209
  helix:  3.06 (0.23), residues: 516
  sheet:  0.66 (0.48), residues: 144
  loop : -0.87 (0.23), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 303 
 HIS   0.001   0.000   HIS B 253 
 PHE   0.008   0.001   PHE B 277 
 TYR   0.032   0.001   TYR C 427 
 ARG   0.001   0.000   ARG B  64 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00435 (    6)
  link_NAG-ASN         : angle       1.70284 (   18)
  hydrogen bonds       : bond        0.03754 (  547)
  hydrogen bonds       : angle       3.98475 ( 1530)
  SS BOND              : bond        0.00209 (   15)
  SS BOND              : angle       1.84357 (   30)
  covalent geometry    : bond        0.00322 ( 9216)
  covalent geometry    : angle       0.55275 (12573)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 64
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  185 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.7035 (tt)
REVERT: C  446 ILE cc_start: 0.8366 (mm) cc_final: 0.7982 (mt)
  outliers start: 29
  outliers final: 28
  residues processed: 89
  average time/residue: 0.1776
  time to fit residues: 24.6524
Evaluate side-chains
  90 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 61
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue   66 CYS
Chi-restraints excluded: chain B residue  144 ASN
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  279 ASN
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain C residue   66 CYS
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  205 ILE
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  298 VAL
Chi-restraints excluded: chain C residue  357 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 67 optimal weight:    0.8980
   chunk 90 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   chunk 118 optimal weight:    0.0870
   chunk 82 optimal weight:    0.9990
   chunk 78 optimal weight:    0.7980
   chunk 117 optimal weight:    1.9990
   chunk 72 optimal weight:    7.9990
   chunk 103 optimal weight:    0.8980
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
B 279 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.140612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.120925 restraints weight = 11751.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.120782 restraints weight = 12485.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.120860 restraints weight = 11875.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.4476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.098   9237  Z= 0.178
  Angle     :  0.594  10.331  12621  Z= 0.307
  Chirality :  0.046   0.168   1563
  Planarity :  0.004   0.045   1614
  Dihedral  :  4.228  17.073   1431
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 15.17 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.25), residues: 1209
  helix:  2.91 (0.23), residues: 516
  sheet:  0.55 (0.49), residues: 144
  loop : -0.95 (0.23), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 303 
 HIS   0.002   0.001   HIS B 253 
 PHE   0.010   0.001   PHE B 277 
 TYR   0.025   0.002   TYR A 427 
 ARG   0.001   0.000   ARG A 314 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00120 (    6)
  link_NAG-ASN         : angle       1.75452 (   18)
  hydrogen bonds       : bond        0.04127 (  547)
  hydrogen bonds       : angle       4.13097 ( 1530)
  SS BOND              : bond        0.00274 (   15)
  SS BOND              : angle       1.89471 (   30)
  covalent geometry    : bond        0.00460 ( 9216)
  covalent geometry    : angle       0.58363 (12573)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3792.36 seconds
wall clock time: 69 minutes 28.62 seconds (4168.62 seconds total)