Starting phenix.real_space_refine
on Mon Apr 28 20:06:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6hn5_0247/04_2025/6hn5_0247.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6hn5_0247/04_2025/6hn5_0247.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6hn5_0247/04_2025/6hn5_0247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6hn5_0247/04_2025/6hn5_0247.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6hn5_0247/04_2025/6hn5_0247.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6hn5_0247/04_2025/6hn5_0247.cif"
  }
  resolution = 3.2
  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=   0.003
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      59      5.16       5
     C    4980      2.51       5
     N    1338      2.21       5
     O    1492      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7869
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 163
          Classifications: {'peptide': 21}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 20}
    Chain: "B"
      Number of atoms: 212
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 25, 200
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
      Conformer: "B"
        Number of residues, atoms: 25, 200
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
          bond proxies already assigned to first conformer: 191
    Chain: "E"
      Number of atoms: 4715
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 584, 4708
          Classifications: {'peptide': 584}
          Link IDs: {'PTRANS': 28, 'TRANS': 555}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 584, 4708
          Classifications: {'peptide': 584}
          Link IDs: {'PTRANS': 28, 'TRANS': 555}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 4812
    Chain: "F"
      Number of atoms: 2625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 2625
          Classifications: {'peptide': 323}
          Link IDs: {'PTRANS': 12, 'TRANS': 310}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "F"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR B  26 " occ=0.50
      ... (22 atoms not shown)
      pdb=" OH BTYR B  26 " occ=0.50
  Time building chain proxies: 7.37, per 1000 atoms: 0.94
  Number of scatterers: 7869
  At special positions: 0
  Unit cell: (105.04, 108.16, 113.36, 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      59     16.00
     O    1492      8.00
     N    1338      7.00
     C    4980      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=23, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   6 " - pdb=" SG  CYS A  11 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A   7 " - pdb=" SG  CYS B   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  20 " - pdb=" SG  CYS B  19 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E   8 " - pdb=" SG  CYS E  26 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E 126 " - pdb=" SG  CYS E 155 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 182 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E 169 " - pdb=" SG  CYS E 188 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 192 " - pdb=" SG  CYS E 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 196 " - pdb=" SG  CYS E 207 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E 208 " - pdb=" SG  CYS E 216 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E 212 " - pdb=" SG  CYS E 225 " distance=2.01
    Simple disulfide: pdb=" SG  CYS E 228 " - pdb=" SG  CYS E 237 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 241 " - pdb=" SG  CYS E 253 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E 259 " - pdb=" SG  CYS E 284 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 266 " - pdb=" SG  CYS E 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 288 " - pdb=" SG  CYS E 301 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 304 " - pdb=" SG  CYS E 308 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 312 " - pdb=" SG  CYS E 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 435 " - pdb=" SG  CYS E 468 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 524 " - pdb=" SG  CYS F 524 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 312 " - pdb=" SG  CYS F 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 435 " - pdb=" SG  CYS F 468 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 682 " - pdb=" SG  CYS F 685 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG C   1 " - " ASN E 111 "
      " NAG E1001 " - " ASN E  25 "
      " NAG E1004 " - " ASN E 215 "
      " NAG E1005 " - " ASN E 255 "
      " NAG E1006 " - " ASN E 397 "
      " NAG E1007 " - " ASN E 418 "
      " NAG E1008 " - " ASN E  16 "
      " NAG F1001 " - " ASN F 337 "
      " NAG F1002 " - " ASN F 397 "
      " NAG F1003 " - " ASN F 514 "
  Time building additional restraints: 2.07
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1794

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 14 sheets defined
      15.0% alpha, 17.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 7
      removed outlier: 3.567A  pdb=" N   CYS A   7 " --> pdb=" O   VAL A   3 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 18
    Processing helix  chain 'B' and resid 9 through 16
    Processing helix  chain 'E' and resid 17 through 24
    Processing helix  chain 'E' and resid 132 through 136
    Processing helix  chain 'E' and resid 255 through 268
      removed outlier: 3.592A  pdb=" N   CYS E 259 " --> pdb=" O   ASN E 255 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 314 through 316
      No H-bonds generated for 'chain 'E' and resid 314 through 316'
    Processing helix  chain 'E' and resid 323 through 329
    Processing helix  chain 'E' and resid 350 through 358
    Processing helix  chain 'E' and resid 378 through 382
      removed outlier: 4.380A  pdb=" N   PHE E 381 " --> pdb=" O   SER E 378 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 435 through 446
      removed outlier: 3.668A  pdb=" N   ILE E 439 " --> pdb=" O   CYS E 435 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 324 through 328
    Processing helix  chain 'F' and resid 349 through 359
      removed outlier: 3.709A  pdb=" N   GLU F 353 " --> pdb=" O   ASN F 349 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 435 through 446
      removed outlier: 3.565A  pdb=" N   ILE F 439 " --> pdb=" O   CYS F 435 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 496 through 498
      No H-bonds generated for 'chain 'F' and resid 496 through 498'
    Processing helix  chain 'F' and resid 688 through 714
      removed outlier: 3.615A  pdb=" N   PHE F 714 " --> pdb=" O   HIS F 710 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 6 through 8
      removed outlier: 7.440A  pdb=" N   GLU E   6 " --> pdb=" O   SER E  27 " (cutoff:3.500A)
      removed outlier: 5.888A  pdb=" N   ILE E  29 " --> pdb=" O   GLU E   6 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   CYS E   8 " --> pdb=" O   ILE E  29 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 11 through 13
      removed outlier: 6.462A  pdb=" N   MET E  11 " --> pdb=" O   GLN E  34 " (cutoff:3.500A)
      removed outlier: 7.623A  pdb=" N   LEU E  36 " --> pdb=" O   MET E  11 " (cutoff:3.500A)
      removed outlier: 5.752A  pdb=" N   ILE E  13 " --> pdb=" O   LEU E  36 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   MET E  38 " --> pdb=" O   ILE E  13 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   LEU E  33 " --> pdb=" O   LEU E  62 " (cutoff:3.500A)
      removed outlier: 7.576A  pdb=" N   PHE E  64 " --> pdb=" O   LEU E  33 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   ILE E  35 " --> pdb=" O   PHE E  64 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   VAL E  66 " --> pdb=" O   ILE E  35 " (cutoff:3.500A)
      removed outlier: 7.623A  pdb=" N   LEU E  37 " --> pdb=" O   VAL E  66 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   ARG E 118 " --> pdb=" O   ALA E  92 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   VAL E  94 " --> pdb=" O   ARG E 118 " (cutoff:3.500A)
      removed outlier: 7.542A  pdb=" N   GLU E 120 " --> pdb=" O   VAL E  94 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   PHE E  96 " --> pdb=" O   GLU E 120 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   ASN E 122 " --> pdb=" O   PHE E  96 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL E 146 " --> pdb=" O   ILE E 119 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LYS E 121 " --> pdb=" O   VAL E 146 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   ASN E 148 " --> pdb=" O   LYS E 121 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 212 through 216
      removed outlier: 3.556A  pdb=" N   ALA E 227 " --> pdb=" O   LEU E 213 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   ASN E 215 " --> pdb=" O   CYS E 225 " (cutoff:3.500A)
      removed outlier: 5.689A  pdb=" N   CYS E 225 " --> pdb=" O   ASN E 215 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 231 through 232
    Processing sheet with id=AA5, first strand: chain 'E' and resid 252 through 254
      removed outlier: 6.739A  pdb=" N   HIS E 247 " --> pdb=" O   CYS E 284 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 292 through 294
    Processing sheet with id=AA7, first strand: chain 'E' and resid 311 through 312
    Processing sheet with id=AA8, first strand: chain 'E' and resid 318 through 321
      removed outlier: 6.232A  pdb=" N   LEU E 340 " --> pdb=" O   LYS E 369 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   ARG E 371 " --> pdb=" O   LEU E 340 " (cutoff:3.500A)
      removed outlier: 5.795A  pdb=" N   ILE E 342 " --> pdb=" O   ARG E 371 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   LEU E 368 " --> pdb=" O   TYR E 401 " (cutoff:3.500A)
      removed outlier: 7.779A  pdb=" N   LEU E 403 " --> pdb=" O   LEU E 368 " (cutoff:3.500A)
      removed outlier: 6.136A  pdb=" N   ILE E 370 " --> pdb=" O   LEU E 403 " (cutoff:3.500A)
      removed outlier: 5.496A  pdb=" N   TYR E 398 " --> pdb=" O   LYS E 425 " (cutoff:3.500A)
      removed outlier: 7.996A  pdb=" N   PHE E 427 " --> pdb=" O   TYR E 398 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   PHE E 400 " --> pdb=" O   PHE E 427 " (cutoff:3.500A)
      removed outlier: 8.332A  pdb=" N   HIS E 429 " --> pdb=" O   PHE E 400 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   ALA E 402 " --> pdb=" O   HIS E 429 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 475 through 479
      removed outlier: 6.454A  pdb=" N   ARG E 488 " --> pdb=" O   SER E 476 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   ILE E 478 " --> pdb=" O   LEU E 486 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   LEU E 486 " --> pdb=" O   ILE E 478 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 530 through 534
    Processing sheet with id=AB2, first strand: chain 'F' and resid 311 through 313
    Processing sheet with id=AB3, first strand: chain 'F' and resid 320 through 321
      removed outlier: 3.658A  pdb=" N   ARG F 371 " --> pdb=" O   ILE F 342 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   HIS F 429 " --> pdb=" O   ALA F 402 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   PHE F 428 " --> pdb=" O   ASP F 456 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 475 through 480
      removed outlier: 6.603A  pdb=" N   ARG F 488 " --> pdb=" O   SER F 476 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ILE F 478 " --> pdb=" O   LEU F 486 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   LEU F 486 " --> pdb=" O   ILE F 478 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 530 through 534
      removed outlier: 3.658A  pdb=" N   GLY F 502 " --> pdb=" O   LEU F 569 " (cutoff:3.500A)

    170 hydrogen bonds defined for protein.
    429 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.15

  Time building geometry restraints manager: 2.45 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2459
        1.33 -     1.46: 2003
        1.46 -     1.59: 3518
        1.59 -     1.71: 0
        1.71 -     1.84: 71
  Bond restraints: 8051
  Sorted by residual:
  bond pdb=" CG1 ILE E 370 "
       pdb=" CD1 ILE E 370 "
    ideal  model  delta    sigma   weight residual
    1.513  1.384  0.129 3.90e-02 6.57e+02 1.09e+01
  bond pdb=" CG  LEU E  36 "
       pdb=" CD1 LEU E  36 "
    ideal  model  delta    sigma   weight residual
    1.521  1.439  0.082 3.30e-02 9.18e+02 6.10e+00
  bond pdb=" CG  LEU E 137 "
       pdb=" CD1 LEU E 137 "
    ideal  model  delta    sigma   weight residual
    1.521  1.444  0.077 3.30e-02 9.18e+02 5.38e+00
  bond pdb=" C   PRO F 494 "
       pdb=" N   PRO F 495 "
    ideal  model  delta    sigma   weight residual
    1.334  1.388 -0.054 2.34e-02 1.83e+03 5.26e+00
  bond pdb=" CG  LEU E  36 "
       pdb=" CD2 LEU E  36 "
    ideal  model  delta    sigma   weight residual
    1.521  1.445  0.076 3.30e-02 9.18e+02 5.26e+00
  ... (remaining 8046 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.43: 10303
        2.43 -     4.85: 514
        4.85 -     7.28: 71
        7.28 -     9.70: 10
        9.70 -    12.13: 6
  Bond angle restraints: 10904
  Sorted by residual:
  angle pdb=" CA  THR E 578 "
        pdb=" CB  THR E 578 "
        pdb=" CG2 THR E 578 "
      ideal   model   delta    sigma   weight residual
     110.50  117.90   -7.40 1.70e+00 3.46e-01 1.89e+01
  angle pdb=" C   TRP E 251 "
        pdb=" N   ARG E 252 "
        pdb=" CA  ARG E 252 "
      ideal   model   delta    sigma   weight residual
     122.29  115.75    6.54 1.65e+00 3.67e-01 1.57e+01
  angle pdb=" C   ILE E  35 "
        pdb=" N   LEU E  36 "
        pdb=" CA  LEU E  36 "
      ideal   model   delta    sigma   weight residual
     121.62  114.38    7.24 1.83e+00 2.99e-01 1.56e+01
  angle pdb=" C   ARG E 577 "
        pdb=" N   THR E 578 "
        pdb=" CA  THR E 578 "
      ideal   model   delta    sigma   weight residual
     122.78  128.67   -5.89 1.52e+00 4.33e-01 1.50e+01
  angle pdb=" N   GLU B  21 "
        pdb=" CA  GLU B  21 "
        pdb=" C   GLU B  21 "
      ideal   model   delta    sigma   weight residual
     114.56  109.88    4.68 1.27e+00 6.20e-01 1.36e+01
  ... (remaining 10899 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.41: 4691
       15.41 -    30.82: 226
       30.82 -    46.22: 64
       46.22 -    61.63: 29
       61.63 -    77.04: 4
  Dihedral angle restraints: 5014
    sinusoidal: 2229
      harmonic: 2785
  Sorted by residual:
  dihedral pdb=" CA  PRO E 243 "
           pdb=" C   PRO E 243 "
           pdb=" N   PRO E 244 "
           pdb=" CA  PRO E 244 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  130.18   49.82     0      5.00e+00 4.00e-02 9.93e+01
  dihedral pdb=" CB  CYS E 524 "
           pdb=" SG  CYS E 524 "
           pdb=" SG  CYS F 524 "
           pdb=" CB  CYS F 524 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  170.04  -77.04     1      1.00e+01 1.00e-02 7.45e+01
  dihedral pdb=" CB  CYS E 126 "
           pdb=" SG  CYS E 126 "
           pdb=" SG  CYS E 155 "
           pdb=" CB  CYS E 155 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   36.84   56.16     1      1.00e+01 1.00e-02 4.25e+01
  ... (remaining 5011 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.113: 1095
       0.113 -    0.225: 113
       0.225 -    0.338: 3
       0.338 -    0.450: 2
       0.450 -    0.563: 1
  Chirality restraints: 1214
  Sorted by residual:
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN E 111 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.84   -0.56 2.00e-01 2.50e+01 7.92e+00
  chirality pdb=" C2  NAG E1007 "
            pdb=" C1  NAG E1007 "
            pdb=" C3  NAG E1007 "
            pdb=" N2  NAG E1007 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.09   -0.40 2.00e-01 2.50e+01 3.95e+00
  chirality pdb=" C2  NAG F1002 "
            pdb=" C1  NAG F1002 "
            pdb=" C3  NAG F1002 "
            pdb=" N2  NAG F1002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.10   -0.39 2.00e-01 2.50e+01 3.88e+00
  ... (remaining 1211 not shown)

  Planarity restraints: 1402
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE F 370 "   -0.023 2.00e-02 2.50e+03   4.68e-02 2.19e+01
        pdb=" C   ILE F 370 "    0.081 2.00e-02 2.50e+03
        pdb=" O   ILE F 370 "   -0.031 2.00e-02 2.50e+03
        pdb=" N   ARG F 371 "   -0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO E 243 "   -0.067 5.00e-02 4.00e+02   1.01e-01 1.62e+01
        pdb=" N   PRO E 244 "    0.174 5.00e-02 4.00e+02
        pdb=" CA  PRO E 244 "   -0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO E 244 "   -0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO E 242 "   -0.064 5.00e-02 4.00e+02   9.82e-02 1.54e+01
        pdb=" N   PRO E 243 "    0.170 5.00e-02 4.00e+02
        pdb=" CA  PRO E 243 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO E 243 "   -0.053 5.00e-02 4.00e+02
  ... (remaining 1399 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2130
        2.80 -     3.33: 6748
        3.33 -     3.85: 13004
        3.85 -     4.38: 15070
        4.38 -     4.90: 25846
  Nonbonded interactions: 62798
  Sorted by model distance:
  nonbonded pdb=" O   MET F 442 "
            pdb=" OG  SER F 446 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" NH2 ARG E  65 "
            pdb=" OE2 GLU E  97 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" OG  SER F 399 "
            pdb=" O   GLN F 423 "
     model   vdw
     2.336 3.040
  nonbonded pdb=" OG  SER F 378 "
            pdb=" OD1 ASP F 522 "
     model   vdw
     2.336 3.040
  nonbonded pdb=" O   ILE E 131 "
            pdb=" NE2 GLN E 189 "
     model   vdw
     2.354 3.120
  ... (remaining 62793 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.290
  Find NCS groups from input model:        0.070
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
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      :  0.012   0.129   8085  Z= 0.504
  Angle     :  1.224  12.131  10983  Z= 0.626
  Chirality :  0.071   0.563   1214
  Planarity :  0.008   0.101   1392
  Dihedral  : 10.560  74.824   3151
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.78 %
    Favored  : 89.22 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.78 %
    Favored  : 97.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.94 (0.22), residues: 940
  helix: -3.18 (0.29), residues: 143
  sheet: -1.88 (0.40), residues: 147
  loop : -2.85 (0.20), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.005   TRP F 529 
 HIS   0.023   0.004   HIS E 264 
 PHE   0.042   0.006   PHE F 701 
 TYR   0.035   0.004   TYR E 277 
 ARG   0.017   0.002   ARG E 118 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01000 (   10)
  link_NAG-ASN         : angle       3.58369 (   30)
  link_BETA1-4         : bond        0.01932 (    1)
  link_BETA1-4         : angle       5.95927 (    3)
  hydrogen bonds       : bond        0.17124 (  170)
  hydrogen bonds       : angle       8.66206 (  429)
  SS BOND              : bond        0.00876 (   23)
  SS BOND              : angle       2.46830 (   46)
  covalent geometry    : bond        0.01201 ( 8051)
  covalent geometry    : angle       1.19966 (10904)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  460 LYS cc_start: 0.7294 (mtpt) cc_final: 0.6543 (pttt)
REVERT: E  509 GLU cc_start: 0.8125 (tt0) cc_final: 0.7750 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.2761
  time to fit residues: 48.2810
Evaluate side-chains
  71 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 24 optimal weight:    8.9990
   chunk 48 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 85 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
E  15 ASN
E 187 HIS
E 247 HIS
E 295 ASN
E 313 HIS
E 405 ASN
E 561 GLN
F 561 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.142865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.112604 restraints weight = 41082.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3905 rms_B_bonded: 6.62
r_work: 0.3644 rms_B_bonded: 5.81 restraints_weight: 2.0000
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3654
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3654 r_free = 0.3654    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3653 r_free = 0.3653    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3653
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8085  Z= 0.171
  Angle     :  0.781  16.887  10983  Z= 0.384
  Chirality :  0.050   0.331   1214
  Planarity :  0.006   0.093   1392
  Dihedral  :  9.382  59.122   1276
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  7.87 %
    Favored  : 90.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.11 (0.24), residues: 940
  helix: -1.79 (0.40), residues: 130
  sheet: -1.48 (0.43), residues: 140
  loop : -2.43 (0.21), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 414 
 HIS   0.009   0.001   HIS E 264 
 PHE   0.029   0.002   PHE E 258 
 TYR   0.015   0.002   TYR F 401 
 ARG   0.007   0.001   ARG E 488 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00754 (   10)
  link_NAG-ASN         : angle       3.70655 (   30)
  link_BETA1-4         : bond        0.00767 (    1)
  link_BETA1-4         : angle       4.26998 (    3)
  hydrogen bonds       : bond        0.04667 (  170)
  hydrogen bonds       : angle       6.51099 (  429)
  SS BOND              : bond        0.00468 (   23)
  SS BOND              : angle       1.83352 (   46)
  covalent geometry    : bond        0.00397 ( 8051)
  covalent geometry    : angle       0.74711 (10904)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  460 LYS cc_start: 0.7575 (mtpt) cc_final: 0.6739 (pttt)
REVERT: E  509 GLU cc_start: 0.8952 (tt0) cc_final: 0.8529 (tt0)
REVERT: E  557 LYS cc_start: 0.8755 (ptpt) cc_final: 0.8110 (ptpt)
REVERT: F  357 ASN cc_start: 0.8943 (m-40) cc_final: 0.8690 (m-40)
REVERT: F  438 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8450 (mm-30)
REVERT: F  504 MET cc_start: 0.8737 (mtt) cc_final: 0.8459 (mtp)
REVERT: F  522 ASP cc_start: 0.6193 (m-30) cc_final: 0.5689 (t0)
  outliers start: 10
  outliers final: 6
  residues processed: 100
  average time/residue: 0.1995
  time to fit residues: 27.6247
Evaluate side-chains
  68 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue  111 ASN
Chi-restraints excluded: chain E residue  459 LEU
Chi-restraints excluded: chain F residue  423 GLN
Chi-restraints excluded: chain F residue  509 GLU
Chi-restraints excluded: chain F residue  688 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0570
   chunk 49 optimal weight:    1.9990
   chunk 85 optimal weight:    0.0000
   chunk 19 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 40 optimal weight:    3.9990
   chunk 84 optimal weight:    1.9990
   overall best weight:    0.4502

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

Flipped N/Q/H residues before XYZ refinement:
E 189 GLN
E 337 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.144463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.114905 restraints weight = 28681.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3946 rms_B_bonded: 5.57
r_work: 0.3702 rms_B_bonded: 5.25 restraints_weight: 2.0000
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3709
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3709 r_free = 0.3709    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3709 r_free = 0.3709    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3709
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8085  Z= 0.141
  Angle     :  0.768  21.676  10983  Z= 0.366
  Chirality :  0.050   0.522   1214
  Planarity :  0.005   0.090   1392
  Dihedral  :  8.767  57.366   1276
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  :  9.14 %
    Favored  : 89.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.81 (0.25), residues: 940
  helix: -1.39 (0.43), residues: 129
  sheet: -1.21 (0.43), residues: 143
  loop : -2.28 (0.22), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP F 414 
 HIS   0.012   0.001   HIS E 264 
 PHE   0.040   0.002   PHE E 258 
 TYR   0.029   0.002   TYR B  16 
 ARG   0.006   0.001   ARG E 229 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00611 (   10)
  link_NAG-ASN         : angle       3.58423 (   30)
  link_BETA1-4         : bond        0.00261 (    1)
  link_BETA1-4         : angle       3.09823 (    3)
  hydrogen bonds       : bond        0.04069 (  170)
  hydrogen bonds       : angle       6.34629 (  429)
  SS BOND              : bond        0.00860 (   23)
  SS BOND              : angle       2.10610 (   46)
  covalent geometry    : bond        0.00328 ( 8051)
  covalent geometry    : angle       0.73273 (10904)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   59 ASP cc_start: 0.8228 (m-30) cc_final: 0.7890 (m-30)
REVERT: E  337 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.8404 (t0)
REVERT: E  460 LYS cc_start: 0.7454 (mtpt) cc_final: 0.6665 (pttt)
REVERT: E  509 GLU cc_start: 0.8914 (tt0) cc_final: 0.8711 (tt0)
REVERT: E  557 LYS cc_start: 0.8811 (ptpt) cc_final: 0.8339 (ptpp)
REVERT: F  353 GLU cc_start: 0.8805 (mp0) cc_final: 0.8509 (mp0)
REVERT: F  423 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7808 (pm20)
  outliers start: 11
  outliers final: 6
  residues processed: 88
  average time/residue: 0.2186
  time to fit residues: 26.4942
Evaluate side-chains
  74 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue  111 ASN
Chi-restraints excluded: chain E residue  337 ASN
Chi-restraints excluded: chain E residue  459 LEU
Chi-restraints excluded: chain E residue  524 CYS
Chi-restraints excluded: chain F residue  423 GLN
Chi-restraints excluded: chain F residue  501 LEU
Chi-restraints excluded: chain F residue  509 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 85 optimal weight:    0.0970
   chunk 69 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 52 optimal weight:    0.4980
   chunk 57 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 65 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
E 313 HIS
E 405 ASN
** F 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.144454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.113664 restraints weight = 32355.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3930 rms_B_bonded: 6.01
r_work: 0.3682 rms_B_bonded: 5.65 restraints_weight: 2.0000
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3692
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3692 r_free = 0.3692    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3692 r_free = 0.3692    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3692
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8085  Z= 0.134
  Angle     :  0.724  16.976  10983  Z= 0.346
  Chirality :  0.050   0.544   1214
  Planarity :  0.005   0.092   1392
  Dihedral  :  8.276  55.916   1276
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  :  8.80 %
    Favored  : 89.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (0.25), residues: 940
  helix: -1.18 (0.44), residues: 131
  sheet: -1.11 (0.45), residues: 133
  loop : -2.20 (0.22), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 412 
 HIS   0.006   0.001   HIS E 264 
 PHE   0.030   0.002   PHE E 258 
 TYR   0.029   0.001   TYR B  16 
 ARG   0.006   0.001   ARG B  22 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00483 (   10)
  link_NAG-ASN         : angle       3.37735 (   30)
  link_BETA1-4         : bond        0.00430 (    1)
  link_BETA1-4         : angle       2.90164 (    3)
  hydrogen bonds       : bond        0.03708 (  170)
  hydrogen bonds       : angle       5.96128 (  429)
  SS BOND              : bond        0.00336 (   23)
  SS BOND              : angle       1.30544 (   46)
  covalent geometry    : bond        0.00311 ( 8051)
  covalent geometry    : angle       0.69741 (10904)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   59 ASP cc_start: 0.8312 (m-30) cc_final: 0.7969 (m-30)
REVERT: E  211 GLU cc_start: 0.7583 (tt0) cc_final: 0.7193 (tm-30)
REVERT: E  460 LYS cc_start: 0.7488 (mtpt) cc_final: 0.6669 (pttt)
REVERT: F  423 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7836 (pm20)
REVERT: F  438 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8408 (mm-30)
REVERT: F  582 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8554 (tmtt)
REVERT: F  693 LEU cc_start: 0.8830 (tp) cc_final: 0.8556 (mm)
  outliers start: 12
  outliers final: 9
  residues processed: 76
  average time/residue: 0.1915
  time to fit residues: 20.7344
Evaluate side-chains
  76 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue  111 ASN
Chi-restraints excluded: chain E residue  262 LEU
Chi-restraints excluded: chain E residue  459 LEU
Chi-restraints excluded: chain E residue  524 CYS
Chi-restraints excluded: chain E residue  585 ILE
Chi-restraints excluded: chain F residue  423 GLN
Chi-restraints excluded: chain F residue  501 LEU
Chi-restraints excluded: chain F residue  509 GLU
Chi-restraints excluded: chain F residue  576 ARG
Chi-restraints excluded: chain F residue  582 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 62 optimal weight:    7.9990
   chunk 75 optimal weight:    4.9990
   chunk 10 optimal weight:    0.5980
   chunk 34 optimal weight:    0.0980
   chunk 69 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
E 313 HIS
** F 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 691 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.142867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.112522 restraints weight = 38043.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3906 rms_B_bonded: 6.48
r_work: 0.3649 rms_B_bonded: 5.72 restraints_weight: 2.0000
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3656
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3656 r_free = 0.3656    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3656 r_free = 0.3656    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3656
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.3038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8085  Z= 0.171
  Angle     :  0.722  17.443  10983  Z= 0.344
  Chirality :  0.050   0.556   1214
  Planarity :  0.005   0.092   1392
  Dihedral  :  8.057  58.258   1276
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  8.91 %
    Favored  : 89.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.25), residues: 940
  helix: -1.02 (0.45), residues: 131
  sheet: -1.11 (0.44), residues: 133
  loop : -2.17 (0.22), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 412 
 HIS   0.007   0.001   HIS E 264 
 PHE   0.026   0.002   PHE E 258 
 TYR   0.021   0.002   TYR B  16 
 ARG   0.006   0.001   ARG E  14 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00469 (   10)
  link_NAG-ASN         : angle       3.34926 (   30)
  link_BETA1-4         : bond        0.00405 (    1)
  link_BETA1-4         : angle       3.10449 (    3)
  hydrogen bonds       : bond        0.03738 (  170)
  hydrogen bonds       : angle       5.86646 (  429)
  SS BOND              : bond        0.00407 (   23)
  SS BOND              : angle       1.37738 (   46)
  covalent geometry    : bond        0.00408 ( 8051)
  covalent geometry    : angle       0.69515 (10904)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.981 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   59 ASP cc_start: 0.8279 (m-30) cc_final: 0.7895 (m-30)
REVERT: E  239 GLU cc_start: 0.4803 (pm20) cc_final: 0.4543 (pm20)
REVERT: E  460 LYS cc_start: 0.7406 (mtpt) cc_final: 0.6594 (pttt)
REVERT: E  509 GLU cc_start: 0.8929 (tt0) cc_final: 0.8536 (tt0)
REVERT: E  557 LYS cc_start: 0.8800 (ptpt) cc_final: 0.8287 (pttm)
REVERT: F  423 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7921 (pm20)
REVERT: F  582 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8628 (tmtt)
  outliers start: 14
  outliers final: 8
  residues processed: 78
  average time/residue: 0.2246
  time to fit residues: 24.0884
Evaluate side-chains
  71 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue  111 ASN
Chi-restraints excluded: chain E residue  459 LEU
Chi-restraints excluded: chain E residue  524 CYS
Chi-restraints excluded: chain F residue  423 GLN
Chi-restraints excluded: chain F residue  509 GLU
Chi-restraints excluded: chain F residue  576 ARG
Chi-restraints excluded: chain F residue  582 LYS
Chi-restraints excluded: chain F residue  685 CYS
Chi-restraints excluded: chain F residue  688 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 36 optimal weight:    0.3980
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 41 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 76 optimal weight:    7.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** F 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.141497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.110223 restraints weight = 33775.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3878 rms_B_bonded: 6.03
r_work: 0.3627 rms_B_bonded: 5.65 restraints_weight: 2.0000
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3637
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3637 r_free = 0.3637    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3637 r_free = 0.3637    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3637
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.3108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8085  Z= 0.194
  Angle     :  0.742  17.464  10983  Z= 0.355
  Chirality :  0.051   0.563   1214
  Planarity :  0.005   0.091   1392
  Dihedral  :  7.969  59.427   1276
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  :  9.72 %
    Favored  : 88.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.58 (0.25), residues: 940
  helix: -1.04 (0.44), residues: 132
  sheet: -1.06 (0.43), residues: 138
  loop : -2.15 (0.22), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP F 529 
 HIS   0.007   0.001   HIS E 264 
 PHE   0.025   0.002   PHE E 258 
 TYR   0.019   0.002   TYR B  16 
 ARG   0.007   0.001   ARG E 498 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00459 (   10)
  link_NAG-ASN         : angle       3.35860 (   30)
  link_BETA1-4         : bond        0.00528 (    1)
  link_BETA1-4         : angle       3.25193 (    3)
  hydrogen bonds       : bond        0.03729 (  170)
  hydrogen bonds       : angle       5.82099 (  429)
  SS BOND              : bond        0.00399 (   23)
  SS BOND              : angle       1.51620 (   46)
  covalent geometry    : bond        0.00464 ( 8051)
  covalent geometry    : angle       0.71449 (10904)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   59 ASP cc_start: 0.8325 (m-30) cc_final: 0.7933 (m-30)
REVERT: E  460 LYS cc_start: 0.7442 (mtpt) cc_final: 0.6597 (pttt)
REVERT: E  509 GLU cc_start: 0.8941 (tt0) cc_final: 0.8669 (tt0)
REVERT: E  557 LYS cc_start: 0.8829 (ptpt) cc_final: 0.8339 (ptpt)
REVERT: F  423 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7939 (pm20)
REVERT: F  582 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8582 (tmtt)
  outliers start: 13
  outliers final: 7
  residues processed: 74
  average time/residue: 0.1968
  time to fit residues: 20.5808
Evaluate side-chains
  67 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue  111 ASN
Chi-restraints excluded: chain E residue  459 LEU
Chi-restraints excluded: chain E residue  524 CYS
Chi-restraints excluded: chain F residue  423 GLN
Chi-restraints excluded: chain F residue  509 GLU
Chi-restraints excluded: chain F residue  582 LYS
Chi-restraints excluded: chain F residue  685 CYS
Chi-restraints excluded: chain F residue  688 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 39 optimal weight:    0.0980
   chunk 61 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0970
   chunk 41 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
B   5 HIS
F 357 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.144259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.113210 restraints weight = 21667.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3932 rms_B_bonded: 3.99
r_work: 0.3766 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3776
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3776 r_free = 0.3776    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3776 r_free = 0.3776    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3776
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.3391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8085  Z= 0.122
  Angle     :  0.686  15.272  10983  Z= 0.331
  Chirality :  0.049   0.574   1214
  Planarity :  0.005   0.094   1392
  Dihedral  :  7.641  56.100   1276
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 10.53 %
    Favored  : 87.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.42 (0.26), residues: 940
  helix: -0.76 (0.45), residues: 132
  sheet: -0.89 (0.45), residues: 133
  loop : -2.09 (0.22), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 493 
 HIS   0.006   0.001   HIS E 264 
 PHE   0.026   0.001   PHE E 258 
 TYR   0.024   0.001   TYR A  14 
 ARG   0.005   0.000   ARG E 498 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00383 (   10)
  link_NAG-ASN         : angle       3.19159 (   30)
  link_BETA1-4         : bond        0.00055 (    1)
  link_BETA1-4         : angle       2.63909 (    3)
  hydrogen bonds       : bond        0.03368 (  170)
  hydrogen bonds       : angle       5.68100 (  429)
  SS BOND              : bond        0.00262 (   23)
  SS BOND              : angle       1.25357 (   46)
  covalent geometry    : bond        0.00287 ( 8051)
  covalent geometry    : angle       0.66170 (10904)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLU cc_start: 0.8200 (tp30) cc_final: 0.7978 (tp30)
REVERT: E   59 ASP cc_start: 0.8057 (m-30) cc_final: 0.7788 (m-30)
REVERT: E  258 PHE cc_start: 0.8687 (t80) cc_final: 0.8293 (t80)
REVERT: E  460 LYS cc_start: 0.7260 (mtpt) cc_final: 0.6471 (pttt)
REVERT: E  509 GLU cc_start: 0.8788 (tt0) cc_final: 0.8474 (tt0)
REVERT: E  557 LYS cc_start: 0.8767 (ptpt) cc_final: 0.8296 (ptpt)
REVERT: F  423 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7897 (pm20)
REVERT: F  582 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8415 (tmtt)
REVERT: F  693 LEU cc_start: 0.8802 (tp) cc_final: 0.8564 (mm)
  outliers start: 15
  outliers final: 9
  residues processed: 83
  average time/residue: 0.2337
  time to fit residues: 28.6246
Evaluate side-chains
  72 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 1.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue  111 ASN
Chi-restraints excluded: chain E residue  293 THR
Chi-restraints excluded: chain E residue  295 ASN
Chi-restraints excluded: chain E residue  459 LEU
Chi-restraints excluded: chain E residue  524 CYS
Chi-restraints excluded: chain F residue  368 LEU
Chi-restraints excluded: chain F residue  423 GLN
Chi-restraints excluded: chain F residue  582 LYS
Chi-restraints excluded: chain F residue  685 CYS
Chi-restraints excluded: chain F residue  688 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 29 optimal weight:    4.9990
   chunk 80 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 83 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
F 357 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.142223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.111016 restraints weight = 44636.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3886 rms_B_bonded: 6.16
r_work: 0.3640 rms_B_bonded: 5.80 restraints_weight: 2.0000
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3650
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3650 r_free = 0.3650    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3650 r_free = 0.3650    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3650
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.3410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8085  Z= 0.167
  Angle     :  0.720  15.675  10983  Z= 0.346
  Chirality :  0.050   0.579   1214
  Planarity :  0.005   0.092   1392
  Dihedral  :  7.548  56.033   1276
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 11.11 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.38 (0.26), residues: 940
  helix: -0.64 (0.46), residues: 132
  sheet: -0.90 (0.44), residues: 133
  loop : -2.07 (0.22), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 412 
 HIS   0.006   0.001   HIS E 264 
 PHE   0.022   0.002   PHE E 258 
 TYR   0.023   0.002   TYR B  16 
 ARG   0.005   0.001   ARG E  14 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00379 (   10)
  link_NAG-ASN         : angle       3.23151 (   30)
  link_BETA1-4         : bond        0.00382 (    1)
  link_BETA1-4         : angle       2.99229 (    3)
  hydrogen bonds       : bond        0.03507 (  170)
  hydrogen bonds       : angle       5.69441 (  429)
  SS BOND              : bond        0.00329 (   23)
  SS BOND              : angle       1.40646 (   46)
  covalent geometry    : bond        0.00401 ( 8051)
  covalent geometry    : angle       0.69484 (10904)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.996 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   38 MET cc_start: 0.7703 (mmp) cc_final: 0.7419 (mmt)
REVERT: E   59 ASP cc_start: 0.8344 (m-30) cc_final: 0.8087 (m-30)
REVERT: E  258 PHE cc_start: 0.8703 (t80) cc_final: 0.8268 (t80)
REVERT: E  460 LYS cc_start: 0.7322 (mtpt) cc_final: 0.6466 (pttt)
REVERT: E  504 MET cc_start: 0.8854 (mtm) cc_final: 0.8547 (mtm)
REVERT: E  509 GLU cc_start: 0.8936 (tt0) cc_final: 0.8650 (tt0)
REVERT: E  557 LYS cc_start: 0.8826 (ptpt) cc_final: 0.8320 (ptpt)
REVERT: F  423 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7921 (pm20)
REVERT: F  582 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8520 (tmtt)
  outliers start: 15
  outliers final: 8
  residues processed: 70
  average time/residue: 0.2047
  time to fit residues: 20.5011
Evaluate side-chains
  66 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue  111 ASN
Chi-restraints excluded: chain E residue  194 THR
Chi-restraints excluded: chain E residue  262 LEU
Chi-restraints excluded: chain E residue  459 LEU
Chi-restraints excluded: chain E residue  524 CYS
Chi-restraints excluded: chain F residue  423 GLN
Chi-restraints excluded: chain F residue  582 LYS
Chi-restraints excluded: chain F residue  685 CYS
Chi-restraints excluded: chain F residue  688 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 58 optimal weight:   20.0000
   chunk 40 optimal weight:    0.7980
   chunk 19 optimal weight:    9.9990
   chunk 48 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0770
   chunk 84 optimal weight:    1.9990
   chunk 90 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
F 548 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.144079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.114304 restraints weight = 30309.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 5.52
r_work: 0.3705 rms_B_bonded: 5.20 restraints_weight: 2.0000
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3714
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3714 r_free = 0.3714    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3714 r_free = 0.3714    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3714
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.3562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8085  Z= 0.132
  Angle     :  0.697  15.186  10983  Z= 0.334
  Chirality :  0.049   0.585   1214
  Planarity :  0.005   0.093   1392
  Dihedral  :  7.358  56.122   1276
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 11.34 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.30 (0.26), residues: 940
  helix: -0.50 (0.46), residues: 132
  sheet: -0.78 (0.44), residues: 133
  loop : -2.05 (0.22), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 412 
 HIS   0.006   0.001   HIS E 264 
 PHE   0.024   0.002   PHE E 231 
 TYR   0.032   0.002   TYR B  16 
 ARG   0.007   0.001   ARG B  22 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00328 (   10)
  link_NAG-ASN         : angle       3.15642 (   30)
  link_BETA1-4         : bond        0.00214 (    1)
  link_BETA1-4         : angle       2.58400 (    3)
  hydrogen bonds       : bond        0.03300 (  170)
  hydrogen bonds       : angle       5.60502 (  429)
  SS BOND              : bond        0.00271 (   23)
  SS BOND              : angle       1.22012 (   46)
  covalent geometry    : bond        0.00316 ( 8051)
  covalent geometry    : angle       0.67350 (10904)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   38 MET cc_start: 0.7325 (mmp) cc_final: 0.7031 (mmt)
REVERT: E   59 ASP cc_start: 0.8203 (m-30) cc_final: 0.7929 (m-30)
REVERT: E  239 GLU cc_start: 0.5082 (pm20) cc_final: 0.4802 (pm20)
REVERT: E  258 PHE cc_start: 0.8685 (t80) cc_final: 0.8289 (t80)
REVERT: E  460 LYS cc_start: 0.7241 (mtpt) cc_final: 0.6411 (pttt)
REVERT: E  509 GLU cc_start: 0.8863 (tt0) cc_final: 0.8569 (tt0)
REVERT: E  557 LYS cc_start: 0.8836 (ptpt) cc_final: 0.8309 (ptpt)
REVERT: F  423 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7946 (pm20)
REVERT: F  582 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8443 (tmtt)
REVERT: F  693 LEU cc_start: 0.8805 (tp) cc_final: 0.8554 (mm)
  outliers start: 13
  outliers final: 9
  residues processed: 67
  average time/residue: 0.2044
  time to fit residues: 19.8758
Evaluate side-chains
  64 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue  111 ASN
Chi-restraints excluded: chain E residue  194 THR
Chi-restraints excluded: chain E residue  262 LEU
Chi-restraints excluded: chain E residue  459 LEU
Chi-restraints excluded: chain E residue  524 CYS
Chi-restraints excluded: chain E residue  533 ASP
Chi-restraints excluded: chain F residue  423 GLN
Chi-restraints excluded: chain F residue  582 LYS
Chi-restraints excluded: chain F residue  685 CYS
Chi-restraints excluded: chain F residue  688 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 31 optimal weight:    0.3980
   chunk 93 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0170
   chunk 38 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
F 548 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.144483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.113728 restraints weight = 20507.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3940 rms_B_bonded: 3.87
r_work: 0.3777 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3786
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3786 r_free = 0.3786    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3786 r_free = 0.3786    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3786
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.3658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8085  Z= 0.123
  Angle     :  0.688  14.207  10983  Z= 0.330
  Chirality :  0.049   0.588   1214
  Planarity :  0.005   0.094   1392
  Dihedral  :  7.206  56.111   1276
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 12.04 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.21 (0.26), residues: 940
  helix: -0.51 (0.46), residues: 133
  sheet: -0.45 (0.46), residues: 122
  loop : -2.02 (0.22), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 412 
 HIS   0.006   0.001   HIS E 264 
 PHE   0.023   0.002   PHE E 231 
 TYR   0.029   0.001   TYR B  16 
 ARG   0.006   0.000   ARG B  22 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00315 (   10)
  link_NAG-ASN         : angle       3.11054 (   30)
  link_BETA1-4         : bond        0.00156 (    1)
  link_BETA1-4         : angle       2.53453 (    3)
  hydrogen bonds       : bond        0.03223 (  170)
  hydrogen bonds       : angle       5.51897 (  429)
  SS BOND              : bond        0.00255 (   23)
  SS BOND              : angle       1.16209 (   46)
  covalent geometry    : bond        0.00296 ( 8051)
  covalent geometry    : angle       0.66544 (10904)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   38 MET cc_start: 0.7414 (mmp) cc_final: 0.7088 (mmm)
REVERT: E   59 ASP cc_start: 0.8071 (m-30) cc_final: 0.7819 (m-30)
REVERT: E  239 GLU cc_start: 0.5007 (pm20) cc_final: 0.4804 (pm20)
REVERT: E  258 PHE cc_start: 0.8634 (t80) cc_final: 0.8277 (t80)
REVERT: E  460 LYS cc_start: 0.7150 (mtpt) cc_final: 0.6358 (pttt)
REVERT: E  557 LYS cc_start: 0.8814 (ptpt) cc_final: 0.8376 (ptpp)
REVERT: F  423 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7962 (pm20)
REVERT: F  582 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8374 (tmtt)
REVERT: F  693 LEU cc_start: 0.8793 (tp) cc_final: 0.8553 (mm)
  outliers start: 10
  outliers final: 8
  residues processed: 69
  average time/residue: 0.1991
  time to fit residues: 20.1579
Evaluate side-chains
  66 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue  111 ASN
Chi-restraints excluded: chain E residue  194 THR
Chi-restraints excluded: chain E residue  262 LEU
Chi-restraints excluded: chain E residue  459 LEU
Chi-restraints excluded: chain E residue  524 CYS
Chi-restraints excluded: chain F residue  423 GLN
Chi-restraints excluded: chain F residue  582 LYS
Chi-restraints excluded: chain F residue  685 CYS
Chi-restraints excluded: chain F residue  688 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 89 optimal weight:    0.0770
   chunk 10 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0980
   chunk 85 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
F 548 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.145202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.115978 restraints weight = 37151.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3959 rms_B_bonded: 6.54
r_work: 0.3700 rms_B_bonded: 5.71 restraints_weight: 2.0000
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3709
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3709 r_free = 0.3709    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3709 r_free = 0.3709    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3709
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.3757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8085  Z= 0.118
  Angle     :  0.690  13.654  10983  Z= 0.328
  Chirality :  0.049   0.587   1214
  Planarity :  0.005   0.094   1392
  Dihedral  :  7.100  56.054   1276
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 12.50 %
    Favored  : 86.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.26), residues: 940
  helix: -0.50 (0.46), residues: 133
  sheet: -0.29 (0.47), residues: 122
  loop : -1.97 (0.22), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 414 
 HIS   0.006   0.001   HIS E 264 
 PHE   0.023   0.002   PHE E 258 
 TYR   0.028   0.001   TYR B  16 
 ARG   0.007   0.000   ARG B  22 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00304 (   10)
  link_NAG-ASN         : angle       3.07252 (   30)
  link_BETA1-4         : bond        0.00165 (    1)
  link_BETA1-4         : angle       2.39513 (    3)
  hydrogen bonds       : bond        0.03183 (  170)
  hydrogen bonds       : angle       5.48109 (  429)
  SS BOND              : bond        0.00246 (   23)
  SS BOND              : angle       1.08487 (   46)
  covalent geometry    : bond        0.00280 ( 8051)
  covalent geometry    : angle       0.66824 (10904)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5291.26 seconds
wall clock time: 91 minutes 40.84 seconds (5500.84 seconds total)