Starting phenix.real_space_refine
on Wed Sep 17 10:15:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6hn5_0247/09_2025/6hn5_0247.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6hn5_0247/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6hn5_0247/09_2025/6hn5_0247.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6hn5_0247/09_2025/6hn5_0247.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6hn5_0247/09_2025/6hn5_0247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6hn5_0247/09_2025/6hn5_0247.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.40, per 1000 atoms: 0.30
  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: 0.65
  Conformation dependent library (CDL) restraints added in 641.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.27
  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: 0.99

  Time building geometry restraints manager: 0.89 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:             1.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.280
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.440
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.017   0.002   ARG E 118 
 TYR   0.035   0.004   TYR E 277 
 PHE   0.042   0.006   PHE F 701 
 TRP   0.035   0.005   TRP F 529 
 HIS   0.023   0.004   HIS E 264 

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

*********************** 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  : 0.276 
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: 0.1231
  time to fit residues: 21.5050
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  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.3980
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.5780

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

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

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.143305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.112139 restraints weight = 33721.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3901 rms_B_bonded: 6.22
r_work: 0.3654 rms_B_bonded: 5.68 restraints_weight: 2.0000
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3665
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3665 r_free = 0.3665    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3664 r_free = 0.3664    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3664
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078   8085  Z= 0.159
  Angle     :  0.785  16.255  10983  Z= 0.386
  Chirality :  0.050   0.312   1214
  Planarity :  0.006   0.093   1392
  Dihedral  :  9.452  59.063   1276
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  7.87 %
    Favored  : 90.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.15 (0.24), residues: 940
  helix: -1.83 (0.40), residues: 130
  sheet: -1.44 (0.43), residues: 142
  loop : -2.47 (0.21), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 488 
 TYR   0.014   0.002   TYR F 401 
 PHE   0.030   0.002   PHE E 258 
 TRP   0.012   0.001   TRP E 414 
 HIS   0.009   0.001   HIS E 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 8051)
  covalent geometry    : angle       0.75161 (10904)
  SS BOND              : bond        0.00648 (   23)
  SS BOND              : angle       1.83741 (   46)
  hydrogen bonds       : bond        0.04804 (  170)
  hydrogen bonds       : angle       6.57103 (  429)
  link_BETA1-4         : bond        0.01726 (    1)
  link_BETA1-4         : angle       3.13719 (    3)
  link_NAG-ASN         : bond        0.00844 (   10)
  link_NAG-ASN         : angle       3.73102 (   30)

*********************** 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: 9
    poor density    : 92
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7987 (tp30)
REVERT: E  460 LYS cc_start: 0.7556 (mtpt) cc_final: 0.6725 (pttt)
REVERT: F  357 ASN cc_start: 0.8909 (m-40) cc_final: 0.8670 (m-40)
REVERT: F  438 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8425 (mm-30)
REVERT: F  504 MET cc_start: 0.8693 (mtt) cc_final: 0.8397 (mtp)
REVERT: F  522 ASP cc_start: 0.6190 (m-30) cc_final: 0.5658 (t0)
  outliers start: 9
  outliers final: 4
  residues processed: 100
  average time/residue: 0.0891
  time to fit residues: 12.1137
Evaluate side-chains
  69 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 28 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 57 optimal weight:    7.9990
   chunk 25 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0770
   chunk 13 optimal weight:    0.0970
   chunk 46 optimal weight:    0.7980
   chunk 54 optimal weight:    0.4980
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.4336

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

Flipped N/Q/H residues before XYZ refinement:
E 189 GLN
E 247 HIS
E 263 HIS
E 337 ASN
E 405 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.144695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.113707 restraints weight = 31991.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3929 rms_B_bonded: 5.95
r_work: 0.3683 rms_B_bonded: 5.61 restraints_weight: 2.0000
r_work (final): 0.3683
-------------------------------------------------------------------------------
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 = 0.06   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: 0.7890
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8085  Z= 0.137
  Angle     :  0.766  20.812  10983  Z= 0.367
  Chirality :  0.050   0.515   1214
  Planarity :  0.005   0.090   1392
  Dihedral  :  8.822  59.366   1276
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  :  9.61 %
    Favored  : 89.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.83 (0.25), residues: 940
  helix: -1.40 (0.43), residues: 128
  sheet: -1.18 (0.44), residues: 143
  loop : -2.30 (0.22), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 717 
 TYR   0.023   0.001   TYR B  16 
 PHE   0.041   0.002   PHE E 258 
 TRP   0.014   0.001   TRP F 414 
 HIS   0.011   0.001   HIS E 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 8051)
  covalent geometry    : angle       0.73272 (10904)
  SS BOND              : bond        0.00527 (   23)
  SS BOND              : angle       1.99520 (   46)
  hydrogen bonds       : bond        0.04180 (  170)
  hydrogen bonds       : angle       6.35366 (  429)
  link_BETA1-4         : bond        0.00034 (    1)
  link_BETA1-4         : angle       3.00167 (    3)
  link_NAG-ASN         : bond        0.00618 (   10)
  link_NAG-ASN         : angle       3.59290 (   30)

*********************** 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
  89 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7908 (tm-30)
REVERT: E   56 MET cc_start: 0.8806 (ttm) cc_final: 0.8560 (ttp)
REVERT: E   59 ASP cc_start: 0.8290 (m-30) cc_final: 0.7962 (m-30)
REVERT: E  337 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8387 (t0)
REVERT: E  460 LYS cc_start: 0.7509 (mtpt) cc_final: 0.6740 (pttt)
REVERT: E  509 GLU cc_start: 0.8917 (tt0) cc_final: 0.8391 (tt0)
REVERT: E  557 LYS cc_start: 0.8818 (ptpt) cc_final: 0.8259 (ptpt)
REVERT: F  423 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7755 (pm20)
  outliers start: 11
  outliers final: 6
  residues processed: 86
  average time/residue: 0.0840
  time to fit residues: 10.3347
Evaluate side-chains
  73 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
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 71 optimal weight:    3.9990
   chunk 2 optimal weight:    0.3980
   chunk 24 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0980
   chunk 41 optimal weight:    0.5980
   chunk 34 optimal weight:    0.1980
   chunk 28 optimal weight:    0.3980
   chunk 90 optimal weight:    0.4980
   chunk 62 optimal weight:    0.0010
   overall best weight:    0.2186

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

Flipped N/Q/H residues before XYZ refinement:
B   5 HIS
** E 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.146268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.115170 restraints weight = 37606.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3953 rms_B_bonded: 6.41
r_work: 0.3698 rms_B_bonded: 5.95 restraints_weight: 2.0000
r_work (final): 0.3698
-------------------------------------------------------------------------------
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: 0.7868
moved from start:          0.3082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8085  Z= 0.114
  Angle     :  0.709  15.819  10983  Z= 0.341
  Chirality :  0.049   0.541   1214
  Planarity :  0.005   0.093   1392
  Dihedral  :  8.285  59.652   1276
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  9.38 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.68 (0.25), residues: 940
  helix: -1.19 (0.44), residues: 131
  sheet: -1.07 (0.46), residues: 133
  loop : -2.21 (0.22), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 488 
 TYR   0.023   0.001   TYR B  16 
 PHE   0.030   0.001   PHE E 258 
 TRP   0.008   0.001   TRP E 412 
 HIS   0.006   0.001   HIS E 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 8051)
  covalent geometry    : angle       0.68360 (10904)
  SS BOND              : bond        0.00325 (   23)
  SS BOND              : angle       1.18777 (   46)
  hydrogen bonds       : bond        0.03708 (  170)
  hydrogen bonds       : angle       5.94879 (  429)
  link_BETA1-4         : bond        0.00118 (    1)
  link_BETA1-4         : angle       2.63569 (    3)
  link_NAG-ASN         : bond        0.00497 (   10)
  link_NAG-ASN         : angle       3.37102 (   30)

*********************** 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
  92 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLU cc_start: 0.8375 (tm-30) cc_final: 0.7965 (tm-30)
REVERT: E   56 MET cc_start: 0.8870 (ttm) cc_final: 0.8605 (ttp)
REVERT: E   59 ASP cc_start: 0.8221 (m-30) cc_final: 0.7928 (m-30)
REVERT: E  211 GLU cc_start: 0.7539 (tt0) cc_final: 0.7066 (tm-30)
REVERT: E  392 THR cc_start: 0.7974 (m) cc_final: 0.7651 (p)
REVERT: E  460 LYS cc_start: 0.7514 (mtpt) cc_final: 0.6660 (pttt)
REVERT: E  486 LEU cc_start: 0.8048 (tp) cc_final: 0.7830 (tt)
REVERT: E  509 GLU cc_start: 0.8931 (tt0) cc_final: 0.8380 (tt0)
REVERT: E  557 LYS cc_start: 0.8742 (ptpt) cc_final: 0.8219 (pttm)
REVERT: F  423 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7743 (pm20)
REVERT: F  438 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8453 (mm-30)
REVERT: F  693 LEU cc_start: 0.8817 (tp) cc_final: 0.8547 (mm)
  outliers start: 9
  outliers final: 5
  residues processed: 88
  average time/residue: 0.0844
  time to fit residues: 10.5065
Evaluate side-chains
  74 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 F residue  423 GLN
Chi-restraints excluded: chain F residue  501 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 57 optimal weight:    9.9990
   chunk 38 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 89 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** E 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 691 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.141772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.110041 restraints weight = 40410.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3868 rms_B_bonded: 5.99
r_work: 0.3624 rms_B_bonded: 5.69 restraints_weight: 2.0000
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3634
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3634 r_free = 0.3634    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 = 0.3634 r_free = 0.3634    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3634
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.3042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8085  Z= 0.210
  Angle     :  0.767  17.685  10983  Z= 0.366
  Chirality :  0.052   0.558   1214
  Planarity :  0.005   0.091   1392
  Dihedral  :  8.088  56.004   1276
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  9.49 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.59 (0.25), residues: 940
  helix: -1.07 (0.44), residues: 131
  sheet: -1.10 (0.44), residues: 138
  loop : -2.14 (0.22), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E  14 
 TYR   0.032   0.002   TYR B  16 
 PHE   0.025   0.002   PHE E 258 
 TRP   0.013   0.002   TRP F 529 
 HIS   0.008   0.001   HIS E 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 ( 8051)
  covalent geometry    : angle       0.73923 (10904)
  SS BOND              : bond        0.00466 (   23)
  SS BOND              : angle       1.53995 (   46)
  hydrogen bonds       : bond        0.03976 (  170)
  hydrogen bonds       : angle       5.93998 (  429)
  link_BETA1-4         : bond        0.00275 (    1)
  link_BETA1-4         : angle       3.43489 (    3)
  link_NAG-ASN         : bond        0.00547 (   10)
  link_NAG-ASN         : angle       3.49386 (   30)

*********************** 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
  80 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8003 (tm-30)
REVERT: E   59 ASP cc_start: 0.8464 (m-30) cc_final: 0.8081 (m-30)
REVERT: E  211 GLU cc_start: 0.7684 (tt0) cc_final: 0.7398 (tm-30)
REVERT: E  239 GLU cc_start: 0.4827 (pm20) cc_final: 0.4594 (pm20)
REVERT: E  460 LYS cc_start: 0.7413 (mtpt) cc_final: 0.6617 (pttt)
REVERT: E  509 GLU cc_start: 0.8952 (tt0) cc_final: 0.8485 (tt0)
REVERT: E  557 LYS cc_start: 0.8827 (ptpt) cc_final: 0.8319 (ptpt)
REVERT: F  423 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7931 (pm20)
REVERT: F  582 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8611 (tmtt)
  outliers start: 15
  outliers final: 5
  residues processed: 77
  average time/residue: 0.1015
  time to fit residues: 10.6303
Evaluate side-chains
  69 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
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  582 LYS
Chi-restraints excluded: chain F residue  685 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 87 optimal weight:    0.0270
   chunk 16 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 89 optimal weight:    0.4980
   chunk 58 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.6238

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

Flipped N/Q/H residues before XYZ refinement:
** E 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 357 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.144041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.113528 restraints weight = 30588.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3933 rms_B_bonded: 5.68
r_work: 0.3695 rms_B_bonded: 5.31 restraints_weight: 2.0000
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3706
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3706 r_free = 0.3706    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 = 0.3706 r_free = 0.3706    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3706
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.3315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8085  Z= 0.134
  Angle     :  0.704  16.222  10983  Z= 0.335
  Chirality :  0.050   0.564   1214
  Planarity :  0.005   0.092   1392
  Dihedral  :  7.710  56.075   1276
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 10.65 %
    Favored  : 87.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.48 (0.25), residues: 940
  helix: -0.96 (0.44), residues: 132
  sheet: -1.01 (0.45), residues: 133
  loop : -2.07 (0.22), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 498 
 TYR   0.022   0.001   TYR B  16 
 PHE   0.026   0.002   PHE E 258 
 TRP   0.009   0.001   TRP E 412 
 HIS   0.006   0.001   HIS E 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8051)
  covalent geometry    : angle       0.67974 (10904)
  SS BOND              : bond        0.00362 (   23)
  SS BOND              : angle       1.14458 (   46)
  hydrogen bonds       : bond        0.03493 (  170)
  hydrogen bonds       : angle       5.68811 (  429)
  link_BETA1-4         : bond        0.00145 (    1)
  link_BETA1-4         : angle       2.73530 (    3)
  link_NAG-ASN         : bond        0.00421 (   10)
  link_NAG-ASN         : angle       3.30499 (   30)

*********************** 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
  76 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8022 (tm-30)
REVERT: E   56 MET cc_start: 0.8729 (ttm) cc_final: 0.8485 (ttp)
REVERT: E   59 ASP cc_start: 0.8191 (m-30) cc_final: 0.7882 (m-30)
REVERT: E  239 GLU cc_start: 0.4844 (pm20) cc_final: 0.4633 (pm20)
REVERT: E  258 PHE cc_start: 0.8715 (t80) cc_final: 0.8258 (t80)
REVERT: E  460 LYS cc_start: 0.7339 (mtpt) cc_final: 0.6545 (pttt)
REVERT: E  509 GLU cc_start: 0.8887 (tt0) cc_final: 0.8504 (tt0)
REVERT: E  557 LYS cc_start: 0.8799 (ptpt) cc_final: 0.8341 (ptpp)
REVERT: F  423 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7850 (pm20)
REVERT: F  582 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8545 (tmtt)
  outliers start: 11
  outliers final: 5
  residues processed: 74
  average time/residue: 0.0870
  time to fit residues: 9.1801
Evaluate side-chains
  65 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
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  582 LYS
Chi-restraints excluded: chain F residue  685 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0060
   chunk 56 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   chunk 76 optimal weight:    0.2980
   chunk 13 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
** E 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 357 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.144704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.114405 restraints weight = 35400.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3938 rms_B_bonded: 6.24
r_work: 0.3692 rms_B_bonded: 5.58 restraints_weight: 2.0000
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3701
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3701 r_free = 0.3701    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 = 0.3701 r_free = 0.3701    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3701
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.3469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8085  Z= 0.122
  Angle     :  0.685  15.307  10983  Z= 0.328
  Chirality :  0.049   0.575   1214
  Planarity :  0.005   0.094   1392
  Dihedral  :  7.390  56.031   1276
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 11.23 %
    Favored  : 87.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.38 (0.26), residues: 940
  helix: -0.76 (0.46), residues: 132
  sheet: -0.87 (0.45), residues: 133
  loop : -2.05 (0.22), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 498 
 TYR   0.021   0.001   TYR A  14 
 PHE   0.025   0.002   PHE E 258 
 TRP   0.009   0.001   TRP E 412 
 HIS   0.006   0.001   HIS E 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8051)
  covalent geometry    : angle       0.66109 (10904)
  SS BOND              : bond        0.00288 (   23)
  SS BOND              : angle       1.09872 (   46)
  hydrogen bonds       : bond        0.03330 (  170)
  hydrogen bonds       : angle       5.54688 (  429)
  link_BETA1-4         : bond        0.00177 (    1)
  link_BETA1-4         : angle       2.71491 (    3)
  link_NAG-ASN         : bond        0.00362 (   10)
  link_NAG-ASN         : angle       3.22337 (   30)

*********************** 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
  76 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8066 (tm-30)
REVERT: E   56 MET cc_start: 0.8746 (ttm) cc_final: 0.8499 (ttp)
REVERT: E   59 ASP cc_start: 0.8236 (m-30) cc_final: 0.8018 (m-30)
REVERT: E  258 PHE cc_start: 0.8693 (t80) cc_final: 0.8266 (t80)
REVERT: E  460 LYS cc_start: 0.7332 (mtpt) cc_final: 0.6492 (pttt)
REVERT: E  509 GLU cc_start: 0.8862 (tt0) cc_final: 0.8476 (tt0)
REVERT: E  557 LYS cc_start: 0.8786 (ptpt) cc_final: 0.8365 (ptpp)
REVERT: F  423 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7872 (pm20)
REVERT: F  582 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8479 (tmtt)
  outliers start: 11
  outliers final: 7
  residues processed: 74
  average time/residue: 0.0852
  time to fit residues: 9.0350
Evaluate side-chains
  65 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
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  582 LYS
Chi-restraints excluded: chain F residue  685 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 90 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 25 optimal weight:    8.9990
   chunk 31 optimal weight:    0.0170
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 69 optimal weight:    0.6980
   overall best weight:    0.6420

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

Flipped N/Q/H residues before XYZ refinement:
** E 263 HIS ** 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 = 0.4378 r_free = 0.4378 target = 0.144362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.114252 restraints weight = 34868.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 6.15
r_work: 0.3689 rms_B_bonded: 5.53 restraints_weight: 2.0000
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3698
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3698 r_free = 0.3698    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 = 0.3698 r_free = 0.3698    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3698
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.3553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8085  Z= 0.135
  Angle     :  0.697  15.122  10983  Z= 0.334
  Chirality :  0.050   0.580   1214
  Planarity :  0.005   0.093   1392
  Dihedral  :  7.279  56.034   1276
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 12.27 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.31 (0.25), residues: 940
  helix: -0.70 (0.45), residues: 132
  sheet: -0.60 (0.46), residues: 123
  loop : -2.04 (0.22), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 498 
 TYR   0.030   0.002   TYR B  16 
 PHE   0.023   0.002   PHE E 258 
 TRP   0.009   0.001   TRP E 412 
 HIS   0.006   0.001   HIS E 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8051)
  covalent geometry    : angle       0.67328 (10904)
  SS BOND              : bond        0.00283 (   23)
  SS BOND              : angle       1.21660 (   46)
  hydrogen bonds       : bond        0.03333 (  170)
  hydrogen bonds       : angle       5.59195 (  429)
  link_BETA1-4         : bond        0.00201 (    1)
  link_BETA1-4         : angle       2.71550 (    3)
  link_NAG-ASN         : bond        0.00341 (   10)
  link_NAG-ASN         : angle       3.20271 (   30)

*********************** 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
  68 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8093 (tm-30)
REVERT: E   56 MET cc_start: 0.8743 (ttm) cc_final: 0.8493 (ttp)
REVERT: E   59 ASP cc_start: 0.8255 (m-30) cc_final: 0.8033 (m-30)
REVERT: E  239 GLU cc_start: 0.4938 (pm20) cc_final: 0.4675 (pm20)
REVERT: E  258 PHE cc_start: 0.8647 (t80) cc_final: 0.8251 (t80)
REVERT: E  460 LYS cc_start: 0.7217 (mtpt) cc_final: 0.6404 (pttt)
REVERT: E  509 GLU cc_start: 0.8822 (tt0) cc_final: 0.8183 (tt0)
REVERT: E  557 LYS cc_start: 0.8585 (ptpt) cc_final: 0.8288 (pttm)
REVERT: F  423 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7855 (pm20)
REVERT: F  582 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8473 (tmtt)
REVERT: F  693 LEU cc_start: 0.8827 (tp) cc_final: 0.8580 (mm)
  outliers start: 10
  outliers final: 7
  residues processed: 66
  average time/residue: 0.0849
  time to fit residues: 8.2161
Evaluate side-chains
  63 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
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  582 LYS
Chi-restraints excluded: chain F residue  685 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 49 optimal weight:    0.2980
   chunk 6 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 87 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
** E 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.143398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.111651 restraints weight = 25518.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3897 rms_B_bonded: 4.33
r_work: 0.3724 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3735
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3735 r_free = 0.3735    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3735 r_free = 0.3735    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3735
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.3566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8085  Z= 0.149
  Angle     :  0.705  15.199  10983  Z= 0.337
  Chirality :  0.050   0.584   1214
  Planarity :  0.005   0.093   1392
  Dihedral  :  7.247  56.072   1276
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 12.04 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.32 (0.25), residues: 940
  helix: -0.85 (0.44), residues: 136
  sheet: -0.44 (0.47), residues: 121
  loop : -2.06 (0.22), residues: 683

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 498 
 TYR   0.029   0.002   TYR B  16 
 PHE   0.022   0.002   PHE E 258 
 TRP   0.010   0.001   TRP E 412 
 HIS   0.006   0.001   HIS E 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 8051)
  covalent geometry    : angle       0.68048 (10904)
  SS BOND              : bond        0.00331 (   23)
  SS BOND              : angle       1.26180 (   46)
  hydrogen bonds       : bond        0.03390 (  170)
  hydrogen bonds       : angle       5.56518 (  429)
  link_BETA1-4         : bond        0.00302 (    1)
  link_BETA1-4         : angle       2.74698 (    3)
  link_NAG-ASN         : bond        0.00339 (   10)
  link_NAG-ASN         : angle       3.20825 (   30)

*********************** 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
  66 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8028 (tm-30)
REVERT: E   56 MET cc_start: 0.8671 (ttm) cc_final: 0.8432 (ttp)
REVERT: E   59 ASP cc_start: 0.8180 (m-30) cc_final: 0.7955 (m-30)
REVERT: E  239 GLU cc_start: 0.4990 (pm20) cc_final: 0.4764 (pm20)
REVERT: E  460 LYS cc_start: 0.7189 (mtpt) cc_final: 0.6385 (pttt)
REVERT: E  504 MET cc_start: 0.8878 (mtm) cc_final: 0.8662 (mtm)
REVERT: E  509 GLU cc_start: 0.8747 (tt0) cc_final: 0.8290 (tt0)
REVERT: E  557 LYS cc_start: 0.8706 (ptpt) cc_final: 0.8260 (ptpp)
REVERT: F  423 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7940 (pm20)
REVERT: F  582 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8432 (tmtt)
  outliers start: 12
  outliers final: 7
  residues processed: 64
  average time/residue: 0.0919
  time to fit residues: 8.2605
Evaluate side-chains
  61 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
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  585 ILE
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 48 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0070
   chunk 80 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   overall best weight:    1.0602

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

Flipped N/Q/H residues before XYZ refinement:
** E 263 HIS ** 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 = 0.4341 r_free = 0.4341 target = 0.141782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.110959 restraints weight = 33246.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3888 rms_B_bonded: 6.05
r_work: 0.3634 rms_B_bonded: 5.72 restraints_weight: 2.0000
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3645
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3645 r_free = 0.3645    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 = 0.3645 r_free = 0.3645    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3645
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.3538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8085  Z= 0.175
  Angle     :  0.731  15.890  10983  Z= 0.350
  Chirality :  0.051   0.585   1214
  Planarity :  0.005   0.092   1392
  Dihedral  :  7.272  56.080   1276
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 12.27 %
    Favored  : 86.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.36 (0.25), residues: 940
  helix: -1.00 (0.43), residues: 136
  sheet: -0.55 (0.45), residues: 127
  loop : -2.04 (0.22), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E  14 
 TYR   0.033   0.002   TYR B  16 
 PHE   0.021   0.002   PHE E 258 
 TRP   0.011   0.001   TRP E 412 
 HIS   0.006   0.001   HIS E 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 8051)
  covalent geometry    : angle       0.70692 (10904)
  SS BOND              : bond        0.00368 (   23)
  SS BOND              : angle       1.34589 (   46)
  hydrogen bonds       : bond        0.03531 (  170)
  hydrogen bonds       : angle       5.63518 (  429)
  link_BETA1-4         : bond        0.00383 (    1)
  link_BETA1-4         : angle       2.84903 (    3)
  link_NAG-ASN         : bond        0.00370 (   10)
  link_NAG-ASN         : angle       3.26452 (   30)

********************** 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
  64 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8128 (tm-30)
REVERT: E   56 MET cc_start: 0.8794 (ttm) cc_final: 0.8515 (ttp)
REVERT: E   59 ASP cc_start: 0.8375 (m-30) cc_final: 0.8124 (m-30)
REVERT: E  239 GLU cc_start: 0.5110 (pm20) cc_final: 0.4860 (pm20)
REVERT: E  460 LYS cc_start: 0.7337 (mtpt) cc_final: 0.6484 (pttt)
REVERT: E  504 MET cc_start: 0.8920 (mtm) cc_final: 0.8688 (mtm)
REVERT: E  509 GLU cc_start: 0.8878 (tt0) cc_final: 0.8490 (tt0)
REVERT: E  557 LYS cc_start: 0.8794 (ptpt) cc_final: 0.8336 (ptpp)
REVERT: F  423 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7896 (pm20)
REVERT: F  582 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8482 (tmtt)
  outliers start: 11
  outliers final: 7
  residues processed: 62
  average time/residue: 0.1007
  time to fit residues: 8.7853
Evaluate side-chains
  60 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
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  585 ILE
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 35 optimal weight:    0.0070
   chunk 16 optimal weight:    0.1980
   chunk 42 optimal weight:    0.0980
   chunk 72 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 71 optimal weight:    3.9990
   chunk 80 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.3598

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

Flipped N/Q/H residues before XYZ refinement:
** E 263 HIS ** 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 = 0.4386 r_free = 0.4386 target = 0.145070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.115574 restraints weight = 30953.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3965 rms_B_bonded: 5.87
r_work: 0.3710 rms_B_bonded: 5.51 restraints_weight: 2.0000
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3721
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3721 r_free = 0.3721    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 = 0.3721 r_free = 0.3721    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3721
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.3776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8085  Z= 0.114
  Angle     :  0.687  13.964  10983  Z= 0.327
  Chirality :  0.049   0.573   1214
  Planarity :  0.004   0.094   1392
  Dihedral  :  7.102  56.116   1276
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 12.96 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.24 (0.26), residues: 940
  helix: -0.79 (0.44), residues: 136
  sheet: -0.39 (0.47), residues: 122
  loop : -1.99 (0.22), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 498 
 TYR   0.026   0.001   TYR B  16 
 PHE   0.023   0.001   PHE E 258 
 TRP   0.008   0.001   TRP E 412 
 HIS   0.005   0.001   HIS E 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8051)
  covalent geometry    : angle       0.66562 (10904)
  SS BOND              : bond        0.00255 (   23)
  SS BOND              : angle       1.03640 (   46)
  hydrogen bonds       : bond        0.03172 (  170)
  hydrogen bonds       : angle       5.49611 (  429)
  link_BETA1-4         : bond        0.00072 (    1)
  link_BETA1-4         : angle       2.21537 (    3)
  link_NAG-ASN         : bond        0.00309 (   10)
  link_NAG-ASN         : angle       3.08979 (   30)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2551.56 seconds
wall clock time: 44 minutes 17.78 seconds (2657.78 seconds total)