Starting phenix.real_space_refine
on Fri Sep 11 05:37:54 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6hn5_0247/09_2026/6hn5_0247.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6hn5_0247/09_2026/6hn5_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 {
    restraint_files = "/net/cci-nas-00/data/ceres_data/6hn5_0247/09_2026/6hn5_0247.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6hn5_0247/09_2026/6hn5_0247.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6hn5_0247/09_2026/6hn5_0247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6hn5_0247/09_2026/6hn5_0247.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6hn5_0247/09_2026/6hn5_0247.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6hn5_0247/09_2026/6hn5_0247.cif"
  }
  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-2.2.1-6174/lib/python3.11/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 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 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 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: 2.60, per 1000 atoms: 0.33
  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: 0.70
  Conformation dependent library (CDL) restraints added in 460.0 milliseconds
  

  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: 0.22
  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: 1.29

  Time building geometry restraints manager: 0.92 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: 4496
       15.41 -    30.82: 219
       30.82 -    46.22: 54
       46.22 -    61.63: 10
       61.63 -    77.04: 4
  Dihedral angle restraints: 4783
    sinusoidal: 1998
      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 4780 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:             1.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     9.340
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
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  :  9.753  74.824   2920
  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 are 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/Z
  covalent geometry    : bond        0.01201 /  0.50 ( 8051)
  covalent geometry    : angle       1.19966 /  0.62 (10904)
  SS BOND              : bond        0.00876 /  0.56 (   23)
  SS BOND              : angle       2.46830 /  1.60 (   46)
  hydrogen bonds       : bond        0.17124 / 10.53 (  170)
  hydrogen bonds       : angle       8.66206 /  5.77 (  429)
  link_BETA1-4         : bond        0.01932 /  1.21 (    1)
  link_BETA1-4         : angle       5.95927 /  2.84 (    3)
  link_NAG-ASN         : bond        0.01000 /  0.73 (   10)
  link_NAG-ASN         : angle       3.58369 /  2.07 (   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  : 0.199 
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: 0.1188
  time to fit residues: 20.9223
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  : 0.353 
-------------------------------------------------------------------------------
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...
E  15 ASN
E 187 HIS
E 247 HIS
E 295 ASN
E 313 HIS
E 405 ASN
E 561 GLN
F 561 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.143525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.114533 restraints weight = 33217.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 5.91
r_work: 0.3681 rms_B_bonded: 5.42 restraints_weight: 2.0000
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3691
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3691 r_free = 0.3691    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3691 r_free = 0.3691    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (9 function evaluations)
r_final: 0.3691
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   8085  Z= 0.157
  Angle     :  0.768  16.592  10983  Z= 0.377
  Chirality :  0.050   0.355   1214
  Planarity :  0.006   0.093   1392
  Dihedral  :  6.384  41.572   1045
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  7.99 %
    Favored  : 90.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.10 (0.24), residues: 940
  helix: -1.77 (0.41), residues: 130
  sheet: -1.46 (0.43), residues: 140
  loop : -2.43 (0.21), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 488 
 TYR   0.014   0.002   TYR F 401 
 PHE   0.029   0.002   PHE E 258 
 TRP   0.013   0.001   TRP E 414 
 HIS   0.009   0.001   HIS E 264 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.16 ( 8051)
  covalent geometry    : angle       0.73628 /  0.37 (10904)
  SS BOND              : bond        0.00420 /  0.26 (   23)
  SS BOND              : angle       1.70759 /  1.13 (   46)
  hydrogen bonds       : bond        0.04573 /  2.74 (  170)
  hydrogen bonds       : angle       6.46409 /  4.19 (  429)
  link_BETA1-4         : bond        0.00407 /  0.25 (    1)
  link_BETA1-4         : angle       3.48142 /  1.42 (    3)
  link_NAG-ASN         : bond        0.00533 /  0.29 (   10)
  link_NAG-ASN         : angle       3.64307 /  1.88 (   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
  100 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  460 LYS cc_start: 0.7516 (mtpt) cc_final: 0.6714 (pttt)
REVERT: E  509 GLU cc_start: 0.8920 (tt0) cc_final: 0.8473 (tt0)
REVERT: E  557 LYS cc_start: 0.8743 (ptpt) cc_final: 0.8095 (ptpt)
REVERT: F  357 ASN cc_start: 0.8910 (m-40) cc_final: 0.8646 (m-40)
REVERT: F  438 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8423 (mm-30)
REVERT: F  522 ASP cc_start: 0.6120 (m-30) cc_final: 0.5632 (t0)
  outliers start: 9
  outliers final: 4
  residues processed: 99
  average time/residue: 0.0954
  time to fit residues: 12.9623
Evaluate side-chains
  68 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 63 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0770
   chunk 54 optimal weight:    4.9990
   chunk 69 optimal weight:    0.5980
   overall best weight:    0.5338

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 189 GLN
E 337 ASN
E 405 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.144255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.114506 restraints weight = 31620.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3940 rms_B_bonded: 5.88
r_work: 0.3692 rms_B_bonded: 5.38 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 = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-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 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (7 function evaluations)
r_final: 0.3701
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   8085  Z= 0.144
  Angle     :  0.761  20.249  10983  Z= 0.363
  Chirality :  0.050   0.482   1214
  Planarity :  0.005   0.090   1392
  Dihedral  :  6.003  39.284   1045
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  :  9.38 %
    Favored  : 89.24 %
  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 are not related in a simple way.
  whole: -2.78 (0.25), residues: 940
  helix: -1.32 (0.43), residues: 129
  sheet: -1.17 (0.43), residues: 143
  loop : -2.27 (0.22), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E 229 
 TYR   0.030   0.002   TYR B  16 
 PHE   0.036   0.002   PHE E 258 
 TRP   0.014   0.001   TRP F 414 
 HIS   0.016   0.001   HIS E 264 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.14 ( 8051)
  covalent geometry    : angle       0.72912 /  0.35 (10904)
  SS BOND              : bond        0.00444 /  0.28 (   23)
  SS BOND              : angle       2.01780 /  1.49 (   46)
  hydrogen bonds       : bond        0.04091 /  2.55 (  170)
  hydrogen bonds       : angle       6.28585 /  4.08 (  429)
  link_BETA1-4         : bond        0.00252 /  0.16 (    1)
  link_BETA1-4         : angle       2.50434 /  1.18 (    3)
  link_NAG-ASN         : bond        0.00610 /  0.32 (   10)
  link_NAG-ASN         : angle       3.45243 /  1.82 (   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
  90 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   59 ASP cc_start: 0.8270 (m-30) cc_final: 0.7931 (m-30)
REVERT: E  337 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8384 (t0)
REVERT: E  460 LYS cc_start: 0.7517 (mtpt) cc_final: 0.6709 (pttt)
REVERT: E  509 GLU cc_start: 0.8950 (tt0) cc_final: 0.8733 (tt0)
REVERT: E  557 LYS cc_start: 0.8824 (ptpt) cc_final: 0.8356 (ptpp)
REVERT: F  423 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7806 (pm20)
  outliers start: 11
  outliers final: 7
  residues processed: 86
  average time/residue: 0.0891
  time to fit residues: 10.9726
Evaluate side-chains
  75 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
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  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:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 44 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 28 optimal weight:    0.4980
   chunk 90 optimal weight:    0.1980
   chunk 62 optimal weight:    5.9990
   overall best weight:    0.6182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 337 ASN
** 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 = 0.4374 r_free = 0.4374 target = 0.144159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.114032 restraints weight = 37707.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3932 rms_B_bonded: 6.51
r_work: 0.3675 rms_B_bonded: 5.69 restraints_weight: 2.0000
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3684
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3684 r_free = 0.3684    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3684 r_free = 0.3684    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3684
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8085  Z= 0.142
  Angle     :  0.727  16.998  10983  Z= 0.348
  Chirality :  0.049   0.490   1214
  Planarity :  0.005   0.091   1392
  Dihedral  :  5.787  37.610   1045
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  :  9.26 %
    Favored  : 89.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.25), residues: 940
  helix: -1.20 (0.44), residues: 131
  sheet: -1.11 (0.45), residues: 133
  loop : -2.19 (0.22), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 488 
 TYR   0.030   0.001   TYR B  16 
 PHE   0.029   0.002   PHE E 258 
 TRP   0.009   0.001   TRP E 412 
 HIS   0.006   0.001   HIS E 264 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00335 /  0.14 ( 8051)
  covalent geometry    : angle       0.70202 /  0.34 (10904)
  SS BOND              : bond        0.00352 /  0.22 (   23)
  SS BOND              : angle       1.41980 /  1.00 (   46)
  hydrogen bonds       : bond        0.03716 /  2.34 (  170)
  hydrogen bonds       : angle       6.00575 /  3.86 (  429)
  link_BETA1-4         : bond        0.00109 /  0.07 (    1)
  link_BETA1-4         : angle       2.55533 /  1.23 (    3)
  link_NAG-ASN         : bond        0.00495 /  0.27 (   10)
  link_NAG-ASN         : angle       3.27970 /  1.71 (   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
  82 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   59 ASP cc_start: 0.8302 (m-30) cc_final: 0.7976 (m-30)
REVERT: E  211 GLU cc_start: 0.7591 (tt0) cc_final: 0.7146 (tm-30)
REVERT: E  258 PHE cc_start: 0.8763 (t80) cc_final: 0.8556 (t80)
REVERT: E  460 LYS cc_start: 0.7491 (mtpt) cc_final: 0.6690 (pttt)
REVERT: E  509 GLU cc_start: 0.8937 (tt0) cc_final: 0.8606 (tt0)
REVERT: E  557 LYS cc_start: 0.8803 (ptpt) cc_final: 0.8350 (ptpt)
REVERT: F  423 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7842 (pm20)
REVERT: F  582 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8595 (tmtt)
REVERT: F  693 LEU cc_start: 0.8854 (tp) cc_final: 0.8589 (mm)
  outliers start: 11
  outliers final: 7
  residues processed: 79
  average time/residue: 0.0855
  time to fit residues: 9.6774
Evaluate side-chains
  77 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
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 F residue  423 GLN
Chi-restraints excluded: chain F residue  501 LEU
Chi-restraints excluded: chain F residue  509 GLU
Chi-restraints excluded: chain F residue  582 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 77 optimal weight:    6.9990
   chunk 57 optimal weight:    9.9990
   chunk 38 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 89 optimal weight:    0.4980
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.4320 r_free = 0.4320 target = 0.140231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.108287 restraints weight = 39932.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3845 rms_B_bonded: 5.61
r_work: 0.3615 rms_B_bonded: 5.53 restraints_weight: 2.0000
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3624
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3624 r_free = 0.3624    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 = 0.3624 r_free = 0.3624    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3624
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.2921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   8085  Z= 0.229
  Angle     :  0.780  18.743  10983  Z= 0.374
  Chirality :  0.051   0.509   1214
  Planarity :  0.005   0.090   1392
  Dihedral  :  5.858  38.404   1045
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  :  9.14 %
    Favored  : 88.89 %
  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 are not related in a simple way.
  whole: -2.66 (0.25), residues: 940
  helix: -1.11 (0.44), residues: 131
  sheet: -1.15 (0.43), residues: 138
  loop : -2.20 (0.22), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E  14 
 TYR   0.022   0.002   TYR B  16 
 PHE   0.026   0.002   PHE E 258 
 TRP   0.015   0.002   TRP F 529 
 HIS   0.007   0.001   HIS E 264 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00546 /  0.23 ( 8051)
  covalent geometry    : angle       0.75272 /  0.37 (10904)
  SS BOND              : bond        0.00478 /  0.28 (   23)
  SS BOND              : angle       1.69815 /  1.18 (   46)
  hydrogen bonds       : bond        0.04040 /  2.57 (  170)
  hydrogen bonds       : angle       5.99293 /  3.90 (  429)
  link_BETA1-4         : bond        0.00279 /  0.17 (    1)
  link_BETA1-4         : angle       3.10472 /  1.55 (    3)
  link_NAG-ASN         : bond        0.00519 /  0.32 (   10)
  link_NAG-ASN         : angle       3.34612 /  1.76 (   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
  81 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   59 ASP cc_start: 0.8483 (m-30) cc_final: 0.8090 (m-30)
REVERT: E  211 GLU cc_start: 0.7642 (tt0) cc_final: 0.7363 (tm-30)
REVERT: E  239 GLU cc_start: 0.4607 (pm20) cc_final: 0.4376 (pm20)
REVERT: E  258 PHE cc_start: 0.8765 (t80) cc_final: 0.8545 (t80)
REVERT: E  460 LYS cc_start: 0.7433 (mtpt) cc_final: 0.6614 (pttt)
REVERT: E  509 GLU cc_start: 0.8848 (tt0) cc_final: 0.8530 (tt0)
REVERT: E  557 LYS cc_start: 0.8829 (ptpt) cc_final: 0.8416 (ptpt)
REVERT: F  423 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7949 (pm20)
REVERT: F  582 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8563 (tmtt)
  outliers start: 16
  outliers final: 7
  residues processed: 77
  average time/residue: 0.0902
  time to fit residues: 9.8161
Evaluate side-chains
  70 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue  111 ASN
Chi-restraints excluded: chain E residue  459 LEU
Chi-restraints excluded: chain E residue  524 CYS
Chi-restraints excluded: chain F residue  423 GLN
Chi-restraints excluded: chain F residue  509 GLU
Chi-restraints excluded: chain F residue  576 ARG
Chi-restraints excluded: chain F residue  582 LYS
Chi-restraints excluded: chain F residue  685 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 42 optimal weight:    0.4980
   chunk 68 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B   5 HIS
E 337 ASN
F 357 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.142442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.112187 restraints weight = 30514.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3903 rms_B_bonded: 5.79
r_work: 0.3653 rms_B_bonded: 5.55 restraints_weight: 2.0000
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3664
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3664 r_free = 0.3664    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3664 r_free = 0.3664    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.3664
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.3166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8085  Z= 0.152
  Angle     :  0.706  17.316  10983  Z= 0.336
  Chirality :  0.049   0.509   1214
  Planarity :  0.005   0.093   1392
  Dihedral  :  5.616  37.614   1045
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 10.42 %
    Favored  : 88.08 %
  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 are not related in a simple way.
  whole: -2.52 (0.25), residues: 940
  helix: -0.91 (0.45), residues: 132
  sheet: -1.01 (0.44), residues: 138
  loop : -2.13 (0.22), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 498 
 TYR   0.017   0.001   TYR B  16 
 PHE   0.026   0.002   PHE E 258 
 TRP   0.010   0.001   TRP E 412 
 HIS   0.007   0.001   HIS E 264 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.15 ( 8051)
  covalent geometry    : angle       0.68216 /  0.33 (10904)
  SS BOND              : bond        0.00350 /  0.20 (   23)
  SS BOND              : angle       1.27479 /  0.90 (   46)
  hydrogen bonds       : bond        0.03608 /  2.27 (  170)
  hydrogen bonds       : angle       5.76421 /  3.72 (  429)
  link_BETA1-4         : bond        0.00107 /  0.07 (    1)
  link_BETA1-4         : angle       2.46275 /  1.26 (    3)
  link_NAG-ASN         : bond        0.00440 /  0.25 (   10)
  link_NAG-ASN         : angle       3.19848 /  1.68 (   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
  77 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   22 ARG cc_start: 0.7294 (ttp-110) cc_final: 0.7062 (ttp-110)
REVERT: E   59 ASP cc_start: 0.8302 (m-30) cc_final: 0.7952 (m-30)
REVERT: E  258 PHE cc_start: 0.8736 (t80) cc_final: 0.8312 (t80)
REVERT: E  460 LYS cc_start: 0.7421 (mtpt) cc_final: 0.6605 (pttt)
REVERT: E  509 GLU cc_start: 0.8849 (tt0) cc_final: 0.8473 (tt0)
REVERT: E  557 LYS cc_start: 0.8826 (ptpt) cc_final: 0.8385 (ptpt)
REVERT: F  423 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7932 (pm20)
REVERT: F  582 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8518 (tmtt)
  outliers start: 12
  outliers final: 6
  residues processed: 75
  average time/residue: 0.0825
  time to fit residues: 8.8697
Evaluate side-chains
  69 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
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  411 LEU
Chi-restraints excluded: chain F residue  423 GLN
Chi-restraints excluded: chain F residue  582 LYS
Chi-restraints excluded: chain F residue  685 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 80 optimal weight:    0.0170
   chunk 36 optimal weight:    0.3980
   chunk 70 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 79 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9990
   chunk 76 optimal weight:    7.9990
   chunk 13 optimal weight:    0.5980
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.4418

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.144096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.113402 restraints weight = 35093.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3921 rms_B_bonded: 6.22
r_work: 0.3665 rms_B_bonded: 5.86 restraints_weight: 2.0000
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3675
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3675 r_free = 0.3675    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3675 r_free = 0.3675    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3675
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.3383

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= 0.118
  Angle     :  0.685  15.687  10983  Z= 0.325
  Chirality :  0.049   0.512   1214
  Planarity :  0.005   0.095   1392
  Dihedral  :  5.381  37.317   1045
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 11.23 %
    Favored  : 87.27 %
  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 are not related in a simple way.
  whole: -2.41 (0.26), residues: 940
  helix: -0.71 (0.46), residues: 132
  sheet: -0.94 (0.44), residues: 133
  loop : -2.07 (0.22), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 498 
 TYR   0.017   0.001   TYR A  14 
 PHE   0.025   0.002   PHE E 258 
 TRP   0.010   0.001   TRP E 412 
 HIS   0.006   0.001   HIS E 264 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.12 ( 8051)
  covalent geometry    : angle       0.66372 /  0.32 (10904)
  SS BOND              : bond        0.00292 /  0.17 (   23)
  SS BOND              : angle       1.09883 /  0.82 (   46)
  hydrogen bonds       : bond        0.03350 /  2.07 (  170)
  hydrogen bonds       : angle       5.55571 /  3.56 (  429)
  link_BETA1-4         : bond        0.00072 /  0.05 (    1)
  link_BETA1-4         : angle       2.25933 /  1.14 (    3)
  link_NAG-ASN         : bond        0.00356 /  0.19 (   10)
  link_NAG-ASN         : angle       3.03991 /  1.59 (   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
  80 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   56 MET cc_start: 0.8634 (ttm) cc_final: 0.8367 (ttp)
REVERT: E   59 ASP cc_start: 0.8336 (m-30) cc_final: 0.8099 (m-30)
REVERT: E  258 PHE cc_start: 0.8676 (t80) cc_final: 0.8257 (t80)
REVERT: E  460 LYS cc_start: 0.7353 (mtpt) cc_final: 0.6525 (pttt)
REVERT: F  423 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7886 (pm20)
  outliers start: 12
  outliers final: 7
  residues processed: 77
  average time/residue: 0.0784
  time to fit residues: 8.7136
Evaluate side-chains
  66 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue  111 ASN
Chi-restraints excluded: chain E residue  293 THR
Chi-restraints excluded: chain E residue  459 LEU
Chi-restraints excluded: chain E residue  524 CYS
Chi-restraints excluded: chain F residue  368 LEU
Chi-restraints excluded: chain F residue  423 GLN
Chi-restraints excluded: chain F residue  685 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 90 optimal weight:    0.0980
   chunk 78 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 84 optimal weight:    0.5980
   chunk 25 optimal weight:    5.9990
   chunk 31 optimal weight:    0.3980
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    0.0670
   chunk 5 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.3718

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.145045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.114315 restraints weight = 34513.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3936 rms_B_bonded: 6.22
r_work: 0.3683 rms_B_bonded: 5.86 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 = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3692 r_free = 0.3692    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3692
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.3536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8085  Z= 0.116
  Angle     :  0.677  14.488  10983  Z= 0.327
  Chirality :  0.048   0.512   1214
  Planarity :  0.005   0.094   1392
  Dihedral  :  5.301  35.955   1045
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 11.11 %
    Favored  : 87.27 %
  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 are not related in a simple way.
  whole: -2.29 (0.26), residues: 940
  helix: -0.54 (0.47), residues: 132
  sheet: -0.82 (0.44), residues: 133
  loop : -2.02 (0.22), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  22 
 TYR   0.023   0.001   TYR A  14 
 PHE   0.024   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/Z
  covalent geometry    : bond        0.00273 /  0.12 ( 8051)
  covalent geometry    : angle       0.65551 /  0.32 (10904)
  SS BOND              : bond        0.00229 /  0.15 (   23)
  SS BOND              : angle       1.29879 /  0.93 (   46)
  hydrogen bonds       : bond        0.03248 /  2.08 (  170)
  hydrogen bonds       : angle       5.52042 /  3.54 (  429)
  link_BETA1-4         : bond        0.00111 /  0.07 (    1)
  link_BETA1-4         : angle       2.19419 /  1.10 (    3)
  link_NAG-ASN         : bond        0.00335 /  0.18 (   10)
  link_NAG-ASN         : angle       2.96274 /  1.54 (   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
  77 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   56 MET cc_start: 0.8623 (ttm) cc_final: 0.8358 (ttp)
REVERT: E   59 ASP cc_start: 0.8282 (m-30) cc_final: 0.8081 (m-30)
REVERT: E  239 GLU cc_start: 0.4738 (pm20) cc_final: 0.4505 (pm20)
REVERT: E  258 PHE cc_start: 0.8637 (t80) cc_final: 0.8278 (t80)
REVERT: E  460 LYS cc_start: 0.7289 (mtpt) cc_final: 0.6440 (pttt)
REVERT: E  509 GLU cc_start: 0.8900 (tt0) cc_final: 0.8397 (tt0)
REVERT: E  557 LYS cc_start: 0.8784 (ptpt) cc_final: 0.8266 (pttm)
REVERT: F  423 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7904 (pm20)
REVERT: F  582 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8438 (tmtt)
REVERT: F  693 LEU cc_start: 0.8842 (tp) cc_final: 0.8573 (mm)
  outliers start: 13
  outliers final: 7
  residues processed: 74
  average time/residue: 0.0758
  time to fit residues: 8.1270
Evaluate side-chains
  64 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue  111 ASN
Chi-restraints excluded: chain E residue  194 THR
Chi-restraints excluded: chain E residue  262 LEU
Chi-restraints excluded: chain E residue  459 LEU
Chi-restraints excluded: chain E residue  524 CYS
Chi-restraints excluded: chain F residue  423 GLN
Chi-restraints excluded: chain F residue  582 LYS
Chi-restraints excluded: chain F residue  685 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 69 optimal weight:    0.6980
   chunk 22 optimal weight:    8.9990
   chunk 59 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0570
   chunk 6 optimal weight:    0.3980
   chunk 3 optimal weight:    3.9990
   chunk 87 optimal weight:    0.0070
   chunk 43 optimal weight:    3.9990
   chunk 63 optimal weight:    0.4980
   overall best weight:    0.3116

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.146101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.115331 restraints weight = 25625.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3951 rms_B_bonded: 4.86
r_work: 0.3762 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3771
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3771 r_free = 0.3771    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3771 r_free = 0.3771    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3771
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.3716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   8085  Z= 0.113
  Angle     :  0.668  13.379  10983  Z= 0.322
  Chirality :  0.048   0.502   1214
  Planarity :  0.005   0.096   1392
  Dihedral  :  5.217  35.927   1045
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 11.34 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.17 (0.26), residues: 940
  helix: -0.36 (0.47), residues: 133
  sheet: -0.62 (0.45), residues: 133
  loop : -1.99 (0.22), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  22 
 TYR   0.031   0.001   TYR B  16 
 PHE   0.026   0.002   PHE E 231 
 TRP   0.008   0.001   TRP E 412 
 HIS   0.006   0.001   HIS E 264 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.11 ( 8051)
  covalent geometry    : angle       0.64871 /  0.32 (10904)
  SS BOND              : bond        0.00218 /  0.14 (   23)
  SS BOND              : angle       1.06932 /  0.78 (   46)
  hydrogen bonds       : bond        0.03156 /  2.01 (  170)
  hydrogen bonds       : angle       5.44413 /  3.47 (  429)
  link_BETA1-4         : bond        0.00030 /  0.02 (    1)
  link_BETA1-4         : angle       2.03836 /  1.00 (    3)
  link_NAG-ASN         : bond        0.00309 /  0.17 (   10)
  link_NAG-ASN         : angle       2.86529 /  1.49 (   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
  76 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   56 MET cc_start: 0.8491 (ttm) cc_final: 0.8261 (ttp)
REVERT: E   59 ASP cc_start: 0.8049 (m-30) cc_final: 0.7849 (m-30)
REVERT: E  258 PHE cc_start: 0.8632 (t80) cc_final: 0.8274 (t80)
REVERT: E  460 LYS cc_start: 0.7188 (mtpt) cc_final: 0.6298 (pttt)
REVERT: E  504 MET cc_start: 0.8842 (mtm) cc_final: 0.8621 (mtm)
REVERT: E  509 GLU cc_start: 0.8833 (tt0) cc_final: 0.8547 (tt0)
REVERT: E  557 LYS cc_start: 0.8535 (ptpt) cc_final: 0.8238 (ptpp)
REVERT: F  430 TYR cc_start: 0.8492 (t80) cc_final: 0.8258 (t80)
REVERT: F  582 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8365 (tmtt)
REVERT: F  693 LEU cc_start: 0.8807 (tp) cc_final: 0.8534 (mm)
  outliers start: 13
  outliers final: 7
  residues processed: 74
  average time/residue: 0.0853
  time to fit residues: 9.0670
Evaluate side-chains
  65 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue  111 ASN
Chi-restraints excluded: chain E residue  194 THR
Chi-restraints excluded: chain E residue  262 LEU
Chi-restraints excluded: chain E residue  459 LEU
Chi-restraints excluded: chain E residue  524 CYS
Chi-restraints excluded: chain F residue  582 LYS
Chi-restraints excluded: chain F residue  685 CYS
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:    0.5980
   chunk 59 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 43 optimal weight:    0.1980
   chunk 9 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0970
   chunk 80 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9980
   overall best weight:    0.4778

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 313 HIS
E 337 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.145882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.115035 restraints weight = 33593.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3952 rms_B_bonded: 6.08
r_work: 0.3704 rms_B_bonded: 5.71 restraints_weight: 2.0000
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3712
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3712 r_free = 0.3712    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 = 0.3712 r_free = 0.3712    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3712
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.3744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   8085  Z= 0.125
  Angle     :  0.692  13.713  10983  Z= 0.331
  Chirality :  0.049   0.502   1214
  Planarity :  0.005   0.095   1392
  Dihedral  :  5.222  36.229   1045
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 11.69 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.13 (0.26), residues: 940
  helix: -0.50 (0.46), residues: 136
  sheet: -0.50 (0.46), residues: 128
  loop : -1.93 (0.22), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG F 451 
 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   0.005   0.001   HIS E 264 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.12 ( 8051)
  covalent geometry    : angle       0.67385 /  0.33 (10904)
  SS BOND              : bond        0.00235 /  0.14 (   23)
  SS BOND              : angle       1.08454 /  0.78 (   46)
  hydrogen bonds       : bond        0.03209 /  2.05 (  170)
  hydrogen bonds       : angle       5.37185 /  3.42 (  429)
  link_BETA1-4         : bond        0.00103 /  0.06 (    1)
  link_BETA1-4         : angle       2.13479 /  1.09 (    3)
  link_NAG-ASN         : bond        0.00298 /  0.16 (   10)
  link_NAG-ASN         : angle       2.83265 /  1.47 (   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
  67 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   56 MET cc_start: 0.8594 (ttm) cc_final: 0.8342 (ttp)
REVERT: E  258 PHE cc_start: 0.8642 (t80) cc_final: 0.8318 (t80)
REVERT: E  460 LYS cc_start: 0.7286 (mtpt) cc_final: 0.6325 (pttt)
REVERT: E  509 GLU cc_start: 0.8906 (tt0) cc_final: 0.8676 (tt0)
REVERT: E  557 LYS cc_start: 0.8698 (ptpt) cc_final: 0.8186 (ptpp)
REVERT: F  430 TYR cc_start: 0.8550 (t80) cc_final: 0.8317 (t80)
REVERT: F  582 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8414 (tmtt)
REVERT: F  693 LEU cc_start: 0.8823 (tp) cc_final: 0.8542 (mm)
  outliers start: 10
  outliers final: 8
  residues processed: 63
  average time/residue: 0.0916
  time to fit residues: 8.1355
Evaluate side-chains
  62 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue  111 ASN
Chi-restraints excluded: chain E residue  194 THR
Chi-restraints excluded: chain E residue  262 LEU
Chi-restraints excluded: chain E residue  459 LEU
Chi-restraints excluded: chain E residue  524 CYS
Chi-restraints excluded: chain E residue  533 ASP
Chi-restraints excluded: chain F residue  582 LYS
Chi-restraints excluded: chain F residue  685 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 71 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 43 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F 548 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.144010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.113827 restraints weight = 31730.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3936 rms_B_bonded: 5.93
r_work: 0.3684 rms_B_bonded: 5.48 restraints_weight: 2.0000
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3694
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3694 r_free = 0.3694    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 = 0.3694 r_free = 0.3694    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3694
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.3705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8085  Z= 0.149
  Angle     :  0.711  14.685  10983  Z= 0.341
  Chirality :  0.050   0.514   1214
  Planarity :  0.005   0.094   1392
  Dihedral  :  5.268  36.557   1045
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 11.69 %
    Favored  : 87.15 %
  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 are not related in a simple way.
  whole: -2.18 (0.26), residues: 940
  helix: -0.59 (0.46), residues: 136
  sheet: -0.62 (0.45), residues: 128
  loop : -1.94 (0.23), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG F 451 
 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 264 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.15 ( 8051)
  covalent geometry    : angle       0.69157 /  0.34 (10904)
  SS BOND              : bond        0.00281 /  0.16 (   23)
  SS BOND              : angle       1.21603 /  0.86 (   46)
  hydrogen bonds       : bond        0.03427 /  2.19 (  170)
  hydrogen bonds       : angle       5.44293 /  3.49 (  429)
  link_BETA1-4         : bond        0.00166 /  0.10 (    1)
  link_BETA1-4         : angle       2.28457 /  1.18 (    3)
  link_NAG-ASN         : bond        0.00315 /  0.18 (   10)
  link_NAG-ASN         : angle       2.90568 /  1.51 (   30)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2458.98 seconds
wall clock time: 42 minutes 44.36 seconds (2564.36 seconds total)