Starting phenix.real_space_refine
on Wed Feb 12 14:23:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6hn5_0247/02_2025/6hn5_0247.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6hn5_0247/02_2025/6hn5_0247.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6hn5_0247/02_2025/6hn5_0247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6hn5_0247/02_2025/6hn5_0247.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6hn5_0247/02_2025/6hn5_0247.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6hn5_0247/02_2025/6hn5_0247.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      59      5.16       5
     C    4980      2.51       5
     N    1338      2.21       5
     O    1492      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7869
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 163
          Classifications: {'peptide': 21}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 20}
    Chain: "B"
      Number of atoms: 212
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 25, 200
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
      Conformer: "B"
        Number of residues, atoms: 25, 200
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
          bond proxies already assigned to first conformer: 191
    Chain: "E"
      Number of atoms: 4715
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 584, 4708
          Classifications: {'peptide': 584}
          Link IDs: {'PTRANS': 28, 'TRANS': 555}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 584, 4708
          Classifications: {'peptide': 584}
          Link IDs: {'PTRANS': 28, 'TRANS': 555}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 4812
    Chain: "F"
      Number of atoms: 2625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 2625
          Classifications: {'peptide': 323}
          Link IDs: {'PTRANS': 12, 'TRANS': 310}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "F"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR B  26 " occ=0.50
      ... (22 atoms not shown)
      pdb=" OH BTYR B  26 " occ=0.50
  Time building chain proxies: 6.76, per 1000 atoms: 0.86
  Number of scatterers: 7869
  At special positions: 0
  Unit cell: (105.04, 108.16, 113.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      59     16.00
     O    1492      8.00
     N    1338      7.00
     C    4980      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG C   1 " - " ASN E 111 "
      " NAG E1001 " - " ASN E  25 "
      " NAG E1004 " - " ASN E 215 "
      " NAG E1005 " - " ASN E 255 "
      " NAG E1006 " - " ASN E 397 "
      " NAG E1007 " - " ASN E 418 "
      " NAG E1008 " - " ASN E  16 "
      " NAG F1001 " - " ASN F 337 "
      " NAG F1002 " - " ASN F 397 "
      " NAG F1003 " - " ASN F 514 "
  Time building additional restraints: 2.00
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 14 sheets defined
      15.0% alpha, 17.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 7
      removed outlier: 3.567A  pdb=" N   CYS A   7 " --> pdb=" O   VAL A   3 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 18
    Processing helix  chain 'B' and resid 9 through 16
    Processing helix  chain 'E' and resid 17 through 24
    Processing helix  chain 'E' and resid 132 through 136
    Processing helix  chain 'E' and resid 255 through 268
      removed outlier: 3.592A  pdb=" N   CYS E 259 " --> pdb=" O   ASN E 255 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 314 through 316
      No H-bonds generated for 'chain 'E' and resid 314 through 316'
    Processing helix  chain 'E' and resid 323 through 329
    Processing helix  chain 'E' and resid 350 through 358
    Processing helix  chain 'E' and resid 378 through 382
      removed outlier: 4.380A  pdb=" N   PHE E 381 " --> pdb=" O   SER E 378 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 435 through 446
      removed outlier: 3.668A  pdb=" N   ILE E 439 " --> pdb=" O   CYS E 435 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 324 through 328
    Processing helix  chain 'F' and resid 349 through 359
      removed outlier: 3.709A  pdb=" N   GLU F 353 " --> pdb=" O   ASN F 349 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 435 through 446
      removed outlier: 3.565A  pdb=" N   ILE F 439 " --> pdb=" O   CYS F 435 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 496 through 498
      No H-bonds generated for 'chain 'F' and resid 496 through 498'
    Processing helix  chain 'F' and resid 688 through 714
      removed outlier: 3.615A  pdb=" N   PHE F 714 " --> pdb=" O   HIS F 710 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 6 through 8
      removed outlier: 7.440A  pdb=" N   GLU E   6 " --> pdb=" O   SER E  27 " (cutoff:3.500A)
      removed outlier: 5.888A  pdb=" N   ILE E  29 " --> pdb=" O   GLU E   6 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   CYS E   8 " --> pdb=" O   ILE E  29 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 11 through 13
      removed outlier: 6.462A  pdb=" N   MET E  11 " --> pdb=" O   GLN E  34 " (cutoff:3.500A)
      removed outlier: 7.623A  pdb=" N   LEU E  36 " --> pdb=" O   MET E  11 " (cutoff:3.500A)
      removed outlier: 5.752A  pdb=" N   ILE E  13 " --> pdb=" O   LEU E  36 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   MET E  38 " --> pdb=" O   ILE E  13 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   LEU E  33 " --> pdb=" O   LEU E  62 " (cutoff:3.500A)
      removed outlier: 7.576A  pdb=" N   PHE E  64 " --> pdb=" O   LEU E  33 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   ILE E  35 " --> pdb=" O   PHE E  64 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   VAL E  66 " --> pdb=" O   ILE E  35 " (cutoff:3.500A)
      removed outlier: 7.623A  pdb=" N   LEU E  37 " --> pdb=" O   VAL E  66 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   ARG E 118 " --> pdb=" O   ALA E  92 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   VAL E  94 " --> pdb=" O   ARG E 118 " (cutoff:3.500A)
      removed outlier: 7.542A  pdb=" N   GLU E 120 " --> pdb=" O   VAL E  94 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   PHE E  96 " --> pdb=" O   GLU E 120 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   ASN E 122 " --> pdb=" O   PHE E  96 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL E 146 " --> pdb=" O   ILE E 119 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LYS E 121 " --> pdb=" O   VAL E 146 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   ASN E 148 " --> pdb=" O   LYS E 121 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 212 through 216
      removed outlier: 3.556A  pdb=" N   ALA E 227 " --> pdb=" O   LEU E 213 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   ASN E 215 " --> pdb=" O   CYS E 225 " (cutoff:3.500A)
      removed outlier: 5.689A  pdb=" N   CYS E 225 " --> pdb=" O   ASN E 215 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 231 through 232
    Processing sheet with id=AA5, first strand: chain 'E' and resid 252 through 254
      removed outlier: 6.739A  pdb=" N   HIS E 247 " --> pdb=" O   CYS E 284 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 292 through 294
    Processing sheet with id=AA7, first strand: chain 'E' and resid 311 through 312
    Processing sheet with id=AA8, first strand: chain 'E' and resid 318 through 321
      removed outlier: 6.232A  pdb=" N   LEU E 340 " --> pdb=" O   LYS E 369 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   ARG E 371 " --> pdb=" O   LEU E 340 " (cutoff:3.500A)
      removed outlier: 5.795A  pdb=" N   ILE E 342 " --> pdb=" O   ARG E 371 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   LEU E 368 " --> pdb=" O   TYR E 401 " (cutoff:3.500A)
      removed outlier: 7.779A  pdb=" N   LEU E 403 " --> pdb=" O   LEU E 368 " (cutoff:3.500A)
      removed outlier: 6.136A  pdb=" N   ILE E 370 " --> pdb=" O   LEU E 403 " (cutoff:3.500A)
      removed outlier: 5.496A  pdb=" N   TYR E 398 " --> pdb=" O   LYS E 425 " (cutoff:3.500A)
      removed outlier: 7.996A  pdb=" N   PHE E 427 " --> pdb=" O   TYR E 398 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   PHE E 400 " --> pdb=" O   PHE E 427 " (cutoff:3.500A)
      removed outlier: 8.332A  pdb=" N   HIS E 429 " --> pdb=" O   PHE E 400 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   ALA E 402 " --> pdb=" O   HIS E 429 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 475 through 479
      removed outlier: 6.454A  pdb=" N   ARG E 488 " --> pdb=" O   SER E 476 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   ILE E 478 " --> pdb=" O   LEU E 486 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   LEU E 486 " --> pdb=" O   ILE E 478 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 530 through 534
    Processing sheet with id=AB2, first strand: chain 'F' and resid 311 through 313
    Processing sheet with id=AB3, first strand: chain 'F' and resid 320 through 321
      removed outlier: 3.658A  pdb=" N   ARG F 371 " --> pdb=" O   ILE F 342 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   HIS F 429 " --> pdb=" O   ALA F 402 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   PHE F 428 " --> pdb=" O   ASP F 456 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 475 through 480
      removed outlier: 6.603A  pdb=" N   ARG F 488 " --> pdb=" O   SER F 476 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ILE F 478 " --> pdb=" O   LEU F 486 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   LEU F 486 " --> pdb=" O   ILE F 478 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 530 through 534
      removed outlier: 3.658A  pdb=" N   GLY F 502 " --> pdb=" O   LEU F 569 " (cutoff:3.500A)

    170 hydrogen bonds defined for protein.
    429 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.29

  Time building geometry restraints manager: 2.33 seconds

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

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

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

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

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

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

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

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     23.750
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.129   8051  Z= 0.792
  Angle     :  1.200  12.131  10904  Z= 0.620
  Chirality :  0.071   0.563   1214
  Planarity :  0.008   0.101   1392
  Dihedral  : 10.560  74.824   3151
  Min Nonbonded Distance : 2.281

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

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

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

*********************** 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  : 0.883 
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: 0.2685
  time to fit residues: 47.1005
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  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 24 optimal weight:    5.9990
   chunk 48 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 85 optimal weight:    0.6980
   overall best weight:    0.7180

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

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

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.142863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.112544 restraints weight = 41082.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.3905 rms_B_bonded: 6.66
r_work: 0.3642 rms_B_bonded: 5.87 restraints_weight: 2.0000
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3649
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3649 r_free = 0.3649    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3649 r_free = 0.3649    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3649
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8051  Z= 0.269
  Angle     :  0.747  16.887  10904  Z= 0.375
  Chirality :  0.050   0.331   1214
  Planarity :  0.006   0.093   1392
  Dihedral  :  9.382  59.122   1276
  Min Nonbonded Distance : 2.373

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

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

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

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

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  460 LYS cc_start: 0.7575 (mtpt) cc_final: 0.6738 (pttt)
REVERT: E  509 GLU cc_start: 0.8962 (tt0) cc_final: 0.8543 (tt0)
REVERT: E  557 LYS cc_start: 0.8759 (ptpt) cc_final: 0.8115 (ptpt)
REVERT: F  357 ASN cc_start: 0.8937 (m-40) cc_final: 0.8685 (m-40)
REVERT: F  438 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8461 (mm-30)
REVERT: F  504 MET cc_start: 0.8745 (mtt) cc_final: 0.8463 (mtp)
REVERT: F  522 ASP cc_start: 0.6190 (m-30) cc_final: 0.5690 (t0)
  outliers start: 10
  outliers final: 6
  residues processed: 100
  average time/residue: 0.2051
  time to fit residues: 28.4954
Evaluate side-chains
  68 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue  111 ASN
Chi-restraints excluded: chain E residue  459 LEU
Chi-restraints excluded: chain F residue  423 GLN
Chi-restraints excluded: chain F residue  509 GLU
Chi-restraints excluded: chain F residue  688 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   chunk 15 optimal weight:    0.0000
   chunk 49 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   chunk 19 optimal weight:    6.9990
   chunk 46 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   overall best weight:    0.5984

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.143950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.114011 restraints weight = 28693.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3934 rms_B_bonded: 5.32
r_work: 0.3695 rms_B_bonded: 5.18 restraints_weight: 2.0000
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3706
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3706 r_free = 0.3706    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3706 r_free = 0.3706    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3706
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8051  Z= 0.225
  Angle     :  0.739  20.261  10904  Z= 0.361
  Chirality :  0.050   0.525   1214
  Planarity :  0.005   0.091   1392
  Dihedral  :  8.755  57.134   1276
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  9.26 %
    Favored  : 89.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.82 (0.25), residues: 940
  helix: -1.40 (0.43), residues: 129
  sheet: -1.21 (0.43), residues: 143
  loop : -2.28 (0.22), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP F 414 
 HIS   0.013   0.001   HIS E 264 
 PHE   0.039   0.002   PHE E 258 
 TYR   0.030   0.002   TYR B  16 
 ARG   0.007   0.001   ARG E 229 

*********************** 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
  87 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   59 ASP cc_start: 0.8264 (m-30) cc_final: 0.7924 (m-30)
REVERT: E  337 ASN cc_start: 0.8632 (OUTLIER) cc_final: 0.8407 (t0)
REVERT: E  460 LYS cc_start: 0.7426 (mtpt) cc_final: 0.6642 (pttt)
REVERT: E  509 GLU cc_start: 0.8911 (tt0) cc_final: 0.8593 (tt0)
REVERT: E  557 LYS cc_start: 0.8814 (ptpt) cc_final: 0.8364 (ptpt)
REVERT: F  423 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7823 (pm20)
  outliers start: 10
  outliers final: 6
  residues processed: 85
  average time/residue: 0.2174
  time to fit residues: 25.5786
Evaluate side-chains
  75 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue  111 ASN
Chi-restraints excluded: chain E residue  337 ASN
Chi-restraints excluded: chain E residue  459 LEU
Chi-restraints excluded: chain E residue  524 CYS
Chi-restraints excluded: chain F residue  423 GLN
Chi-restraints excluded: chain F residue  501 LEU
Chi-restraints excluded: chain F residue  509 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 85 optimal weight:    0.0670
   chunk 69 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 57 optimal weight:    7.9990
   chunk 28 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.9320

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4348 r_free = 0.4348 target = 0.142277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.112616 restraints weight = 31935.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.3909 rms_B_bonded: 5.82
r_work: 0.3661 rms_B_bonded: 5.40 restraints_weight: 2.0000
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3669
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3669 r_free = 0.3669    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 = 0.3669 r_free = 0.3669    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3669
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8051  Z= 0.262
  Angle     :  0.723  17.800  10904  Z= 0.352
  Chirality :  0.050   0.542   1214
  Planarity :  0.005   0.091   1392
  Dihedral  :  8.412  58.398   1276
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  :  9.38 %
    Favored  : 89.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.75 (0.25), residues: 940
  helix: -1.26 (0.43), residues: 131
  sheet: -1.23 (0.45), residues: 133
  loop : -2.23 (0.22), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 412 
 HIS   0.006   0.001   HIS E 264 
 PHE   0.029   0.002   PHE E 258 
 TYR   0.023   0.002   TYR B  16 
 ARG   0.005   0.001   ARG E 372 

*********************** 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: 12
    poor density    : 70
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   59 ASP cc_start: 0.8399 (m-30) cc_final: 0.8041 (m-30)
REVERT: E  211 GLU cc_start: 0.7525 (tt0) cc_final: 0.7189 (tm-30)
REVERT: E  460 LYS cc_start: 0.7454 (mtpt) cc_final: 0.6636 (pttt)
REVERT: E  509 GLU cc_start: 0.8899 (tt0) cc_final: 0.8586 (tt0)
REVERT: E  557 LYS cc_start: 0.8811 (ptpt) cc_final: 0.8366 (ptpt)
REVERT: F  423 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7925 (pm20)
REVERT: F  582 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8574 (tmtt)
  outliers start: 12
  outliers final: 8
  residues processed: 78
  average time/residue: 0.2096
  time to fit residues: 22.9112
Evaluate side-chains
  75 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue  111 ASN
Chi-restraints excluded: chain E residue  262 LEU
Chi-restraints excluded: chain E residue  459 LEU
Chi-restraints excluded: chain E residue  524 CYS
Chi-restraints excluded: chain E residue  585 ILE
Chi-restraints excluded: chain F residue  423 GLN
Chi-restraints excluded: chain F residue  509 GLU
Chi-restraints excluded: chain F residue  576 ARG
Chi-restraints excluded: chain F residue  582 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 58 optimal weight:    9.9990
   chunk 8 optimal weight:    0.7980
   chunk 62 optimal weight:    0.0670
   chunk 75 optimal weight:    4.9990
   chunk 10 optimal weight:    0.6980
   chunk 34 optimal weight:    0.2980
   chunk 69 optimal weight:    0.8980
   chunk 19 optimal weight:    7.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
B   5 HIS
F 357 ASN
F 691 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.144455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.114104 restraints weight = 37871.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3932 rms_B_bonded: 6.39
r_work: 0.3681 rms_B_bonded: 5.68 restraints_weight: 2.0000
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3690
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3690 r_free = 0.3690    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 = 0.3690 r_free = 0.3690    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3690
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.3143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8051  Z= 0.190
  Angle     :  0.673  16.455  10904  Z= 0.327
  Chirality :  0.050   0.558   1214
  Planarity :  0.005   0.093   1392
  Dihedral  :  8.038  58.823   1276
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  9.14 %
    Favored  : 89.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.56 (0.25), residues: 940
  helix: -0.99 (0.45), residues: 131
  sheet: -1.03 (0.45), residues: 133
  loop : -2.14 (0.22), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 412 
 HIS   0.007   0.001   HIS E 264 
 PHE   0.028   0.002   PHE E 258 
 TYR   0.027   0.001   TYR B  16 
 ARG   0.006   0.001   ARG E 498 

*********************** 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
  82 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   59 ASP cc_start: 0.8274 (m-30) cc_final: 0.7949 (m-30)
REVERT: E  239 GLU cc_start: 0.4930 (pm20) cc_final: 0.4598 (pm20)
REVERT: E  460 LYS cc_start: 0.7407 (mtpt) cc_final: 0.6606 (pttt)
REVERT: E  509 GLU cc_start: 0.8887 (tt0) cc_final: 0.8546 (tt0)
REVERT: E  557 LYS cc_start: 0.8796 (ptpt) cc_final: 0.8372 (ptpt)
REVERT: F  423 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7825 (pm20)
REVERT: F  582 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8600 (tmtt)
REVERT: F  693 LEU cc_start: 0.8824 (tp) cc_final: 0.8564 (mm)
  outliers start: 14
  outliers final: 6
  residues processed: 80
  average time/residue: 0.1901
  time to fit residues: 21.7191
Evaluate side-chains
  74 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue  111 ASN
Chi-restraints excluded: chain E residue  459 LEU
Chi-restraints excluded: chain E residue  524 CYS
Chi-restraints excluded: chain F residue  423 GLN
Chi-restraints excluded: chain F residue  509 GLU
Chi-restraints excluded: chain F residue  582 LYS
Chi-restraints excluded: chain F residue  685 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 77 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   chunk 30 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 59 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4356 r_free = 0.4356 target = 0.142833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.112001 restraints weight = 33271.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3902 rms_B_bonded: 6.12
r_work: 0.3650 rms_B_bonded: 5.74 restraints_weight: 2.0000
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3660
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3660 r_free = 0.3660    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 = 0.3660 r_free = 0.3660    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3660
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.3230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8051  Z= 0.236
  Angle     :  0.676  16.601  10904  Z= 0.329
  Chirality :  0.050   0.566   1214
  Planarity :  0.005   0.092   1392
  Dihedral  :  7.787  56.735   1276
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  9.72 %
    Favored  : 88.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.50 (0.25), residues: 940
  helix: -0.89 (0.45), residues: 132
  sheet: -0.96 (0.44), residues: 133
  loop : -2.13 (0.22), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 412 
 HIS   0.006   0.001   HIS E 264 
 PHE   0.016   0.002   PHE E  39 
 TYR   0.037   0.002   TYR B  16 
 ARG   0.005   0.001   ARG E  14 

*********************** 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
  80 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   59 ASP cc_start: 0.8288 (m-30) cc_final: 0.7900 (m-30)
REVERT: E  460 LYS cc_start: 0.7402 (mtpt) cc_final: 0.6525 (pttt)
REVERT: E  509 GLU cc_start: 0.8893 (tt0) cc_final: 0.8581 (tt0)
REVERT: E  557 LYS cc_start: 0.8805 (ptpt) cc_final: 0.8389 (ptpt)
REVERT: F  423 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7845 (pm20)
REVERT: F  582 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8532 (tmtt)
  outliers start: 15
  outliers final: 7
  residues processed: 76
  average time/residue: 0.2109
  time to fit residues: 22.4682
Evaluate side-chains
  66 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
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  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 43 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 56 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 89 optimal weight:    0.3980
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.5780

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.144411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.113143 restraints weight = 21751.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3922 rms_B_bonded: 4.04
r_work: 0.3759 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3769
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3769 r_free = 0.3769    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 = 0.3769 r_free = 0.3769    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3769
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.3397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8051  Z= 0.196
  Angle     :  0.663  15.414  10904  Z= 0.323
  Chirality :  0.050   0.575   1214
  Planarity :  0.005   0.093   1392
  Dihedral  :  7.549  56.102   1276
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 11.00 %
    Favored  : 87.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.35 (0.26), residues: 940
  helix: -0.76 (0.45), residues: 132
  sheet: -0.68 (0.46), residues: 123
  loop : -2.05 (0.22), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 412 
 HIS   0.006   0.001   HIS E 264 
 PHE   0.033   0.002   PHE E 258 
 TYR   0.025   0.001   TYR B  16 
 ARG   0.004   0.000   ARG E 498 

*********************** 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
  75 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   16 TYR cc_start: 0.8233 (t80) cc_final: 0.7969 (t80)
REVERT: E   59 ASP cc_start: 0.8028 (m-30) cc_final: 0.7648 (m-30)
REVERT: E  258 PHE cc_start: 0.8636 (t80) cc_final: 0.8262 (t80)
REVERT: E  460 LYS cc_start: 0.7173 (mtpt) cc_final: 0.6393 (pttt)
REVERT: E  509 GLU cc_start: 0.8769 (tt0) cc_final: 0.8436 (tt0)
REVERT: E  557 LYS cc_start: 0.8805 (ptpt) cc_final: 0.8415 (ptpt)
REVERT: F  423 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7835 (pm20)
REVERT: F  582 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8461 (tmtt)
REVERT: F  693 LEU cc_start: 0.8811 (tp) cc_final: 0.8564 (mm)
  outliers start: 9
  outliers final: 6
  residues processed: 73
  average time/residue: 0.2107
  time to fit residues: 21.6682
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  : 0.974 
-------------------------------------------------------------------------------
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  582 LYS
Chi-restraints excluded: chain F residue  685 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 7 optimal weight:    0.4980
   chunk 81 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   chunk 67 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 35 optimal weight:    0.0070
   chunk 63 optimal weight:    3.9990
   overall best weight:    0.6198

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.144255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.113225 restraints weight = 44857.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3914 rms_B_bonded: 6.24
r_work: 0.3667 rms_B_bonded: 5.88 restraints_weight: 2.0000
r_work (final): 0.3667
-------------------------------------------------------------------------------
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 |
|-----------------------------------------------------------------------------|
r_final: 0.3675
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.3505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8051  Z= 0.204
  Angle     :  0.662  15.058  10904  Z= 0.327
  Chirality :  0.049   0.582   1214
  Planarity :  0.005   0.094   1392
  Dihedral  :  7.369  56.061   1276
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 10.88 %
    Favored  : 87.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.30 (0.26), residues: 940
  helix: -0.71 (0.46), residues: 132
  sheet: -0.58 (0.46), residues: 123
  loop : -2.03 (0.22), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 412 
 HIS   0.006   0.001   HIS E 264 
 PHE   0.030   0.002   PHE E 258 
 TYR   0.026   0.001   TYR A  14 
 ARG   0.008   0.001   ARG B  22 

*********************** 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
  70 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   59 ASP cc_start: 0.8288 (m-30) cc_final: 0.8044 (m-30)
REVERT: E  239 GLU cc_start: 0.5060 (pm20) cc_final: 0.4777 (pm20)
REVERT: E  258 PHE cc_start: 0.8592 (t80) cc_final: 0.8231 (t80)
REVERT: E  460 LYS cc_start: 0.7299 (mtpt) cc_final: 0.6434 (pttt)
REVERT: E  504 MET cc_start: 0.8848 (mtm) cc_final: 0.8592 (mtm)
REVERT: E  509 GLU cc_start: 0.8902 (tt0) cc_final: 0.8581 (tt0)
REVERT: E  557 LYS cc_start: 0.8829 (ptpt) cc_final: 0.8421 (ptpt)
REVERT: F  423 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7874 (pm20)
REVERT: F  582 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8468 (tmtt)
  outliers start: 12
  outliers final: 8
  residues processed: 68
  average time/residue: 0.1958
  time to fit residues: 19.3778
Evaluate side-chains
  66 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue  111 ASN
Chi-restraints excluded: chain E residue  194 THR
Chi-restraints excluded: chain E residue  262 LEU
Chi-restraints excluded: chain E residue  459 LEU
Chi-restraints excluded: chain E residue  524 CYS
Chi-restraints excluded: chain F residue  423 GLN
Chi-restraints excluded: chain F residue  582 LYS
Chi-restraints excluded: chain F residue  685 CYS
Chi-restraints excluded: chain F residue  688 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9980
   chunk 90 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0980
   chunk 45 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
E  78 ASN
F 357 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.144423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.114741 restraints weight = 30563.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 5.91
r_work: 0.3695 rms_B_bonded: 5.45 restraints_weight: 2.0000
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3706
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3706 r_free = 0.3706    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3706 r_free = 0.3706    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3706
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.3573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8051  Z= 0.203
  Angle     :  0.659  14.323  10904  Z= 0.323
  Chirality :  0.049   0.583   1214
  Planarity :  0.005   0.094   1392
  Dihedral  :  7.238  56.102   1276
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.32 (0.26), residues: 940
  helix: -0.73 (0.45), residues: 138
  sheet: -0.53 (0.46), residues: 123
  loop : -2.07 (0.22), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 412 
 HIS   0.006   0.001   HIS E 264 
 PHE   0.030   0.002   PHE E 258 
 TYR   0.023   0.001   TYR A  14 
 ARG   0.008   0.001   ARG B  22 

*********************** 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
  68 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   59 ASP cc_start: 0.8170 (m-30) cc_final: 0.7833 (m-30)
REVERT: E  239 GLU cc_start: 0.5096 (pm20) cc_final: 0.4816 (pm20)
REVERT: E  258 PHE cc_start: 0.8587 (t80) cc_final: 0.8224 (t80)
REVERT: E  460 LYS cc_start: 0.7244 (mtpt) cc_final: 0.6411 (pttt)
REVERT: F  423 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7866 (pm20)
REVERT: F  582 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8457 (tmtt)
REVERT: F  693 LEU cc_start: 0.8833 (tp) cc_final: 0.8587 (mm)
  outliers start: 12
  outliers final: 8
  residues processed: 66
  average time/residue: 0.1945
  time to fit residues: 18.5395
Evaluate side-chains
  63 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 SER
Chi-restraints excluded: chain E residue  111 ASN
Chi-restraints excluded: chain E residue  194 THR
Chi-restraints excluded: chain E residue  262 LEU
Chi-restraints excluded: chain E residue  459 LEU
Chi-restraints excluded: chain E residue  524 CYS
Chi-restraints excluded: chain F residue  423 GLN
Chi-restraints excluded: chain F residue  582 LYS
Chi-restraints excluded: chain F residue  685 CYS
Chi-restraints excluded: chain F residue  688 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0030
   chunk 93 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 73 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9980
   chunk 44 optimal weight:    0.1980
   chunk 38 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.4790

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.145134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.114414 restraints weight = 20649.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3944 rms_B_bonded: 3.93
r_work: 0.3781 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3791
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3791 r_free = 0.3791    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3791 r_free = 0.3791    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3791
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.3673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   8051  Z= 0.212
  Angle     :  0.662  13.730  10904  Z= 0.322
  Chirality :  0.049   0.587   1214
  Planarity :  0.005   0.095   1392
  Dihedral  :  7.166  56.100   1276
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 11.57 %
    Favored  : 86.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.26 (0.26), residues: 940
  helix: -0.65 (0.45), residues: 138
  sheet: -0.39 (0.47), residues: 122
  loop : -2.06 (0.22), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 412 
 HIS   0.006   0.001   HIS E 264 
 PHE   0.030   0.002   PHE E 258 
 TYR   0.031   0.002   TYR B  16 
 ARG   0.008   0.000   ARG B  22 

********************** 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
  72 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   59 ASP cc_start: 0.8009 (m-30) cc_final: 0.7679 (m-30)
REVERT: E  258 PHE cc_start: 0.8554 (t80) cc_final: 0.8244 (t80)
REVERT: E  460 LYS cc_start: 0.7130 (mtpt) cc_final: 0.6348 (pttt)
REVERT: E  509 GLU cc_start: 0.8642 (tt0) cc_final: 0.7967 (tt0)
REVERT: E  557 LYS cc_start: 0.8514 (ptpt) cc_final: 0.8168 (pttm)
REVERT: F  423 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7836 (pm20)
REVERT: F  582 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8360 (tmtt)
REVERT: F  693 LEU cc_start: 0.8792 (tp) cc_final: 0.8556 (mm)
  outliers start: 12
  outliers final: 9
  residues processed: 70
  average time/residue: 0.1916
  time to fit residues: 19.5775
Evaluate side-chains
  67 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
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  140 VAL
Chi-restraints excluded: chain E residue  194 THR
Chi-restraints excluded: chain E residue  262 LEU
Chi-restraints excluded: chain E residue  459 LEU
Chi-restraints excluded: chain E residue  524 CYS
Chi-restraints excluded: chain F residue  423 GLN
Chi-restraints excluded: chain F residue  582 LYS
Chi-restraints excluded: chain F residue  685 CYS
Chi-restraints excluded: chain F residue  688 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 2 optimal weight:    0.0060
   chunk 89 optimal weight:    0.4980
   chunk 10 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 84 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 81 optimal weight:    0.6980
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
E 313 HIS
E 337 ASN
F 548 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.144332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.114732 restraints weight = 37290.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3942 rms_B_bonded: 6.29
r_work: 0.3689 rms_B_bonded: 5.65 restraints_weight: 2.0000
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3699
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3699 r_free = 0.3699    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 = 0.3699 r_free = 0.3699    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3699
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.3691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8051  Z= 0.216
  Angle     :  0.676  14.000  10904  Z= 0.327
  Chirality :  0.050   0.587   1214
  Planarity :  0.005   0.095   1392
  Dihedral  :  7.107  56.097   1276
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 11.69 %
    Favored  : 86.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.26), residues: 940
  helix: -0.60 (0.45), residues: 139
  sheet: -0.35 (0.47), residues: 122
  loop : -2.06 (0.22), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 412 
 HIS   0.006   0.001   HIS E 264 
 PHE   0.029   0.002   PHE E 258 
 TYR   0.029   0.002   TYR B  16 
 ARG   0.008   0.001   ARG B  22 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5038.50 seconds
wall clock time: 89 minutes 41.67 seconds (5381.67 seconds total)