Starting phenix.real_space_refine
on Sat Aug 23 02:23:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tve_41639/08_2025/8tve_41639.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tve_41639/08_2025/8tve_41639.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tve_41639/08_2025/8tve_41639.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tve_41639/08_2025/8tve_41639.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tve_41639/08_2025/8tve_41639.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tve_41639/08_2025/8tve_41639.cif"
  }
  resolution = 3.9
  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=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    5799      2.51       5
     N    1536      2.21       5
     O    1707      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9090
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3002
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 409, 3002
          Classifications: {'peptide': 409}
          Incomplete info: {'truncation_to_alanine': 64}
          Link IDs: {'PTRANS': 15, 'TRANS': 393}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 159
          Unresolved non-hydrogen angles: 202
          Unresolved non-hydrogen dihedrals: 116
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'ASP:plan': 13, 'GLU:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 73
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 1.69, per 1000 atoms: 0.19
  Number of scatterers: 9090
  At special positions: 0
  Unit cell: (84.96, 85.845, 171.69, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      48     16.00
     O    1707      8.00
     N    1536      7.00
     C    5799      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  66 " - pdb=" SG  CYS A 187 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A 326 " - pdb=" SG  CYS A 335 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 350 " - pdb=" SG  CYS A 358 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 382 " - pdb=" SG  CYS A 387 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 389 " - pdb=" SG  CYS A 412 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  66 " - pdb=" SG  CYS B 187 " distance=2.06
    Simple disulfide: pdb=" SG  CYS C  66 " - pdb=" SG  CYS C 187 " distance=2.06
    Simple disulfide: pdb=" SG  CYS B 326 " - pdb=" SG  CYS B 335 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 326 " - pdb=" SG  CYS C 335 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 350 " - pdb=" SG  CYS B 358 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 350 " - pdb=" SG  CYS C 358 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 382 " - pdb=" SG  CYS B 387 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 382 " - pdb=" SG  CYS C 387 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 389 " - pdb=" SG  CYS B 412 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 389 " - pdb=" SG  CYS C 412 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 601 " - " ASN A  65 "
      " NAG A 602 " - " ASN A 459 "
      " NAG B 601 " - " ASN B  65 "
      " NAG B 602 " - " ASN B 459 "
      " NAG C 601 " - " ASN C  65 "
      " NAG C 602 " - " ASN C 459 "
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 221.1 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 18 sheets defined
      42.8% alpha, 17.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 32
      removed outlier: 4.997A  pdb=" N   LYS A  30 " --> pdb=" O   ASP A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 92
      Proline residue:  A  84  - end of helix
    Processing helix  chain 'A' and resid 141 through 178
    Processing helix  chain 'A' and resid 178 through 207
    Processing helix  chain 'A' and resid 209 through 215
    Processing helix  chain 'A' and resid 222 through 230
    Processing helix  chain 'A' and resid 233 through 242
    Processing helix  chain 'A' and resid 244 through 254
    Processing helix  chain 'A' and resid 344 through 353
      removed outlier: 4.237A  pdb=" N   CYS A 350 " --> pdb=" O   GLU A 346 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LEU A 351 " --> pdb=" O   LEU A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 476
    Processing helix  chain 'B' and resid 24 through 32
      removed outlier: 4.997A  pdb=" N   LYS B  30 " --> pdb=" O   ASP B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 92
      Proline residue:  B  84  - end of helix
    Processing helix  chain 'B' and resid 141 through 178
    Processing helix  chain 'B' and resid 178 through 207
    Processing helix  chain 'B' and resid 209 through 215
    Processing helix  chain 'B' and resid 222 through 230
    Processing helix  chain 'B' and resid 233 through 242
    Processing helix  chain 'B' and resid 244 through 254
    Processing helix  chain 'B' and resid 344 through 353
      removed outlier: 4.237A  pdb=" N   CYS B 350 " --> pdb=" O   GLU B 346 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LEU B 351 " --> pdb=" O   LEU B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 476
    Processing helix  chain 'C' and resid 24 through 32
      removed outlier: 4.997A  pdb=" N   LYS C  30 " --> pdb=" O   ASP C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 92
      Proline residue:  C  84  - end of helix
    Processing helix  chain 'C' and resid 141 through 178
    Processing helix  chain 'C' and resid 178 through 207
    Processing helix  chain 'C' and resid 209 through 215
    Processing helix  chain 'C' and resid 222 through 230
    Processing helix  chain 'C' and resid 233 through 242
    Processing helix  chain 'C' and resid 244 through 254
    Processing helix  chain 'C' and resid 344 through 353
      removed outlier: 4.237A  pdb=" N   CYS C 350 " --> pdb=" O   GLU C 346 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   LEU C 351 " --> pdb=" O   LEU C 347 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 452 through 476
    Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 38
      removed outlier: 5.344A  pdb=" N   GLU A 290 " --> pdb=" O   GLY A  36 " (cutoff:3.500A)
      removed outlier: 4.829A  pdb=" N   THR A  38 " --> pdb=" O   VAL A 288 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   VAL A 288 " --> pdb=" O   THR A  38 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   PHE A 310 " --> pdb=" O   ILE A 321 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ILE A 321 " --> pdb=" O   PHE A 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 281 through 282
    Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 220
      removed outlier: 7.012A  pdb=" N   ALA A 272 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   VAL A 264 " --> pdb=" O   TYR A 270 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   TYR A 270 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
      removed outlier: 8.957A  pdb=" N   GLY B 431 " --> pdb=" O   THR A  49 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   LEU A  51 " --> pdb=" O   GLY B 431 " (cutoff:3.500A)
      removed outlier: 7.965A  pdb=" N   TYR B 433 " --> pdb=" O   LEU A  51 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   VAL A  53 " --> pdb=" O   TYR B 433 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 298
    Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 374
      removed outlier: 4.031A  pdb=" N   VAL A 378 " --> pdb=" O   LEU A 407 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 394 through 395
      removed outlier: 3.526A  pdb=" N   THR A 394 " --> pdb=" O   CYS A 389 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 433
      removed outlier: 6.900A  pdb=" N   TYR C 270 " --> pdb=" O   VAL C 264 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   VAL C 264 " --> pdb=" O   TYR C 270 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   ALA C 272 " --> pdb=" O   ILE C 262 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 33 through 38
      removed outlier: 5.345A  pdb=" N   GLU B 290 " --> pdb=" O   GLY B  36 " (cutoff:3.500A)
      removed outlier: 4.828A  pdb=" N   THR B  38 " --> pdb=" O   VAL B 288 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   VAL B 288 " --> pdb=" O   THR B  38 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   PHE B 310 " --> pdb=" O   ILE B 321 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ILE B 321 " --> pdb=" O   PHE B 310 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 281 through 282
    Processing sheet with id=AB1, first strand: chain 'B' and resid 219 through 220
      removed outlier: 7.012A  pdb=" N   ALA B 272 " --> pdb=" O   ILE B 262 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   VAL B 264 " --> pdb=" O   TYR B 270 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   TYR B 270 " --> pdb=" O   VAL B 264 " (cutoff:3.500A)
      removed outlier: 8.957A  pdb=" N   GLY C 431 " --> pdb=" O   THR B  49 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   LEU B  51 " --> pdb=" O   GLY C 431 " (cutoff:3.500A)
      removed outlier: 7.965A  pdb=" N   TYR C 433 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   VAL B  53 " --> pdb=" O   TYR C 433 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 296 through 298
    Processing sheet with id=AB3, first strand: chain 'B' and resid 371 through 374
      removed outlier: 4.032A  pdb=" N   VAL B 378 " --> pdb=" O   LEU B 407 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 394 through 395
      removed outlier: 3.525A  pdb=" N   THR B 394 " --> pdb=" O   CYS B 389 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 33 through 38
      removed outlier: 5.344A  pdb=" N   GLU C 290 " --> pdb=" O   GLY C  36 " (cutoff:3.500A)
      removed outlier: 4.829A  pdb=" N   THR C  38 " --> pdb=" O   VAL C 288 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   VAL C 288 " --> pdb=" O   THR C  38 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   PHE C 310 " --> pdb=" O   ILE C 321 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ILE C 321 " --> pdb=" O   PHE C 310 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 281 through 282
    Processing sheet with id=AB7, first strand: chain 'C' and resid 296 through 298
    Processing sheet with id=AB8, first strand: chain 'C' and resid 371 through 374
      removed outlier: 4.031A  pdb=" N   VAL C 378 " --> pdb=" O   LEU C 407 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 394 through 395
      removed outlier: 3.525A  pdb=" N   THR C 394 " --> pdb=" O   CYS C 389 " (cutoff:3.500A)

    547 hydrogen bonds defined for protein.
    1530 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.20

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2310
        1.33 -     1.46: 2146
        1.46 -     1.59: 4691
        1.59 -     1.71: 3
        1.71 -     1.84: 66
  Bond restraints: 9216
  Sorted by residual:
  bond pdb=" CB  LEU A  23 "
       pdb=" CG  LEU A  23 "
    ideal  model  delta    sigma   weight residual
    1.530  1.602 -0.072 2.00e-02 2.50e+03 1.28e+01
  bond pdb=" CB  LEU B  23 "
       pdb=" CG  LEU B  23 "
    ideal  model  delta    sigma   weight residual
    1.530  1.601 -0.071 2.00e-02 2.50e+03 1.28e+01
  bond pdb=" CB  LEU C  23 "
       pdb=" CG  LEU C  23 "
    ideal  model  delta    sigma   weight residual
    1.530  1.601 -0.071 2.00e-02 2.50e+03 1.26e+01
  bond pdb=" NE  ARG C 171 "
       pdb=" CZ  ARG C 171 "
    ideal  model  delta    sigma   weight residual
    1.326  1.362 -0.036 1.10e-02 8.26e+03 1.07e+01
  bond pdb=" NE  ARG A 171 "
       pdb=" CZ  ARG A 171 "
    ideal  model  delta    sigma   weight residual
    1.326  1.362 -0.036 1.10e-02 8.26e+03 1.05e+01
  ... (remaining 9211 not shown)

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.43 -     2.93: 3860
        2.93 -     3.42: 8456
        3.42 -     3.91: 14542
        3.91 -     4.41: 15317
        4.41 -     4.90: 25936
  Nonbonded interactions: 68111
  Sorted by model distance:
  nonbonded pdb=" N   THR B 392 "
            pdb=" N   ASP B 393 "
     model   vdw
     2.433 2.560
  nonbonded pdb=" N   THR C 392 "
            pdb=" N   ASP C 393 "
     model   vdw
     2.433 2.560
  nonbonded pdb=" N   THR A 392 "
            pdb=" N   ASP A 393 "
     model   vdw
     2.433 2.560
  nonbonded pdb=" N   SER B 356 "
            pdb=" O   SER B 356 "
     model   vdw
     2.513 2.496
  nonbonded pdb=" N   SER C 356 "
            pdb=" O   SER C 356 "
     model   vdw
     2.513 2.496
  ... (remaining 68106 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             11.470
  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:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     7.170
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.072   9237  Z= 0.713
  Angle     :  1.541  11.571  12621  Z= 1.078
  Chirality :  0.087   0.347   1563
  Planarity :  0.005   0.020   1614
  Dihedral  :  9.806  79.964   3345
  Min Nonbonded Distance : 2.433

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

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.21), residues: 1209
  helix:  0.53 (0.20), residues: 504
  sheet:  0.73 (0.40), residues: 159
  loop : -0.14 (0.23), residues: 546

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

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

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

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 156
  time to evaluate  : 0.208 
Fit side-chains
REVERT: B  217 VAL cc_start: 0.9116 (t) cc_final: 0.8912 (m)
REVERT: B  404 VAL cc_start: 0.8501 (t) cc_final: 0.8275 (t)
REVERT: B  473 GLU cc_start: 0.7893 (tt0) cc_final: 0.7653 (tt0)
REVERT: C  463 GLN cc_start: 0.7851 (mm110) cc_final: 0.7644 (mm110)
  outliers start: 3
  outliers final: 0
  residues processed: 159
  average time/residue: 0.0961
  time to fit residues: 20.1643
Evaluate side-chains
  85 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    0.4980
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.4980
   chunk 117 optimal weight:    4.9990
   overall best weight:    0.4380

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

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

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.146731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.122863 restraints weight = 11195.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.123186 restraints weight = 9458.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.124304 restraints weight = 9138.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.125173 restraints weight = 7611.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.125457 restraints weight = 6804.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9237  Z= 0.167
  Angle     :  0.610   6.393  12621  Z= 0.335
  Chirality :  0.046   0.135   1563
  Planarity :  0.004   0.029   1614
  Dihedral  :  4.876  18.930   1431
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  :  6.76 %
    Favored  : 90.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.23), residues: 1209
  helix:  2.56 (0.23), residues: 510
  sheet:  0.50 (0.38), residues: 150
  loop : -0.36 (0.22), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 232 
 TYR   0.020   0.002   TYR C 427 
 PHE   0.011   0.002   PHE B 209 
 TRP   0.009   0.002   TRP C 303 
 HIS   0.001   0.000   HIS B 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 9216)
  covalent geometry    : angle       0.60311 (12573)
  SS BOND              : bond        0.00190 (   15)
  SS BOND              : angle       1.59141 (   30)
  hydrogen bonds       : bond        0.05669 (  547)
  hydrogen bonds       : angle       4.86910 ( 1530)
  link_NAG-ASN         : bond        0.00343 (    6)
  link_NAG-ASN         : angle       1.50780 (   18)

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

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 0.237 
Fit side-chains
REVERT: B  217 VAL cc_start: 0.9108 (t) cc_final: 0.8848 (m)
REVERT: B  447 ASP cc_start: 0.8176 (m-30) cc_final: 0.7940 (m-30)
REVERT: C  427 TYR cc_start: 0.8298 (t80) cc_final: 0.8011 (t80)
  outliers start: 23
  outliers final: 9
  residues processed: 102
  average time/residue: 0.0751
  time to fit residues: 11.4404
Evaluate side-chains
  70 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  357 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 89 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0060
   chunk 60 optimal weight:    0.1980
   chunk 2 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0970
   chunk 103 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.3394

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.146703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 90)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.125802 restraints weight = 11232.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.126381 restraints weight = 9792.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.127359 restraints weight = 8853.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.128592 restraints weight = 7978.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.128642 restraints weight = 7427.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.2999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9237  Z= 0.136
  Angle     :  0.519   5.399  12621  Z= 0.285
  Chirality :  0.044   0.139   1563
  Planarity :  0.003   0.036   1614
  Dihedral  :  4.271  17.729   1431
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  :  6.87 %
    Favored  : 90.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.24), residues: 1209
  helix:  3.07 (0.24), residues: 510
  sheet:  0.76 (0.40), residues: 150
  loop : -0.29 (0.23), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 360 
 TYR   0.015   0.001   TYR C 427 
 PHE   0.007   0.001   PHE A 277 
 TRP   0.003   0.001   TRP C 303 
 HIS   0.001   0.000   HIS C  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 9216)
  covalent geometry    : angle       0.51546 (12573)
  SS BOND              : bond        0.00094 (   15)
  SS BOND              : angle       0.85133 (   30)
  hydrogen bonds       : bond        0.04549 (  547)
  hydrogen bonds       : angle       4.30505 ( 1530)
  link_NAG-ASN         : bond        0.00215 (    6)
  link_NAG-ASN         : angle       1.41323 (   18)

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

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 76
  time to evaluate  : 0.210 
Fit side-chains
REVERT: B  154 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7511 (ttmm)
REVERT: B  217 VAL cc_start: 0.9174 (t) cc_final: 0.8816 (m)
REVERT: C  427 TYR cc_start: 0.8215 (t80) cc_final: 0.7804 (t80)
  outliers start: 26
  outliers final: 17
  residues processed: 99
  average time/residue: 0.0679
  time to fit residues: 9.8611
Evaluate side-chains
  81 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  154 LYS
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  357 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 1 optimal weight:    0.2980
   chunk 111 optimal weight:    2.9990
   chunk 113 optimal weight:    0.0020
   chunk 9 optimal weight:    0.7980
   chunk 87 optimal weight:    0.0050
   chunk 25 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9990
   chunk 16 optimal weight:    0.3980
   chunk 73 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   overall best weight:    0.2602

-------------------------------------------------------------------------------
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 = 0.3626 r_free = 0.3626 target = 0.144879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.121272 restraints weight = 11229.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.121749 restraints weight = 9075.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.123274 restraints weight = 7886.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.123891 restraints weight = 6929.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.124014 restraints weight = 6072.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.3430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   9237  Z= 0.112
  Angle     :  0.480   4.810  12621  Z= 0.260
  Chirality :  0.043   0.136   1563
  Planarity :  0.003   0.039   1614
  Dihedral  :  4.065  17.397   1431
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  :  8.42 %
    Favored  : 88.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.12 (0.24), residues: 1209
  helix:  3.18 (0.23), residues: 516
  sheet:  0.95 (0.42), residues: 150
  loop : -0.25 (0.23), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 388 
 TYR   0.021   0.001   TYR A 427 
 PHE   0.008   0.001   PHE C 277 
 TRP   0.004   0.001   TRP B 303 
 HIS   0.001   0.000   HIS C  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 9216)
  covalent geometry    : angle       0.47778 (12573)
  SS BOND              : bond        0.00118 (   15)
  SS BOND              : angle       0.64742 (   30)
  hydrogen bonds       : bond        0.03756 (  547)
  hydrogen bonds       : angle       3.97063 ( 1530)
  link_NAG-ASN         : bond        0.00181 (    6)
  link_NAG-ASN         : angle       1.20043 (   18)

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

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 76
  time to evaluate  : 0.262 
Fit side-chains
REVERT: B  217 VAL cc_start: 0.9135 (t) cc_final: 0.8771 (m)
REVERT: C  427 TYR cc_start: 0.8255 (t80) cc_final: 0.7831 (t80)
  outliers start: 27
  outliers final: 14
  residues processed: 100
  average time/residue: 0.0560
  time to fit residues: 8.8085
Evaluate side-chains
  77 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  432 GLU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue   94 ASP
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  357 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 89 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 58 optimal weight:    0.3980
   chunk 80 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 1 optimal weight:    0.1980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.6380

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.141343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.120571 restraints weight = 11466.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.120383 restraints weight = 11179.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.120515 restraints weight = 10364.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.120764 restraints weight = 9872.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.120881 restraints weight = 9489.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.3680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   9237  Z= 0.183
  Angle     :  0.563   6.583  12621  Z= 0.302
  Chirality :  0.045   0.147   1563
  Planarity :  0.004   0.039   1614
  Dihedral  :  4.210  17.433   1431
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 10.19 %
    Favored  : 85.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.78 (0.24), residues: 1209
  helix:  2.89 (0.23), residues: 516
  sheet:  0.88 (0.44), residues: 144
  loop : -0.43 (0.23), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 388 
 TYR   0.021   0.002   TYR B 427 
 PHE   0.009   0.001   PHE C 310 
 TRP   0.006   0.001   TRP B 303 
 HIS   0.003   0.001   HIS C 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 9216)
  covalent geometry    : angle       0.56021 (12573)
  SS BOND              : bond        0.00201 (   15)
  SS BOND              : angle       0.55273 (   30)
  hydrogen bonds       : bond        0.04437 (  547)
  hydrogen bonds       : angle       4.22188 ( 1530)
  link_NAG-ASN         : bond        0.00155 (    6)
  link_NAG-ASN         : angle       1.52076 (   18)

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

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 72
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  233 ASN cc_start: 0.8694 (t0) cc_final: 0.8475 (t0)
REVERT: B  233 ASN cc_start: 0.8734 (t0) cc_final: 0.8445 (t0)
REVERT: C  233 ASN cc_start: 0.8841 (t0) cc_final: 0.8591 (t0)
REVERT: C  424 VAL cc_start: 0.8240 (t) cc_final: 0.7944 (p)
  outliers start: 38
  outliers final: 30
  residues processed: 106
  average time/residue: 0.0632
  time to fit residues: 10.1724
Evaluate side-chains
  97 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 67
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  207 THR
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  430 GLU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  262 ILE
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  348 ILE
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  166 VAL
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain C residue  190 ILE
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  348 ILE
Chi-restraints excluded: chain C residue  357 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 30 optimal weight:    0.3980
   chunk 88 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 96 optimal weight:    0.3980
   chunk 18 optimal weight:    0.4980
   chunk 32 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0570
   chunk 61 optimal weight:    0.6980
   chunk 79 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 119 optimal weight:    0.5980
   overall best weight:    0.3898

-------------------------------------------------------------------------------
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 = 0.3632 r_free = 0.3632 target = 0.144183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.124426 restraints weight = 11476.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.124005 restraints weight = 11387.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.124663 restraints weight = 10888.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.124912 restraints weight = 10373.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.125077 restraints weight = 9715.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.3874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   9237  Z= 0.133
  Angle     :  0.514   7.805  12621  Z= 0.269
  Chirality :  0.044   0.191   1563
  Planarity :  0.003   0.042   1614
  Dihedral  :  4.111  17.212   1431
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 10.63 %
    Favored  : 85.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.90 (0.24), residues: 1209
  helix:  3.09 (0.23), residues: 516
  sheet:  0.94 (0.46), residues: 144
  loop : -0.50 (0.23), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 388 
 TYR   0.016   0.001   TYR A 427 
 PHE   0.007   0.001   PHE C 277 
 TRP   0.004   0.001   TRP B 303 
 HIS   0.001   0.001   HIS C 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 9216)
  covalent geometry    : angle       0.51017 (12573)
  SS BOND              : bond        0.00142 (   15)
  SS BOND              : angle       0.94844 (   30)
  hydrogen bonds       : bond        0.03904 (  547)
  hydrogen bonds       : angle       3.99474 ( 1530)
  link_NAG-ASN         : bond        0.00133 (    6)
  link_NAG-ASN         : angle       1.26264 (   18)

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

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 70
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  233 ASN cc_start: 0.8652 (t0) cc_final: 0.8446 (t0)
REVERT: C  233 ASN cc_start: 0.8807 (t0) cc_final: 0.8551 (t0)
REVERT: C  424 VAL cc_start: 0.8236 (t) cc_final: 0.7916 (p)
  outliers start: 35
  outliers final: 21
  residues processed: 100
  average time/residue: 0.0713
  time to fit residues: 10.4570
Evaluate side-chains
  85 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  207 THR
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  430 GLU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  190 ILE
Chi-restraints excluded: chain C residue  205 ILE
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  357 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 67 optimal weight:    0.5980
   chunk 111 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 82 optimal weight:    0.2980
   chunk 65 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0980
   chunk 36 optimal weight:    0.6980
   chunk 23 optimal weight:    0.3980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.3619 r_free = 0.3619 target = 0.143357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.122768 restraints weight = 11360.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.122699 restraints weight = 10619.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.122791 restraints weight = 9992.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.122791 restraints weight = 9616.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.122791 restraints weight = 9616.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.4014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9237  Z= 0.135
  Angle     :  0.520   7.941  12621  Z= 0.271
  Chirality :  0.044   0.145   1563
  Planarity :  0.004   0.041   1614
  Dihedral  :  4.075  16.847   1431
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 12.62 %
    Favored  : 84.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.88 (0.24), residues: 1209
  helix:  3.12 (0.23), residues: 516
  sheet:  0.94 (0.46), residues: 144
  loop : -0.56 (0.23), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 388 
 TYR   0.019   0.002   TYR B 427 
 PHE   0.008   0.001   PHE C 277 
 TRP   0.005   0.001   TRP B 303 
 HIS   0.001   0.001   HIS C 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 9216)
  covalent geometry    : angle       0.51766 (12573)
  SS BOND              : bond        0.00163 (   15)
  SS BOND              : angle       0.71800 (   30)
  hydrogen bonds       : bond        0.03815 (  547)
  hydrogen bonds       : angle       3.97985 ( 1530)
  link_NAG-ASN         : bond        0.00111 (    6)
  link_NAG-ASN         : angle       1.28839 (   18)

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

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 68
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  388 ARG cc_start: 0.8449 (ttp-110) cc_final: 0.8076 (mtm-85)
REVERT: C  233 ASN cc_start: 0.8851 (t0) cc_final: 0.8624 (t0)
  outliers start: 28
  outliers final: 25
  residues processed: 91
  average time/residue: 0.0842
  time to fit residues: 11.0016
Evaluate side-chains
  86 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 61
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  430 GLU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain C residue  158 LEU
Chi-restraints excluded: chain C residue  190 ILE
Chi-restraints excluded: chain C residue  205 ILE
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  357 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 41 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 75 optimal weight:    0.4980
   chunk 32 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 108 optimal weight:    0.6980
   overall best weight:    0.6980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.140359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.119487 restraints weight = 11461.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.119597 restraints weight = 11132.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.119502 restraints weight = 11412.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.120298 restraints weight = 10803.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.120386 restraints weight = 9865.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.4131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   9237  Z= 0.189
  Angle     :  0.582   8.681  12621  Z= 0.305
  Chirality :  0.046   0.235   1563
  Planarity :  0.004   0.048   1614
  Dihedral  :  4.208  16.911   1431
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 12.85 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.24), residues: 1209
  helix:  2.91 (0.23), residues: 516
  sheet:  0.75 (0.47), residues: 144
  loop : -0.73 (0.23), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 388 
 TYR   0.021   0.002   TYR A 427 
 PHE   0.009   0.001   PHE C 277 
 TRP   0.006   0.001   TRP B 303 
 HIS   0.002   0.001   HIS C 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 ( 9216)
  covalent geometry    : angle       0.57466 (12573)
  SS BOND              : bond        0.00225 (   15)
  SS BOND              : angle       1.63695 (   30)
  hydrogen bonds       : bond        0.04297 (  547)
  hydrogen bonds       : angle       4.17291 ( 1530)
  link_NAG-ASN         : bond        0.00395 (    6)
  link_NAG-ASN         : angle       1.50903 (   18)

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

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 63
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  233 ASN cc_start: 0.8764 (t0) cc_final: 0.8546 (t0)
REVERT: C  233 ASN cc_start: 0.8935 (t0) cc_final: 0.8666 (t0)
  outliers start: 29
  outliers final: 25
  residues processed: 88
  average time/residue: 0.0736
  time to fit residues: 10.2187
Evaluate side-chains
  87 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 62
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  430 GLU
Chi-restraints excluded: chain A residue  432 GLU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain C residue   66 CYS
Chi-restraints excluded: chain C residue  190 ILE
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  357 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 88 optimal weight:    3.9990
   chunk 46 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 101 optimal weight:    0.3980
   chunk 119 optimal weight:    3.9990
   chunk 83 optimal weight:    0.8980
   chunk 71 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3586 r_free = 0.3586 target = 0.140608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.120073 restraints weight = 11434.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.119028 restraints weight = 12497.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.119102 restraints weight = 13326.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.119410 restraints weight = 12140.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.119526 restraints weight = 11015.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.4204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   9237  Z= 0.171
  Angle     :  0.586   9.611  12621  Z= 0.305
  Chirality :  0.046   0.238   1563
  Planarity :  0.004   0.046   1614
  Dihedral  :  4.236  16.962   1431
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 12.62 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.58 (0.24), residues: 1209
  helix:  2.96 (0.23), residues: 516
  sheet:  0.67 (0.47), residues: 144
  loop : -0.79 (0.23), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 388 
 TYR   0.023   0.002   TYR B 427 
 PHE   0.008   0.001   PHE C 277 
 TRP   0.006   0.001   TRP B 303 
 HIS   0.002   0.001   HIS C 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 9216)
  covalent geometry    : angle       0.57629 (12573)
  SS BOND              : bond        0.00233 (   15)
  SS BOND              : angle       1.90690 (   30)
  hydrogen bonds       : bond        0.04239 (  547)
  hydrogen bonds       : angle       4.15985 ( 1530)
  link_NAG-ASN         : bond        0.00375 (    6)
  link_NAG-ASN         : angle       1.53949 (   18)

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

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 65
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  233 ASN cc_start: 0.8933 (t0) cc_final: 0.8666 (t0)
  outliers start: 34
  outliers final: 31
  residues processed: 94
  average time/residue: 0.0727
  time to fit residues: 10.8191
Evaluate side-chains
  93 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 62
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 MET
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  207 THR
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  430 GLU
Chi-restraints excluded: chain A residue  432 GLU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue   66 CYS
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain C residue   66 CYS
Chi-restraints excluded: chain C residue  190 ILE
Chi-restraints excluded: chain C residue  205 ILE
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  357 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 46 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0270
   chunk 102 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 85 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 106 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 87 optimal weight:    0.8980
   chunk 58 optimal weight:    0.4980
   overall best weight:    0.4638

-------------------------------------------------------------------------------
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 = 0.3599 r_free = 0.3599 target = 0.141782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.120714 restraints weight = 11553.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.120491 restraints weight = 11109.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.120359 restraints weight = 12214.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.120359 restraints weight = 11281.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.120359 restraints weight = 11281.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.4321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9237  Z= 0.144
  Angle     :  0.563   9.931  12621  Z= 0.290
  Chirality :  0.045   0.195   1563
  Planarity :  0.004   0.044   1614
  Dihedral  :  4.170  16.996   1431
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 12.85 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.25), residues: 1209
  helix:  3.10 (0.24), residues: 516
  sheet:  0.67 (0.48), residues: 144
  loop : -0.83 (0.23), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 388 
 TYR   0.025   0.002   TYR A 427 
 PHE   0.007   0.001   PHE B 277 
 TRP   0.005   0.001   TRP B 303 
 HIS   0.001   0.001   HIS B 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 9216)
  covalent geometry    : angle       0.55425 (12573)
  SS BOND              : bond        0.00245 (   15)
  SS BOND              : angle       1.75616 (   30)
  hydrogen bonds       : bond        0.03988 (  547)
  hydrogen bonds       : angle       4.04853 ( 1530)
  link_NAG-ASN         : bond        0.00188 (    6)
  link_NAG-ASN         : angle       1.57724 (   18)

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

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 67
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  233 ASN cc_start: 0.8956 (t0) cc_final: 0.8676 (t0)
REVERT: C  345 TYR cc_start: 0.7144 (t80) cc_final: 0.6935 (t80)
  outliers start: 30
  outliers final: 29
  residues processed: 93
  average time/residue: 0.0749
  time to fit residues: 11.0462
Evaluate side-chains
  92 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 63
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  207 THR
Chi-restraints excluded: chain A residue  215 ASN
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  357 LYS
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  430 GLU
Chi-restraints excluded: chain A residue  432 GLU
Chi-restraints excluded: chain A residue  469 ILE
Chi-restraints excluded: chain B residue   66 CYS
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  357 LYS
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain C residue   66 CYS
Chi-restraints excluded: chain C residue  190 ILE
Chi-restraints excluded: chain C residue  205 ILE
Chi-restraints excluded: chain C residue  266 VAL
Chi-restraints excluded: chain C residue  357 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 27 optimal weight:    0.1980
   chunk 58 optimal weight:    0.7980
   chunk 116 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 13 optimal weight:    0.1980
   chunk 114 optimal weight:    1.9990
   chunk 91 optimal weight:    0.4980
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3598 r_free = 0.3598 target = 0.141792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.120832 restraints weight = 11446.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.120077 restraints weight = 12299.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.120170 restraints weight = 12866.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.120536 restraints weight = 11981.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.120750 restraints weight = 11019.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.4376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9237  Z= 0.153
  Angle     :  0.599   9.647  12621  Z= 0.307
  Chirality :  0.046   0.228   1563
  Planarity :  0.004   0.044   1614
  Dihedral  :  4.202  16.983   1431
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 12.96 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.25), residues: 1209
  helix:  3.08 (0.23), residues: 513
  sheet:  0.64 (0.48), residues: 144
  loop : -0.80 (0.23), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 388 
 TYR   0.022   0.002   TYR B 427 
 PHE   0.008   0.001   PHE B 277 
 TRP   0.005   0.001   TRP B 303 
 HIS   0.001   0.001   HIS C 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 9216)
  covalent geometry    : angle       0.58659 (12573)
  SS BOND              : bond        0.00242 (   15)
  SS BOND              : angle       2.24550 (   30)
  hydrogen bonds       : bond        0.04050 (  547)
  hydrogen bonds       : angle       4.09296 ( 1530)
  link_NAG-ASN         : bond        0.00378 (    6)
  link_NAG-ASN         : angle       1.67485 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1354.13 seconds
wall clock time: 24 minutes 2.71 seconds (1442.71 seconds total)