Starting phenix.real_space_refine
on Wed Mar  4 10:51:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tw2_26148/03_2026/7tw2_26148.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tw2_26148/03_2026/7tw2_26148.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tw2_26148/03_2026/7tw2_26148.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tw2_26148/03_2026/7tw2_26148.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tw2_26148/03_2026/7tw2_26148.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tw2_26148/03_2026/7tw2_26148.cif"
  }
  resolution = 4.8
  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=   0.002
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    8429      2.51       5
     N    2122      2.21       5
     O    2239      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12838
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 6435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 814, 6435
          Classifications: {'peptide': 814}
          Link IDs: {'PTRANS': 49, 'TRANS': 764}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 6375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 805, 6375
          Classifications: {'peptide': 805}
          Link IDs: {'PTRANS': 47, 'TRANS': 757}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.57, per 1000 atoms: 0.20
  Number of scatterers: 12838
  At special positions: 0
  Unit cell: (120.006, 96.642, 147.618, 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    2239      8.00
     N    2122      7.00
     C    8429      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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 A1000 " - " ASN A 642 "
      " NAG B1000 " - " ASN B 642 "
  Time building additional restraints: 0.99
  Conformation dependent library (CDL) restraints added in 459.6 milliseconds
  

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3030

  Finding SS restraints...
    Secondary structure from input PDB file:
      75 helices and 8 sheets defined
      61.1% alpha, 4.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'B' and resid 103 through 116
      removed outlier: 4.084A  pdb=" N   LYS B 116 " --> pdb=" O   ARG B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 142
    Processing helix  chain 'B' and resid 149 through 158
      removed outlier: 3.975A  pdb=" N   ARG B 155 " --> pdb=" O   GLU B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 163 through 165
      No H-bonds generated for 'chain 'B' and resid 163 through 165'
    Processing helix  chain 'B' and resid 166 through 171
    Processing helix  chain 'B' and resid 195 through 200
    Processing helix  chain 'B' and resid 212 through 220
    Processing helix  chain 'B' and resid 277 through 291
    Processing helix  chain 'B' and resid 291 through 301
    Processing helix  chain 'B' and resid 303 through 317
      removed outlier: 4.265A  pdb=" N   LEU B 307 " --> pdb=" O   SER B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 334
    Processing helix  chain 'B' and resid 335 through 349
      removed outlier: 4.116A  pdb=" N   SER B 349 " --> pdb=" O   ARG B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 390
    Processing helix  chain 'B' and resid 392 through 399
    Processing helix  chain 'B' and resid 402 through 431
      removed outlier: 4.062A  pdb=" N   LEU B 406 " --> pdb=" O   SER B 402 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   PHE B 414 " --> pdb=" O   ILE B 410 " (cutoff:3.500A)
      Proline residue:  B 419  - end of helix
    Processing helix  chain 'B' and resid 436 through 455
      removed outlier: 3.684A  pdb=" N   LEU B 440 " --> pdb=" O   GLY B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 483
      removed outlier: 3.622A  pdb=" N   LEU B 469 " --> pdb=" O   SER B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 488 through 507
      removed outlier: 3.667A  pdb=" N   TRP B 492 " --> pdb=" O   VAL B 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 515
    Processing helix  chain 'B' and resid 517 through 547
      removed outlier: 3.615A  pdb=" N   GLN B 521 " --> pdb=" O   SER B 517 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 569 through 593
      removed outlier: 3.976A  pdb=" N   ASN B 593 " --> pdb=" O   ARG B 589 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 598 through 608
    Processing helix  chain 'B' and resid 608 through 624
      removed outlier: 3.529A  pdb=" N   ILE B 624 " --> pdb=" O   VAL B 620 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 667
    Processing helix  chain 'B' and resid 667 through 690
      removed outlier: 3.734A  pdb=" N   ALA B 671 " --> pdb=" O   SER B 667 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   LEU B 673 " --> pdb=" O   LEU B 669 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 702 through 719
    Processing helix  chain 'B' and resid 727 through 738
    Processing helix  chain 'B' and resid 760 through 773
      removed outlier: 3.597A  pdb=" N   LEU B 764 " --> pdb=" O   ARG B 760 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 776 through 781
    Processing helix  chain 'B' and resid 786 through 799
      removed outlier: 3.987A  pdb=" N   GLY B 790 " --> pdb=" O   ALA B 786 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ILE B 791 " --> pdb=" O   VAL B 787 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 803 through 811
      removed outlier: 3.675A  pdb=" N   ASP B 807 " --> pdb=" O   ILE B 803 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 822 through 827
      removed outlier: 3.580A  pdb=" N   LYS B 826 " --> pdb=" O   VAL B 822 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 829 through 853
    Processing helix  chain 'B' and resid 855 through 857
      No H-bonds generated for 'chain 'B' and resid 855 through 857'
    Processing helix  chain 'B' and resid 858 through 865
      removed outlier: 3.698A  pdb=" N   VAL B 862 " --> pdb=" O   ALA B 858 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 865 through 872
      removed outlier: 3.617A  pdb=" N   LEU B 869 " --> pdb=" O   LEU B 865 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 873 through 877
    Processing helix  chain 'B' and resid 879 through 887
    Processing helix  chain 'A' and resid 103 through 115
    Processing helix  chain 'A' and resid 127 through 142
    Processing helix  chain 'A' and resid 149 through 158
    Processing helix  chain 'A' and resid 164 through 168
      removed outlier: 3.826A  pdb=" N   GLU A 168 " --> pdb=" O   GLY A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 201
      removed outlier: 3.507A  pdb=" N   GLN A 198 " --> pdb=" O   SER A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 220
    Processing helix  chain 'A' and resid 277 through 291
      removed outlier: 3.578A  pdb=" N   GLU A 291 " --> pdb=" O   THR A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 301
    Processing helix  chain 'A' and resid 303 through 317
      removed outlier: 4.025A  pdb=" N   LEU A 307 " --> pdb=" O   SER A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 334
    Processing helix  chain 'A' and resid 335 through 347
    Processing helix  chain 'A' and resid 379 through 390
      removed outlier: 3.553A  pdb=" N   VAL A 383 " --> pdb=" O   PHE A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 399
    Processing helix  chain 'A' and resid 402 through 431
      removed outlier: 4.016A  pdb=" N   LEU A 406 " --> pdb=" O   SER A 402 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   PHE A 414 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      Proline residue:  A 419  - end of helix
    Processing helix  chain 'A' and resid 436 through 455
      removed outlier: 3.731A  pdb=" N   LEU A 440 " --> pdb=" O   GLY A 436 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   PHE A 451 " --> pdb=" O   GLN A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 483
      removed outlier: 3.574A  pdb=" N   LEU A 469 " --> pdb=" O   SER A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 507
      removed outlier: 3.706A  pdb=" N   TRP A 492 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 516
    Processing helix  chain 'A' and resid 517 through 547
      removed outlier: 3.662A  pdb=" N   GLN A 521 " --> pdb=" O   SER A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 593
      removed outlier: 3.862A  pdb=" N   ASN A 593 " --> pdb=" O   ARG A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 608
      removed outlier: 3.522A  pdb=" N   PHE A 608 " --> pdb=" O   VAL A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 624
    Processing helix  chain 'A' and resid 660 through 667
      removed outlier: 3.530A  pdb=" N   MET A 664 " --> pdb=" O   PRO A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 667 through 690
      removed outlier: 3.635A  pdb=" N   ALA A 671 " --> pdb=" O   SER A 667 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LEU A 673 " --> pdb=" O   LEU A 669 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 691 through 695
      removed outlier: 3.832A  pdb=" N   LYS A 695 " --> pdb=" O   PRO A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 702 through 719
    Processing helix  chain 'A' and resid 727 through 738
    Processing helix  chain 'A' and resid 760 through 773
    Processing helix  chain 'A' and resid 776 through 781
    Processing helix  chain 'A' and resid 786 through 799
      removed outlier: 3.980A  pdb=" N   GLY A 790 " --> pdb=" O   ALA A 786 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ILE A 791 " --> pdb=" O   VAL A 787 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 803 through 811
      removed outlier: 3.579A  pdb=" N   ASP A 807 " --> pdb=" O   ILE A 803 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 827
      removed outlier: 3.784A  pdb=" N   LYS A 826 " --> pdb=" O   VAL A 822 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 829 through 853
      removed outlier: 3.635A  pdb=" N   LEU A 835 " --> pdb=" O   TRP A 831 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 857
      No H-bonds generated for 'chain 'A' and resid 855 through 857'
    Processing helix  chain 'A' and resid 858 through 872
      removed outlier: 3.947A  pdb=" N   VAL A 862 " --> pdb=" O   ALA A 858 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   VAL A 867 " --> pdb=" O   LEU A 863 " (cutoff:3.500A)
      Proline residue:  A 868  - end of helix
    Processing helix  chain 'A' and resid 873 through 877
    Processing helix  chain 'A' and resid 879 through 887
    Processing sheet with id=AA1, first strand: chain 'B' and resid 58 through 67
      removed outlier: 6.585A  pdb=" N   VAL B  59 " --> pdb=" O   ARG B  80 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   ARG B  80 " --> pdb=" O   VAL B  59 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   LEU B  61 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 85 through 87
    current: chain 'B' and resid 226 through 234
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 226 through 234
    current: chain 'B' and resid 262 through 270
    Processing sheet with id=AA2, first strand: chain 'B' and resid 319 through 321
      removed outlier: 3.620A  pdb=" N   LEU B 319 " --> pdb=" O   LEU A 321 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU A 319 " --> pdb=" O   LEU B 321 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 462 through 463
    Processing sheet with id=AA4, first strand: chain 'B' and resid 739 through 740
    Processing sheet with id=AA5, first strand: chain 'A' and resid 56 through 67
      removed outlier: 7.025A  pdb=" N   VAL A  59 " --> pdb=" O   ARG A  80 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   ARG A  80 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   LEU A  61 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 86 through 87
    current: chain 'A' and resid 262 through 269
    Processing sheet with id=AA6, first strand: chain 'A' and resid 177 through 178
    Processing sheet with id=AA7, first strand: chain 'A' and resid 462 through 463
    Processing sheet with id=AA8, first strand: chain 'A' and resid 739 through 742
      removed outlier: 6.747A  pdb=" N   VAL A 740 " --> pdb=" O   GLN A 754 " (cutoff:3.500A)

    670 hydrogen bonds defined for protein.
    1950 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: 1.96

  Time building geometry restraints manager: 1.32 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4038
        1.34 -     1.46: 2842
        1.46 -     1.58: 6176
        1.58 -     1.70: 0
        1.70 -     1.82: 86
  Bond restraints: 13142
  Sorted by residual:
  bond pdb=" N   LEU B 706 "
       pdb=" CA  LEU B 706 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.19e-02 7.06e+03 5.91e+00
  bond pdb=" N   TRP B 662 "
       pdb=" CA  TRP B 662 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.026 1.23e-02 6.61e+03 4.62e+00
  bond pdb=" C1  NAG B1000 "
       pdb=" O5  NAG B1000 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.09e+00
  bond pdb=" C1  NAG A1000 "
       pdb=" O5  NAG A1000 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.95e+00
  bond pdb=" C   VAL A 560 "
       pdb=" N   PRO A 561 "
    ideal  model  delta    sigma   weight residual
    1.334  1.364 -0.030 2.34e-02 1.83e+03 1.66e+00
  ... (remaining 13137 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 17429
        2.05 -     4.11: 347
        4.11 -     6.16: 55
        6.16 -     8.22: 20
        8.22 -    10.27: 8
  Bond angle restraints: 17859
  Sorted by residual:
  angle pdb=" N   TRP B 662 "
        pdb=" CA  TRP B 662 "
        pdb=" C   TRP B 662 "
      ideal   model   delta    sigma   weight residual
     111.36  107.14    4.22 1.09e+00 8.42e-01 1.50e+01
  angle pdb=" N   LYS A 695 "
        pdb=" CA  LYS A 695 "
        pdb=" C   LYS A 695 "
      ideal   model   delta    sigma   weight residual
     111.30  116.42   -5.12 1.36e+00 5.41e-01 1.42e+01
  angle pdb=" CB  MET B 586 "
        pdb=" CG  MET B 586 "
        pdb=" SD  MET B 586 "
      ideal   model   delta    sigma   weight residual
     112.70  122.94  -10.24 3.00e+00 1.11e-01 1.17e+01
  angle pdb=" CA  GLU B 254 "
        pdb=" CB  GLU B 254 "
        pdb=" CG  GLU B 254 "
      ideal   model   delta    sigma   weight residual
     114.10  120.66   -6.56 2.00e+00 2.50e-01 1.07e+01
  angle pdb=" CB  MET B 712 "
        pdb=" CG  MET B 712 "
        pdb=" SD  MET B 712 "
      ideal   model   delta    sigma   weight residual
     112.70  122.19   -9.49 3.00e+00 1.11e-01 1.00e+01
  ... (remaining 17854 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 7182
       17.95 -    35.91: 577
       35.91 -    53.86: 90
       53.86 -    71.81: 12
       71.81 -    89.76: 18
  Dihedral angle restraints: 7879
    sinusoidal: 3202
      harmonic: 4677
  Sorted by residual:
  dihedral pdb=" CA  TRP B  81 "
           pdb=" C   TRP B  81 "
           pdb=" N   VAL B  82 "
           pdb=" CA  VAL B  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.11   20.89     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" CA  TYR A 555 "
           pdb=" C   TYR A 555 "
           pdb=" N   ASN A 556 "
           pdb=" CA  ASN A 556 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.28   18.72     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" CA  TYR B 555 "
           pdb=" C   TYR B 555 "
           pdb=" N   ASN B 556 "
           pdb=" CA  ASN B 556 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.76   18.24     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 7876 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1722
       0.057 -    0.113: 332
       0.113 -    0.170: 38
       0.170 -    0.226: 2
       0.226 -    0.283: 1
  Chirality restraints: 2095
  Sorted by residual:
  chirality pdb=" CA  MET B 300 "
            pdb=" N   MET B 300 "
            pdb=" C   MET B 300 "
            pdb=" CB  MET B 300 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" CA  LYS A 219 "
            pdb=" N   LYS A 219 "
            pdb=" C   LYS A 219 "
            pdb=" CB  LYS A 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CB  ILE B 296 "
            pdb=" CA  ILE B 296 "
            pdb=" CG1 ILE B 296 "
            pdb=" CG2 ILE B 296 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.37e-01
  ... (remaining 2092 not shown)

  Planarity restraints: 2242
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B 447 "   -0.023 2.00e-02 2.50e+03   4.63e-02 2.14e+01
        pdb=" C   GLN B 447 "    0.080 2.00e-02 2.50e+03
        pdb=" O   GLN B 447 "   -0.030 2.00e-02 2.50e+03
        pdb=" N   GLY B 448 "   -0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP B 831 "   -0.022 2.00e-02 2.50e+03   4.47e-02 2.00e+01
        pdb=" C   TRP B 831 "    0.077 2.00e-02 2.50e+03
        pdb=" O   TRP B 831 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   ARG B 832 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 197 "   -0.016 2.00e-02 2.50e+03   3.28e-02 1.07e+01
        pdb=" C   THR A 197 "    0.057 2.00e-02 2.50e+03
        pdb=" O   THR A 197 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   GLN A 198 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 2239 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 611
        2.72 -     3.27: 12954
        3.27 -     3.81: 20545
        3.81 -     4.36: 24058
        4.36 -     4.90: 41847
  Nonbonded interactions: 100015
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B  63 "
            pdb=" OG1 THR B 279 "
     model   vdw
     2.177 3.040
  nonbonded pdb=" NH1 ARG A 646 "
            pdb=" O   GLY A 647 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" ND2 ASN B 569 "
            pdb=" O   PRO A 568 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" OE2 GLU B 291 "
            pdb=" NE  ARG B 346 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" NH1 ARG B 646 "
            pdb=" O   GLY B 647 "
     model   vdw
     2.260 3.120
  ... (remaining 100010 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 55 through 348 or resid 369 through 1000))
}

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:             2.770
  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:             0.020
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.530
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
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      :  0.003   0.030  13144  Z= 0.143
  Angle     :  0.749  10.273  17865  Z= 0.377
  Chirality :  0.043   0.283   2095
  Planarity :  0.005   0.058   2240
  Dihedral  : 13.669  89.764   4849
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.21 %
    Favored  : 99.72 %
  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 are not related in a simple way.
  whole: -1.27 (0.19), residues: 1603
  helix:  0.08 (0.17), residues: 903
  sheet: -0.26 (0.54), residues: 85
  loop : -2.33 (0.20), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 387 
 TYR   0.033   0.002   TYR B  58 
 PHE   0.022   0.001   PHE B 244 
 TRP   0.013   0.001   TRP B 492 
 HIS   0.004   0.001   HIS B  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (13142)
  covalent geometry    : angle       0.74943 (17859)
  hydrogen bonds       : bond        0.13588 (  670)
  hydrogen bonds       : angle       5.20485 ( 1950)
  link_NAG-ASN         : bond        0.00176 (    2)
  link_NAG-ASN         : angle       0.83533 (    6)

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

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

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  578 MET cc_start: 0.9141 (tmm) cc_final: 0.8731 (tmm)
REVERT: B  776 MET cc_start: 0.8765 (mpp) cc_final: 0.8464 (mpp)
REVERT: A  264 PHE cc_start: 0.7663 (m-80) cc_final: 0.7022 (m-80)
REVERT: A  741 MET cc_start: 0.7191 (mtp) cc_final: 0.6716 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 79
  average time/residue: 0.0791
  time to fit residues: 10.4012
Evaluate side-chains
  57 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:   30.0000
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:   40.0000
   chunk 149 optimal weight:    7.9990
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
B 569 ASN
B 651 HIS
A  87 ASN
A 569 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.070793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.048978 restraints weight = 131774.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.049797 restraints weight = 80001.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.050270 restraints weight = 50250.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.050547 restraints weight = 36214.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.050854 restraints weight = 27067.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.1400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  13144  Z= 0.146
  Angle     :  0.589   6.802  17865  Z= 0.285
  Chirality :  0.039   0.143   2095
  Planarity :  0.005   0.050   2240
  Dihedral  :  4.355  59.231   1777
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  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 are not related in a simple way.
  whole:  0.40 (0.21), residues: 1603
  helix:  1.37 (0.17), residues: 925
  sheet:  0.35 (0.58), residues: 81
  loop : -1.55 (0.22), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 760 
 TYR   0.017   0.002   TYR B  58 
 PHE   0.017   0.001   PHE A 471 
 TRP   0.011   0.001   TRP B 492 
 HIS   0.004   0.001   HIS A 547 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (13142)
  covalent geometry    : angle       0.58911 (17859)
  hydrogen bonds       : bond        0.03717 (  670)
  hydrogen bonds       : angle       4.06883 ( 1950)
  link_NAG-ASN         : bond        0.00472 (    2)
  link_NAG-ASN         : angle       1.23386 (    6)

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

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

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.286 
Fit side-chains
REVERT: B  578 MET cc_start: 0.9194 (tmm) cc_final: 0.8759 (tmm)
REVERT: A  471 PHE cc_start: 0.9674 (t80) cc_final: 0.9373 (t80)
REVERT: A  498 ILE cc_start: 0.9798 (mm) cc_final: 0.9595 (pt)
REVERT: A  741 MET cc_start: 0.7488 (mtp) cc_final: 0.7011 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.0754
  time to fit residues: 8.5740
Evaluate side-chains
  52 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 86 optimal weight:   30.0000
   chunk 144 optimal weight:    9.9990
   chunk 4 optimal weight:    0.0870
   chunk 104 optimal weight:    0.9980
   chunk 8 optimal weight:   30.0000
   chunk 73 optimal weight:    0.7980
   chunk 151 optimal weight:    7.9990
   chunk 116 optimal weight:    8.9990
   chunk 106 optimal weight:    8.9990
   chunk 60 optimal weight:    8.9990
   chunk 33 optimal weight:   10.0000
   overall best weight:    3.7762

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

Flipped N/Q/H residues before XYZ refinement:
B 133 ASN
** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 569 ASN
A 651 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.068971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.047552 restraints weight = 133331.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.048459 restraints weight = 80350.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.048987 restraints weight = 51146.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.049645 restraints weight = 36130.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.049719 restraints weight = 27932.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.2271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  13144  Z= 0.165
  Angle     :  0.594   7.794  17865  Z= 0.288
  Chirality :  0.040   0.163   2095
  Planarity :  0.004   0.044   2240
  Dihedral  :  4.333  53.381   1777
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  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 are not related in a simple way.
  whole:  0.88 (0.21), residues: 1603
  helix:  1.59 (0.17), residues: 940
  sheet:  0.21 (0.57), residues: 81
  loop : -1.03 (0.23), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 730 
 TYR   0.014   0.002   TYR B 278 
 PHE   0.017   0.002   PHE A 792 
 TRP   0.011   0.001   TRP B 492 
 HIS   0.005   0.001   HIS B 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (13142)
  covalent geometry    : angle       0.59306 (17859)
  hydrogen bonds       : bond        0.03625 (  670)
  hydrogen bonds       : angle       4.11929 ( 1950)
  link_NAG-ASN         : bond        0.00326 (    2)
  link_NAG-ASN         : angle       1.38458 (    6)

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

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

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  578 MET cc_start: 0.9116 (tmm) cc_final: 0.8586 (tmm)
REVERT: B  861 PHE cc_start: 0.9435 (t80) cc_final: 0.9191 (t80)
REVERT: A  471 PHE cc_start: 0.9683 (t80) cc_final: 0.9371 (t80)
REVERT: A  741 MET cc_start: 0.7484 (mtp) cc_final: 0.7041 (mtp)
REVERT: A  833 MET cc_start: 0.8992 (ptp) cc_final: 0.8182 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0776
  time to fit residues: 8.6226
Evaluate side-chains
  54 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 136 optimal weight:    0.0870
   chunk 111 optimal weight:    3.9990
   chunk 88 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 134 optimal weight:    7.9990
   chunk 118 optimal weight:    7.9990
   chunk 140 optimal weight:    0.7980
   chunk 82 optimal weight:    0.0870
   chunk 101 optimal weight:   10.0000
   chunk 117 optimal weight:    9.9990
   overall best weight:    1.5940

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

Flipped N/Q/H residues before XYZ refinement:
A 163 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.070404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.048787 restraints weight = 131469.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.049565 restraints weight = 78216.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.050093 restraints weight = 49990.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.050522 restraints weight = 35635.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.050778 restraints weight = 26473.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.2460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  13144  Z= 0.101
  Angle     :  0.531   7.113  17865  Z= 0.250
  Chirality :  0.038   0.167   2095
  Planarity :  0.004   0.044   2240
  Dihedral  :  4.118  49.427   1777
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  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 are not related in a simple way.
  whole:  1.32 (0.21), residues: 1603
  helix:  1.96 (0.17), residues: 944
  sheet:  0.20 (0.57), residues: 82
  loop : -0.87 (0.23), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 389 
 TYR   0.013   0.001   TYR B 278 
 PHE   0.033   0.001   PHE B 266 
 TRP   0.034   0.001   TRP B 662 
 HIS   0.008   0.001   HIS B 834 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 (13142)
  covalent geometry    : angle       0.53031 (17859)
  hydrogen bonds       : bond        0.03295 (  670)
  hydrogen bonds       : angle       3.84473 ( 1950)
  link_NAG-ASN         : bond        0.00296 (    2)
  link_NAG-ASN         : angle       1.00654 (    6)

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

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

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
REVERT: B  578 MET cc_start: 0.9148 (tmm) cc_final: 0.8747 (tmm)
REVERT: B  776 MET cc_start: 0.8844 (mpp) cc_final: 0.8623 (mpp)
REVERT: B  861 PHE cc_start: 0.9433 (t80) cc_final: 0.9153 (t80)
REVERT: A  471 PHE cc_start: 0.9652 (t80) cc_final: 0.9364 (t80)
REVERT: A  675 PHE cc_start: 0.9183 (t80) cc_final: 0.8853 (t80)
REVERT: A  712 MET cc_start: 0.8606 (ptp) cc_final: 0.8282 (ptp)
REVERT: A  741 MET cc_start: 0.7461 (mtp) cc_final: 0.7205 (mtp)
REVERT: A  805 LEU cc_start: 0.9533 (tt) cc_final: 0.9299 (mt)
REVERT: A  833 MET cc_start: 0.8968 (ptp) cc_final: 0.8159 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0828
  time to fit residues: 9.1701
Evaluate side-chains
  51 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 102 optimal weight:    0.9980
   chunk 120 optimal weight:   10.0000
   chunk 146 optimal weight:    9.9990
   chunk 12 optimal weight:    8.9990
   chunk 9 optimal weight:    3.9990
   chunk 151 optimal weight:    7.9990
   chunk 3 optimal weight:   20.0000
   chunk 64 optimal weight:   20.0000
   chunk 107 optimal weight:   30.0000
   chunk 22 optimal weight:    5.9990
   overall best weight:    3.9386

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

Flipped N/Q/H residues before XYZ refinement:
B 433 ASN
B 550 GLN
** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.068087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.046842 restraints weight = 134646.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.047566 restraints weight = 81462.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.048075 restraints weight = 52915.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.048604 restraints weight = 37875.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.048774 restraints weight = 27524.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.3098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13144  Z= 0.169
  Angle     :  0.604   7.477  17865  Z= 0.292
  Chirality :  0.040   0.177   2095
  Planarity :  0.004   0.037   2240
  Dihedral  :  4.312  49.643   1777
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  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 are not related in a simple way.
  whole:  1.30 (0.21), residues: 1603
  helix:  1.85 (0.17), residues: 946
  sheet: -0.10 (0.57), residues: 82
  loop : -0.66 (0.24), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 730 
 TYR   0.016   0.002   TYR B 278 
 PHE   0.013   0.002   PHE A 464 
 TRP   0.032   0.002   TRP B 662 
 HIS   0.004   0.001   HIS B 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (13142)
  covalent geometry    : angle       0.60376 (17859)
  hydrogen bonds       : bond        0.03617 (  670)
  hydrogen bonds       : angle       4.11752 ( 1950)
  link_NAG-ASN         : bond        0.00323 (    2)
  link_NAG-ASN         : angle       1.57458 (    6)

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

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

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  559 MET cc_start: 0.8706 (tpp) cc_final: 0.8474 (tpp)
REVERT: B  578 MET cc_start: 0.9121 (tmm) cc_final: 0.8732 (tmm)
REVERT: B  861 PHE cc_start: 0.9385 (t80) cc_final: 0.9116 (t80)
REVERT: A  471 PHE cc_start: 0.9621 (t80) cc_final: 0.9332 (t80)
REVERT: A  663 MET cc_start: 0.9439 (tpt) cc_final: 0.9233 (tpt)
REVERT: A  675 PHE cc_start: 0.9175 (t80) cc_final: 0.8795 (t80)
REVERT: A  741 MET cc_start: 0.7390 (mtp) cc_final: 0.7186 (mtp)
REVERT: A  833 MET cc_start: 0.8995 (ptp) cc_final: 0.8202 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0789
  time to fit residues: 8.1762
Evaluate side-chains
  52 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 153 optimal weight:   10.0000
   chunk 82 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 102 optimal weight:    7.9990
   chunk 120 optimal weight:    7.9990
   chunk 26 optimal weight:    4.9990
   chunk 157 optimal weight:   10.0000
   chunk 60 optimal weight:    7.9990
   chunk 121 optimal weight:    6.9990
   chunk 5 optimal weight:   10.0000
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 374 GLN
B 434 GLN
** B 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  71 GLN
A 547 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.065704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.045224 restraints weight = 132124.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.045878 restraints weight = 84397.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.046474 restraints weight = 54397.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.046743 restraints weight = 39873.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.046850 restraints weight = 30296.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.4471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  13144  Z= 0.275
  Angle     :  0.784   9.697  17865  Z= 0.390
  Chirality :  0.044   0.189   2095
  Planarity :  0.006   0.058   2240
  Dihedral  :  5.251  53.809   1777
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 16.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  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 are not related in a simple way.
  whole:  0.41 (0.20), residues: 1603
  helix:  1.00 (0.17), residues: 944
  sheet: -0.50 (0.56), residues: 83
  loop : -0.74 (0.24), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 603 
 TYR   0.022   0.003   TYR B 278 
 PHE   0.031   0.003   PHE B 584 
 TRP   0.032   0.003   TRP B 662 
 HIS   0.007   0.002   HIS B 834 

Details of bonding type rmsd
  covalent geometry    : bond        0.00549 (13142)
  covalent geometry    : angle       0.78192 (17859)
  hydrogen bonds       : bond        0.04507 (  670)
  hydrogen bonds       : angle       4.80616 ( 1950)
  link_NAG-ASN         : bond        0.00294 (    2)
  link_NAG-ASN         : angle       3.30393 (    6)

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

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

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.463 
Fit side-chains
REVERT: B  435 MET cc_start: 0.7826 (tpp) cc_final: 0.7564 (tpp)
REVERT: B  578 MET cc_start: 0.9186 (tmm) cc_final: 0.8854 (tmm)
REVERT: B  696 MET cc_start: 0.8445 (mtp) cc_final: 0.7987 (mpp)
REVERT: B  776 MET cc_start: 0.8821 (mpp) cc_final: 0.8605 (mpp)
REVERT: A  471 PHE cc_start: 0.9620 (t80) cc_final: 0.9247 (t80)
REVERT: A  663 MET cc_start: 0.9464 (tpt) cc_final: 0.9227 (tpt)
REVERT: A  675 PHE cc_start: 0.9155 (t80) cc_final: 0.8805 (t80)
REVERT: A  696 MET cc_start: 0.8675 (pmm) cc_final: 0.8436 (pmm)
REVERT: A  833 MET cc_start: 0.9162 (ptp) cc_final: 0.8952 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0888
  time to fit residues: 9.0021
Evaluate side-chains
  51 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   chunk 121 optimal weight:    9.9990
   chunk 0 optimal weight:   30.0000
   chunk 48 optimal weight:    6.9990
   chunk 128 optimal weight:    0.5980
   chunk 93 optimal weight:    7.9990
   chunk 125 optimal weight:    1.9990
   chunk 142 optimal weight:    6.9990
   chunk 16 optimal weight:    8.9990
   chunk 89 optimal weight:   30.0000
   overall best weight:    4.7188

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

Flipped N/Q/H residues before XYZ refinement:
** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 840 GLN ** 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 = 0.3694 r_free = 0.3694 target = 0.066762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.045717 restraints weight = 130386.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.046310 restraints weight = 78502.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.046786 restraints weight = 56434.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 62)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.047452 restraints weight = 40862.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.047609 restraints weight = 31067.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.4630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  13144  Z= 0.194
  Angle     :  0.672   8.647  17865  Z= 0.327
  Chirality :  0.041   0.180   2095
  Planarity :  0.005   0.052   2240
  Dihedral  :  4.955  52.827   1777
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  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 are not related in a simple way.
  whole:  0.71 (0.21), residues: 1603
  helix:  1.29 (0.17), residues: 942
  sheet: -0.50 (0.57), residues: 82
  loop : -0.67 (0.25), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 295 
 TYR   0.020   0.002   TYR B 278 
 PHE   0.023   0.002   PHE B 266 
 TRP   0.033   0.002   TRP B 662 
 HIS   0.005   0.001   HIS B 834 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (13142)
  covalent geometry    : angle       0.67088 (17859)
  hydrogen bonds       : bond        0.04007 (  670)
  hydrogen bonds       : angle       4.55024 ( 1950)
  link_NAG-ASN         : bond        0.00296 (    2)
  link_NAG-ASN         : angle       2.46431 (    6)

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

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

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
REVERT: B  578 MET cc_start: 0.9132 (tmm) cc_final: 0.8751 (tmm)
REVERT: B  721 MET cc_start: 0.8691 (mpp) cc_final: 0.7991 (mtm)
REVERT: B  776 MET cc_start: 0.8754 (mpp) cc_final: 0.8525 (mpp)
REVERT: A  471 PHE cc_start: 0.9594 (t80) cc_final: 0.9302 (t80)
REVERT: A  663 MET cc_start: 0.9420 (tpt) cc_final: 0.9137 (tpt)
REVERT: A  675 PHE cc_start: 0.9031 (t80) cc_final: 0.8783 (t80)
REVERT: A  696 MET cc_start: 0.8686 (pmm) cc_final: 0.8417 (pmm)
REVERT: A  833 MET cc_start: 0.9105 (ptp) cc_final: 0.8898 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.0790
  time to fit residues: 8.4576
Evaluate side-chains
  49 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 72 optimal weight:    6.9990
   chunk 6 optimal weight:    0.8980
   chunk 136 optimal weight:    9.9990
   chunk 50 optimal weight:    8.9990
   chunk 87 optimal weight:   50.0000
   chunk 97 optimal weight:    6.9990
   chunk 110 optimal weight:    0.1980
   chunk 59 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 148 optimal weight:    7.9990
   chunk 109 optimal weight:   20.0000
   overall best weight:    3.0186

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

Flipped N/Q/H residues before XYZ refinement:
** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 840 GLN ** 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 = 0.3711 r_free = 0.3711 target = 0.067341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.046961 restraints weight = 129325.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.047467 restraints weight = 77931.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.048101 restraints weight = 54936.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.048411 restraints weight = 38601.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.048962 restraints weight = 30610.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.4703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13144  Z= 0.147
  Angle     :  0.634  13.526  17865  Z= 0.301
  Chirality :  0.040   0.218   2095
  Planarity :  0.004   0.047   2240
  Dihedral  :  4.734  50.044   1777
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  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 are not related in a simple way.
  whole:  1.08 (0.21), residues: 1603
  helix:  1.61 (0.17), residues: 937
  sheet: -0.41 (0.58), residues: 82
  loop : -0.53 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 295 
 TYR   0.018   0.002   TYR B 278 
 PHE   0.028   0.001   PHE B 236 
 TRP   0.029   0.002   TRP B 662 
 HIS   0.005   0.001   HIS B 834 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (13142)
  covalent geometry    : angle       0.63290 (17859)
  hydrogen bonds       : bond        0.03741 (  670)
  hydrogen bonds       : angle       4.32664 ( 1950)
  link_NAG-ASN         : bond        0.00359 (    2)
  link_NAG-ASN         : angle       1.83183 (    6)

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

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

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: B  578 MET cc_start: 0.9109 (tmm) cc_final: 0.8616 (tmm)
REVERT: B  776 MET cc_start: 0.8824 (mpp) cc_final: 0.8529 (mpp)
REVERT: B  861 PHE cc_start: 0.9457 (t80) cc_final: 0.9197 (t80)
REVERT: A  663 MET cc_start: 0.9425 (tpt) cc_final: 0.9111 (tpt)
REVERT: A  675 PHE cc_start: 0.9132 (t80) cc_final: 0.8790 (t80)
REVERT: A  696 MET cc_start: 0.8621 (pmm) cc_final: 0.8326 (pmm)
REVERT: A  741 MET cc_start: 0.6266 (mmp) cc_final: 0.6061 (mmm)
REVERT: A  795 MET cc_start: 0.9023 (mtm) cc_final: 0.8789 (mtm)
REVERT: A  833 MET cc_start: 0.9125 (ptp) cc_final: 0.8875 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0823
  time to fit residues: 8.5912
Evaluate side-chains
  51 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 27 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 87 optimal weight:   40.0000
   chunk 154 optimal weight:    3.9990
   chunk 7 optimal weight:   20.0000
   chunk 80 optimal weight:    9.9990
   chunk 122 optimal weight:    0.9990
   chunk 64 optimal weight:    7.9990
   chunk 3 optimal weight:   20.0000
   chunk 38 optimal weight:    0.5980
   overall best weight:    3.7188

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

Flipped N/Q/H residues before XYZ refinement:
** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 840 GLN ** 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 = 0.3704 r_free = 0.3704 target = 0.066945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.046700 restraints weight = 129334.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.047437 restraints weight = 78921.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.047840 restraints weight = 50128.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.048124 restraints weight = 35748.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.048377 restraints weight = 26049.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.4934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13144  Z= 0.163
  Angle     :  0.650  10.756  17865  Z= 0.313
  Chirality :  0.041   0.179   2095
  Planarity :  0.004   0.047   2240
  Dihedral  :  4.741  49.380   1777
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  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 are not related in a simple way.
  whole:  1.09 (0.21), residues: 1603
  helix:  1.61 (0.17), residues: 936
  sheet: -0.23 (0.59), residues: 80
  loop : -0.53 (0.25), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 295 
 TYR   0.017   0.002   TYR B 278 
 PHE   0.018   0.001   PHE A 464 
 TRP   0.038   0.002   TRP B 662 
 HIS   0.005   0.001   HIS B 834 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (13142)
  covalent geometry    : angle       0.64923 (17859)
  hydrogen bonds       : bond        0.03764 (  670)
  hydrogen bonds       : angle       4.39511 ( 1950)
  link_NAG-ASN         : bond        0.00335 (    2)
  link_NAG-ASN         : angle       1.73791 (    6)

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

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

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  578 MET cc_start: 0.9117 (tmm) cc_final: 0.8535 (tmm)
REVERT: B  586 MET cc_start: 0.6083 (tmm) cc_final: 0.5834 (tmm)
REVERT: B  696 MET cc_start: 0.8417 (mtp) cc_final: 0.8055 (mpp)
REVERT: B  776 MET cc_start: 0.8875 (mpp) cc_final: 0.8568 (mpp)
REVERT: B  861 PHE cc_start: 0.9425 (t80) cc_final: 0.9204 (t80)
REVERT: A  663 MET cc_start: 0.9392 (tpt) cc_final: 0.9077 (tpt)
REVERT: A  696 MET cc_start: 0.8602 (pmm) cc_final: 0.8338 (pmm)
REVERT: A  795 MET cc_start: 0.9020 (mtm) cc_final: 0.8757 (mtm)
REVERT: A  833 MET cc_start: 0.9119 (ptp) cc_final: 0.8868 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.0829
  time to fit residues: 8.6366
Evaluate side-chains
  52 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 88 optimal weight:    9.9990
   chunk 101 optimal weight:   30.0000
   chunk 151 optimal weight:    0.8980
   chunk 48 optimal weight:    7.9990
   chunk 16 optimal weight:   40.0000
   chunk 31 optimal weight:    3.9990
   chunk 117 optimal weight:    8.9990
   chunk 86 optimal weight:    7.9990
   chunk 130 optimal weight:    0.9990
   chunk 155 optimal weight:    8.9990
   chunk 66 optimal weight:    0.1980
   overall best weight:    2.8186

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

Flipped N/Q/H residues before XYZ refinement:
** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 840 GLN ** 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 = 0.3718 r_free = 0.3718 target = 0.067353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.047253 restraints weight = 128705.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.047799 restraints weight = 77920.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.048321 restraints weight = 50329.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.048590 restraints weight = 35942.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.048945 restraints weight = 27386.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.5003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  13144  Z= 0.134
  Angle     :  0.616  10.693  17865  Z= 0.293
  Chirality :  0.040   0.174   2095
  Planarity :  0.004   0.044   2240
  Dihedral  :  4.630  49.414   1777
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  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 are not related in a simple way.
  whole:  1.27 (0.21), residues: 1603
  helix:  1.75 (0.17), residues: 938
  sheet: -0.29 (0.56), residues: 90
  loop : -0.44 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 295 
 TYR   0.016   0.001   TYR B 390 
 PHE   0.016   0.001   PHE B 266 
 TRP   0.031   0.002   TRP B 662 
 HIS   0.004   0.001   HIS B 834 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (13142)
  covalent geometry    : angle       0.61579 (17859)
  hydrogen bonds       : bond        0.03588 (  670)
  hydrogen bonds       : angle       4.25333 ( 1950)
  link_NAG-ASN         : bond        0.00390 (    2)
  link_NAG-ASN         : angle       1.49072 (    6)

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

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

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  578 MET cc_start: 0.9163 (tmm) cc_final: 0.8828 (tmm)
REVERT: B  586 MET cc_start: 0.5819 (tmm) cc_final: 0.5609 (tmm)
REVERT: B  696 MET cc_start: 0.8386 (mtp) cc_final: 0.8026 (mpp)
REVERT: B  721 MET cc_start: 0.8342 (pmm) cc_final: 0.8086 (pmm)
REVERT: B  776 MET cc_start: 0.8869 (mpp) cc_final: 0.8579 (mpp)
REVERT: B  795 MET cc_start: 0.9159 (ptp) cc_final: 0.8943 (ptp)
REVERT: A  663 MET cc_start: 0.9388 (tpt) cc_final: 0.9081 (tpt)
REVERT: A  696 MET cc_start: 0.8537 (pmm) cc_final: 0.8264 (pmm)
REVERT: A  795 MET cc_start: 0.8984 (mtm) cc_final: 0.8740 (mtm)
REVERT: A  833 MET cc_start: 0.9095 (ptp) cc_final: 0.8808 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.0884
  time to fit residues: 9.1856
Evaluate side-chains
  50 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 110 optimal weight:    0.0470
   chunk 8 optimal weight:    3.9990
   chunk 91 optimal weight:   30.0000
   chunk 150 optimal weight:    0.0470
   chunk 3 optimal weight:   10.0000
   chunk 64 optimal weight:    0.9990
   chunk 117 optimal weight:    9.9990
   chunk 138 optimal weight:    0.0020
   chunk 43 optimal weight:   20.0000
   chunk 123 optimal weight:    0.8980
   overall best weight:    0.3984

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

Flipped N/Q/H residues before XYZ refinement:
** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 840 GLN ** 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 = 0.3765 r_free = 0.3765 target = 0.069230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.048691 restraints weight = 130085.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.048979 restraints weight = 78241.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.049638 restraints weight = 54845.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.049812 restraints weight = 39914.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.050130 restraints weight = 30591.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.4890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  13144  Z= 0.100
  Angle     :  0.591  10.285  17865  Z= 0.272
  Chirality :  0.040   0.172   2095
  Planarity :  0.004   0.043   2240
  Dihedral  :  4.237  39.106   1777
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  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 are not related in a simple way.
  whole:  1.59 (0.22), residues: 1603
  helix:  2.03 (0.17), residues: 937
  sheet: -0.10 (0.56), residues: 96
  loop : -0.35 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 340 
 TYR   0.015   0.001   TYR B 390 
 PHE   0.014   0.001   PHE B 266 
 TRP   0.025   0.001   TRP B 662 
 HIS   0.006   0.001   HIS B 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 (13142)
  covalent geometry    : angle       0.59112 (17859)
  hydrogen bonds       : bond        0.03212 (  670)
  hydrogen bonds       : angle       3.96684 ( 1950)
  link_NAG-ASN         : bond        0.00343 (    2)
  link_NAG-ASN         : angle       0.76639 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2564.18 seconds
wall clock time: 44 minutes 46.67 seconds (2686.67 seconds total)