Starting phenix.real_space_refine
on Wed Jun 11 16:34:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tw2_26148/06_2025/7tw2_26148.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tw2_26148/06_2025/7tw2_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_26148/06_2025/7tw2_26148.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tw2_26148/06_2025/7tw2_26148.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tw2_26148/06_2025/7tw2_26148.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tw2_26148/06_2025/7tw2_26148.cif"
  }
  resolution = 4.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.38, per 1000 atoms: 0.65
  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: 3.24
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  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: 1.28
  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: 3.89

  Time building geometry restraints manager: 3.88 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 894 or resid 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:             2.110
  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:          0.550
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     31.860
  Find NCS groups from input model:        0.540
  Set up NCS constraints:                  0.050
  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:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.260
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.013   0.001   TRP B 492 
 HIS   0.004   0.001   HIS B  98 
 PHE   0.022   0.001   PHE B 244 
 TYR   0.033   0.002   TYR B  58 
 ARG   0.005   0.000   ARG A 387 

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

*********************** 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  : 1.513 
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: 0.7021 (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: 0.1971
  time to fit residues: 25.8597
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  : 1.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 135 optimal weight:    9.9990
   chunk 122 optimal weight:    8.9990
   chunk 67 optimal weight:    8.9990
   chunk 41 optimal weight:    9.9990
   chunk 82 optimal weight:    0.6980
   chunk 65 optimal weight:    6.9990
   chunk 126 optimal weight:    7.9990
   chunk 48 optimal weight:   10.0000
   chunk 76 optimal weight:    9.9990
   chunk 93 optimal weight:    0.0070
   chunk 146 optimal weight:   10.0000
   overall best weight:    4.9404

-------------------------------------------------------------------------------
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 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 547 HIS
A 569 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.068728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.047355 restraints weight = 131950.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.047934 restraints weight = 79754.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.048800 restraints weight = 53397.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  13144  Z= 0.212
  Angle     :  0.678   7.614  17865  Z= 0.333
  Chirality :  0.041   0.156   2095
  Planarity :  0.005   0.048   2240
  Dihedral  :  4.497  48.752   1777
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.21), residues: 1603
  helix:  1.06 (0.17), residues: 937
  sheet: -0.02 (0.57), residues: 81
  loop : -1.48 (0.22), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 492 
 HIS   0.005   0.001   HIS B 703 
 PHE   0.020   0.002   PHE A 792 
 TYR   0.017   0.002   TYR B  58 
 ARG   0.006   0.001   ARG A 760 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00472 (    2)
  link_NAG-ASN         : angle       2.17347 (    6)
  hydrogen bonds       : bond        0.04184 (  670)
  hydrogen bonds       : angle       4.32732 ( 1950)
  covalent geometry    : bond        0.00425 (13142)
  covalent geometry    : angle       0.67701 (17859)

*********************** 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
  65 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 1.517 
Fit side-chains
REVERT: B  578 MET cc_start: 0.9123 (tmm) cc_final: 0.8684 (tmm)
REVERT: A  471 PHE cc_start: 0.9670 (t80) cc_final: 0.9330 (t80)
REVERT: A  498 ILE cc_start: 0.9821 (mm) cc_final: 0.9608 (pt)
REVERT: A  663 MET cc_start: 0.9433 (tpt) cc_final: 0.9204 (tpt)
REVERT: A  741 MET cc_start: 0.7308 (mtp) cc_final: 0.6829 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.2047
  time to fit residues: 22.2164
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  : 1.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 131 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 126 optimal weight:    6.9990
   chunk 142 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 33 optimal weight:   10.0000
   chunk 147 optimal weight:    5.9990
   chunk 13 optimal weight:   30.0000
   chunk 74 optimal weight:    9.9990
   chunk 153 optimal weight:    6.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 133 ASN
** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 569 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.067559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.046495 restraints weight = 131182.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.047396 restraints weight = 80089.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.047741 restraints weight = 51236.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13144  Z= 0.217
  Angle     :  0.671   7.717  17865  Z= 0.331
  Chirality :  0.041   0.168   2095
  Planarity :  0.005   0.045   2240
  Dihedral  :  4.623  50.678   1777
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.21), residues: 1603
  helix:  1.26 (0.17), residues: 936
  sheet: -0.08 (0.59), residues: 81
  loop : -1.04 (0.24), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 831 
 HIS   0.004   0.001   HIS B 703 
 PHE   0.014   0.002   PHE A 471 
 TYR   0.018   0.002   TYR B 278 
 ARG   0.005   0.001   ARG B 730 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00328 (    2)
  link_NAG-ASN         : angle       2.21826 (    6)
  hydrogen bonds       : bond        0.04022 (  670)
  hydrogen bonds       : angle       4.48080 ( 1950)
  covalent geometry    : bond        0.00435 (13142)
  covalent geometry    : angle       0.66994 (17859)

*********************** 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
  66 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 1.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  578 MET cc_start: 0.9177 (tmm) cc_final: 0.8673 (tmm)
REVERT: B  861 PHE cc_start: 0.9494 (t80) cc_final: 0.9256 (t80)
REVERT: A  471 PHE cc_start: 0.9690 (t80) cc_final: 0.9366 (t80)
REVERT: A  663 MET cc_start: 0.9492 (tpt) cc_final: 0.9183 (tpt)
REVERT: A  741 MET cc_start: 0.7405 (mtp) cc_final: 0.6965 (mtp)
REVERT: A  795 MET cc_start: 0.9031 (mtm) cc_final: 0.8700 (mtm)
REVERT: A  833 MET cc_start: 0.9001 (ptp) cc_final: 0.8257 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1992
  time to fit residues: 21.9904
Evaluate side-chains
  53 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 1.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 69 optimal weight:    8.9990
   chunk 109 optimal weight:   30.0000
   chunk 80 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9990
   chunk 29 optimal weight:   30.0000
   chunk 6 optimal weight:    0.6980
   chunk 106 optimal weight:   20.0000
   chunk 111 optimal weight:    8.9990
   chunk 147 optimal weight:    7.9990
   chunk 91 optimal weight:   20.0000
   chunk 146 optimal weight:    3.9990
   overall best weight:    4.1388

-------------------------------------------------------------------------------
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**
** A 163 HIS ** 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 = 0.3726 r_free = 0.3726 target = 0.067797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.046616 restraints weight = 130420.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.047497 restraints weight = 78280.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.047874 restraints weight = 49172.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.3276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13144  Z= 0.175
  Angle     :  0.618   7.102  17865  Z= 0.302
  Chirality :  0.040   0.175   2095
  Planarity :  0.004   0.041   2240
  Dihedral  :  4.555  48.061   1777
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.21), residues: 1603
  helix:  1.45 (0.17), residues: 940
  sheet: -0.36 (0.58), residues: 82
  loop : -0.88 (0.24), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 662 
 HIS   0.005   0.001   HIS B 834 
 PHE   0.031   0.002   PHE B 266 
 TYR   0.019   0.002   TYR B 278 
 ARG   0.004   0.001   ARG A 389 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00307 (    2)
  link_NAG-ASN         : angle       1.97416 (    6)
  hydrogen bonds       : bond        0.03751 (  670)
  hydrogen bonds       : angle       4.34603 ( 1950)
  covalent geometry    : bond        0.00357 (13142)
  covalent geometry    : angle       0.61703 (17859)

*********************** 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
  62 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 1.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  578 MET cc_start: 0.9120 (tmm) cc_final: 0.8753 (tmm)
REVERT: B  861 PHE cc_start: 0.9368 (t80) cc_final: 0.9139 (t80)
REVERT: A  471 PHE cc_start: 0.9641 (t80) cc_final: 0.9381 (t80)
REVERT: A  663 MET cc_start: 0.9397 (tpt) cc_final: 0.9089 (tpt)
REVERT: A  741 MET cc_start: 0.7271 (mtp) cc_final: 0.7022 (mtp)
REVERT: A  795 MET cc_start: 0.8991 (mtm) cc_final: 0.8777 (mtm)
REVERT: A  833 MET cc_start: 0.8991 (ptp) cc_final: 0.8133 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.2195
  time to fit residues: 22.4079
Evaluate side-chains
  53 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 1.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 30 optimal weight:   20.0000
   chunk 144 optimal weight:   20.0000
   chunk 100 optimal weight:    0.8980
   chunk 86 optimal weight:   20.0000
   chunk 112 optimal weight:    5.9990
   chunk 105 optimal weight:   20.0000
   chunk 83 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 160 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    3.9788

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

Flipped N/Q/H residues before XYZ refinement:
** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.067544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.047135 restraints weight = 132610.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.047706 restraints weight = 81960.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.048147 restraints weight = 52097.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.3780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13144  Z= 0.168
  Angle     :  0.623   7.142  17865  Z= 0.303
  Chirality :  0.040   0.176   2095
  Planarity :  0.004   0.039   2240
  Dihedral  :  4.565  46.634   1777
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.21), residues: 1603
  helix:  1.56 (0.17), residues: 945
  sheet: -0.43 (0.58), residues: 82
  loop : -0.66 (0.25), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 662 
 HIS   0.004   0.001   HIS B 703 
 PHE   0.013   0.002   PHE A 471 
 TYR   0.018   0.002   TYR B 278 
 ARG   0.004   0.001   ARG A 389 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00298 (    2)
  link_NAG-ASN         : angle       1.94111 (    6)
  hydrogen bonds       : bond        0.03706 (  670)
  hydrogen bonds       : angle       4.29343 ( 1950)
  covalent geometry    : bond        0.00344 (13142)
  covalent geometry    : angle       0.62165 (17859)

*********************** 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  : 1.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  578 MET cc_start: 0.9153 (tmm) cc_final: 0.8647 (tmm)
REVERT: B  776 MET cc_start: 0.8871 (mpp) cc_final: 0.8600 (mpp)
REVERT: B  861 PHE cc_start: 0.9471 (t80) cc_final: 0.9202 (t80)
REVERT: A  471 PHE cc_start: 0.9681 (t80) cc_final: 0.9406 (t80)
REVERT: A  663 MET cc_start: 0.9457 (tpt) cc_final: 0.9167 (tpt)
REVERT: A  795 MET cc_start: 0.8993 (mtm) cc_final: 0.8781 (mtm)
REVERT: A  833 MET cc_start: 0.9061 (ptp) cc_final: 0.8271 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.2073
  time to fit residues: 21.4511
Evaluate side-chains
  53 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 1.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 119 optimal weight:    1.9990
   chunk 12 optimal weight:   20.0000
   chunk 49 optimal weight:    0.3980
   chunk 81 optimal weight:   50.0000
   chunk 135 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9980
   chunk 50 optimal weight:    4.9990
   chunk 142 optimal weight:   20.0000
   chunk 80 optimal weight:   10.0000
   chunk 110 optimal weight:    0.1980
   chunk 145 optimal weight:    5.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
B 434 GLN
A 163 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.069106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.049856 restraints weight = 128792.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.049463 restraints weight = 86850.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.050608 restraints weight = 55324.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.3828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  13144  Z= 0.105
  Angle     :  0.559   6.657  17865  Z= 0.264
  Chirality :  0.039   0.177   2095
  Planarity :  0.004   0.050   2240
  Dihedral  :  4.283  42.319   1777
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.21), residues: 1603
  helix:  1.95 (0.17), residues: 935
  sheet: -0.23 (0.59), residues: 82
  loop : -0.54 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP B 662 
 HIS   0.003   0.001   HIS B 734 
 PHE   0.019   0.001   PHE B 266 
 TYR   0.015   0.001   TYR B 278 
 ARG   0.006   0.000   ARG B 295 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00345 (    2)
  link_NAG-ASN         : angle       1.31679 (    6)
  hydrogen bonds       : bond        0.03364 (  670)
  hydrogen bonds       : angle       4.01738 ( 1950)
  covalent geometry    : bond        0.00226 (13142)
  covalent geometry    : angle       0.55809 (17859)

*********************** 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
  64 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 1.481 
Fit side-chains
REVERT: B  578 MET cc_start: 0.9082 (tmm) cc_final: 0.8756 (tmm)
REVERT: B  776 MET cc_start: 0.8933 (mpp) cc_final: 0.8578 (mpp)
REVERT: B  861 PHE cc_start: 0.9423 (t80) cc_final: 0.9146 (t80)
REVERT: A  663 MET cc_start: 0.9499 (tpt) cc_final: 0.9246 (tpt)
REVERT: A  795 MET cc_start: 0.9021 (mtm) cc_final: 0.8765 (mtm)
REVERT: A  833 MET cc_start: 0.9003 (ptp) cc_final: 0.8238 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.2008
  time to fit residues: 21.7215
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  : 1.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 84 optimal weight:   40.0000
   chunk 96 optimal weight:    1.9990
   chunk 99 optimal weight:   30.0000
   chunk 95 optimal weight:    8.9990
   chunk 2 optimal weight:   40.0000
   chunk 35 optimal weight:    8.9990
   chunk 53 optimal weight:    9.9990
   chunk 154 optimal weight:    7.9990
   chunk 103 optimal weight:    6.9990
   chunk 93 optimal weight:    0.9980
   chunk 90 optimal weight:    8.9990
   overall best weight:    5.3988

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.066503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.046278 restraints weight = 131195.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.046768 restraints weight = 81600.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.047305 restraints weight = 53506.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.4419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  13144  Z= 0.221
  Angle     :  0.691  11.302  17865  Z= 0.339
  Chirality :  0.041   0.186   2095
  Planarity :  0.005   0.047   2240
  Dihedral  :  4.654  45.787   1777
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.21), residues: 1603
  helix:  1.47 (0.17), residues: 942
  sheet: -0.33 (0.58), residues: 82
  loop : -0.52 (0.25), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 662 
 HIS   0.004   0.001   HIS A 309 
 PHE   0.022   0.002   PHE A 836 
 TYR   0.018   0.002   TYR B 278 
 ARG   0.005   0.001   ARG B 295 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00269 (    2)
  link_NAG-ASN         : angle       2.08078 (    6)
  hydrogen bonds       : bond        0.03904 (  670)
  hydrogen bonds       : angle       4.47122 ( 1950)
  covalent geometry    : bond        0.00450 (13142)
  covalent geometry    : angle       0.69034 (17859)

*********************** 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
  62 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 1.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  578 MET cc_start: 0.8993 (tmm) cc_final: 0.8650 (tmm)
REVERT: B  776 MET cc_start: 0.8764 (mpp) cc_final: 0.8524 (mpp)
REVERT: B  861 PHE cc_start: 0.9427 (t80) cc_final: 0.9134 (t80)
REVERT: A  663 MET cc_start: 0.9324 (tpt) cc_final: 0.9001 (tpt)
REVERT: A  696 MET cc_start: 0.8644 (pmm) cc_final: 0.8436 (pmm)
REVERT: A  795 MET cc_start: 0.8999 (mtm) cc_final: 0.8775 (mtm)
REVERT: A  833 MET cc_start: 0.9146 (ptp) cc_final: 0.8890 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.1960
  time to fit residues: 20.5447
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  : 1.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 115 optimal weight:   10.0000
   chunk 44 optimal weight:   10.0000
   chunk 158 optimal weight:    0.8980
   chunk 48 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 145 optimal weight:   10.0000
   chunk 132 optimal weight:    7.9990
   chunk 103 optimal weight:    6.9990
   chunk 1 optimal weight:    0.8980
   chunk 124 optimal weight:    0.7980
   chunk 14 optimal weight:    8.9990
   overall best weight:    3.5184

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.067388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.046744 restraints weight = 133691.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.047518 restraints weight = 80816.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.048116 restraints weight = 48782.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.4549

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= 0.152
  Angle     :  0.613   9.147  17865  Z= 0.296
  Chirality :  0.040   0.174   2095
  Planarity :  0.004   0.044   2240
  Dihedral  :  4.598  47.916   1777
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.21), residues: 1603
  helix:  1.61 (0.17), residues: 941
  sheet: -0.31 (0.58), residues: 82
  loop : -0.43 (0.25), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 662 
 HIS   0.003   0.001   HIS A 101 
 PHE   0.018   0.001   PHE A 836 
 TYR   0.017   0.002   TYR B 278 
 ARG   0.006   0.000   ARG B 295 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00337 (    2)
  link_NAG-ASN         : angle       1.59176 (    6)
  hydrogen bonds       : bond        0.03594 (  670)
  hydrogen bonds       : angle       4.28279 ( 1950)
  covalent geometry    : bond        0.00318 (13142)
  covalent geometry    : angle       0.61269 (17859)

*********************** 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
  64 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 1.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  435 MET cc_start: 0.8223 (mmt) cc_final: 0.8010 (mmt)
REVERT: B  475 PHE cc_start: 0.9280 (t80) cc_final: 0.8945 (t80)
REVERT: B  578 MET cc_start: 0.9057 (tmm) cc_final: 0.8729 (tmm)
REVERT: B  776 MET cc_start: 0.8784 (mpp) cc_final: 0.8501 (mpp)
REVERT: B  861 PHE cc_start: 0.9401 (t80) cc_final: 0.9114 (t80)
REVERT: A  663 MET cc_start: 0.9440 (tpt) cc_final: 0.9059 (tpt)
REVERT: A  696 MET cc_start: 0.8557 (pmm) cc_final: 0.8345 (pmm)
REVERT: A  741 MET cc_start: 0.7024 (mmm) cc_final: 0.6812 (mmm)
REVERT: A  795 MET cc_start: 0.8949 (mtm) cc_final: 0.8736 (mtm)
REVERT: A  833 MET cc_start: 0.9151 (ptp) cc_final: 0.8509 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.2127
  time to fit residues: 22.9420
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  : 1.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 126 optimal weight:    4.9990
   chunk 2 optimal weight:   20.0000
   chunk 73 optimal weight:    9.9990
   chunk 45 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 43 optimal weight:    8.9990
   chunk 105 optimal weight:   20.0000
   chunk 8 optimal weight:   10.0000
   chunk 157 optimal weight:    0.7980
   chunk 148 optimal weight:    9.9990
   overall best weight:    4.1588

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

Flipped N/Q/H residues before XYZ refinement:
B 734 HIS
** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.066645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.046318 restraints weight = 130169.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.047040 restraints weight = 78114.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.047412 restraints weight = 52066.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.4892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13144  Z= 0.176
  Angle     :  0.645   9.447  17865  Z= 0.313
  Chirality :  0.041   0.183   2095
  Planarity :  0.004   0.044   2240
  Dihedral  :  4.712  50.083   1777
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.21), residues: 1603
  helix:  1.52 (0.17), residues: 935
  sheet: -0.35 (0.58), residues: 82
  loop : -0.42 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 662 
 HIS   0.005   0.001   HIS B 734 
 PHE   0.028   0.002   PHE B 236 
 TYR   0.016   0.002   TYR B 278 
 ARG   0.005   0.001   ARG B 295 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00344 (    2)
  link_NAG-ASN         : angle       1.65683 (    6)
  hydrogen bonds       : bond        0.03712 (  670)
  hydrogen bonds       : angle       4.37890 ( 1950)
  covalent geometry    : bond        0.00362 (13142)
  covalent geometry    : angle       0.64402 (17859)

*********************** 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
  60 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 1.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  435 MET cc_start: 0.8240 (mmt) cc_final: 0.7965 (mmt)
REVERT: B  578 MET cc_start: 0.9061 (tmm) cc_final: 0.8729 (tmm)
REVERT: B  776 MET cc_start: 0.8725 (mpp) cc_final: 0.8515 (mpp)
REVERT: B  861 PHE cc_start: 0.9381 (t80) cc_final: 0.9093 (t80)
REVERT: A  663 MET cc_start: 0.9324 (tpt) cc_final: 0.8947 (tpt)
REVERT: A  696 MET cc_start: 0.8596 (pmm) cc_final: 0.8362 (pmm)
REVERT: A  741 MET cc_start: 0.7001 (mmm) cc_final: 0.6770 (mmm)
REVERT: A  795 MET cc_start: 0.8960 (mtm) cc_final: 0.8740 (mtm)
REVERT: A  833 MET cc_start: 0.9127 (ptp) cc_final: 0.8849 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.2025
  time to fit residues: 20.7193
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  : 1.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 99 optimal weight:    4.9990
   chunk 82 optimal weight:    0.3980
   chunk 118 optimal weight:    8.9990
   chunk 142 optimal weight:    5.9990
   chunk 85 optimal weight:   50.0000
   chunk 107 optimal weight:   30.0000
   chunk 41 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 129 optimal weight:    1.9990
   chunk 153 optimal weight:    5.9990
   overall best weight:    2.2586

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.067765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.047748 restraints weight = 128282.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.048288 restraints weight = 78636.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.048898 restraints weight = 50368.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.4907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13144  Z= 0.122
  Angle     :  0.593   9.265  17865  Z= 0.282
  Chirality :  0.040   0.176   2095
  Planarity :  0.004   0.042   2240
  Dihedral  :  4.522  48.689   1777
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.21), residues: 1603
  helix:  1.87 (0.17), residues: 929
  sheet: -0.34 (0.55), residues: 92
  loop : -0.35 (0.26), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 662 
 HIS   0.004   0.001   HIS A 101 
 PHE   0.018   0.001   PHE A 836 
 TYR   0.015   0.001   TYR B 278 
 ARG   0.005   0.000   ARG B 295 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00345 (    2)
  link_NAG-ASN         : angle       1.26087 (    6)
  hydrogen bonds       : bond        0.03416 (  670)
  hydrogen bonds       : angle       4.16921 ( 1950)
  covalent geometry    : bond        0.00261 (13142)
  covalent geometry    : angle       0.59254 (17859)

********************** 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
  61 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 3.555 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  435 MET cc_start: 0.8239 (mmt) cc_final: 0.7966 (mmt)
REVERT: B  578 MET cc_start: 0.9070 (tmm) cc_final: 0.8732 (tmm)
REVERT: B  776 MET cc_start: 0.8910 (mpp) cc_final: 0.8625 (mpp)
REVERT: B  861 PHE cc_start: 0.9394 (t80) cc_final: 0.9101 (t80)
REVERT: A  663 MET cc_start: 0.9458 (tpt) cc_final: 0.9113 (tpt)
REVERT: A  696 MET cc_start: 0.8564 (pmm) cc_final: 0.8283 (pmm)
REVERT: A  795 MET cc_start: 0.8942 (mtm) cc_final: 0.8733 (mtm)
REVERT: A  833 MET cc_start: 0.9063 (ptp) cc_final: 0.8407 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.2233
  time to fit residues: 24.6061
Evaluate side-chains
  48 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 1.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 42 optimal weight:    6.9990
   chunk 96 optimal weight:    8.9990
   chunk 125 optimal weight:    2.9990
   chunk 85 optimal weight:   50.0000
   chunk 14 optimal weight:   20.0000
   chunk 69 optimal weight:   10.0000
   chunk 130 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 148 optimal weight:    5.9990
   chunk 108 optimal weight:    9.9990
   chunk 118 optimal weight:    6.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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 734 HIS
** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.065825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.046063 restraints weight = 131442.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.046668 restraints weight = 80101.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.047276 restraints weight = 50314.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.5431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  13144  Z= 0.235
  Angle     :  0.717   9.102  17865  Z= 0.354
  Chirality :  0.043   0.211   2095
  Planarity :  0.005   0.054   2240
  Dihedral  :  4.979  53.603   1777
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 14.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.07 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.21), residues: 1603
  helix:  1.19 (0.17), residues: 936
  sheet: -0.48 (0.54), residues: 92
  loop : -0.52 (0.25), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 662 
 HIS   0.008   0.001   HIS B 734 
 PHE   0.023   0.002   PHE A 464 
 TYR   0.017   0.002   TYR B 390 
 ARG   0.007   0.001   ARG B 603 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00435 (    2)
  link_NAG-ASN         : angle       2.12257 (    6)
  hydrogen bonds       : bond        0.04047 (  670)
  hydrogen bonds       : angle       4.61239 ( 1950)
  covalent geometry    : bond        0.00473 (13142)
  covalent geometry    : angle       0.71568 (17859)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4374.45 seconds
wall clock time: 77 minutes 0.16 seconds (4620.16 seconds total)