Starting phenix.real_space_refine
on Sat Aug 23 04:50:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jag_36113/08_2025/8jag_36113.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jag_36113/08_2025/8jag_36113.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jag_36113/08_2025/8jag_36113.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jag_36113/08_2025/8jag_36113.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jag_36113/08_2025/8jag_36113.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jag_36113/08_2025/8jag_36113.cif"
  }
  resolution = 3.55
  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=   0.001 sd=   0.079
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      50      5.16       5
     C    6243      2.51       5
     N    1607      2.21       5
     O    1872      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9772
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8037
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1028, 8037
          Classifications: {'peptide': 1028}
          Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 979}
          Chain breaks: 10
    Chain: "H"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 809
          Classifications: {'peptide': 105}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 100}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 856
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 856
          Classifications: {'peptide': 111}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 103}
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 2.06, per 1000 atoms: 0.21
  Number of scatterers: 9772
  At special positions: 0
  Unit cell: (118.34, 90.21, 193.03, 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      50     16.00
     O    1872      8.00
     N    1607      7.00
     C    6243      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  19 " - pdb=" SG  CYS A 133 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 128 " - pdb=" SG  CYS A 159 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 278 " - pdb=" SG  CYS A 288 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 323 " - pdb=" SG  CYS A 348 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 366 " - pdb=" SG  CYS A 419 " distance=2.08
    Simple disulfide: pdb=" SG  CYS A 378 " - pdb=" SG  CYS A 511 " distance=2.11
    Simple disulfide: pdb=" SG  CYS A 524 " - pdb=" SG  CYS A 576 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 603 " - pdb=" SG  CYS A 635 " distance=2.07
    Simple disulfide: pdb=" SG  CYS A 648 " - pdb=" SG  CYS A 657 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 720 " - pdb=" SG  CYS A 742 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 725 " - pdb=" SG  CYS A 731 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A1014 " - pdb=" SG  CYS A1025 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A1064 " - pdb=" SG  CYS A1108 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  89 " distance=2.07
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  92 " distance=2.05

  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 A1301 " - " ASN A 330 "
      " NAG A1302 " - " ASN A 227 "
      " NAG A1303 " - " ASN A 269 "
      " NAG A1304 " - " ASN A 783 "
      " NAG A1305 " - " ASN A  65 "
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 237.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2316

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 20 sheets defined
      21.6% alpha, 27.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 281 through 290
    Processing helix  chain 'A' and resid 325 through 330
    Processing helix  chain 'A' and resid 336 through 340
      removed outlier: 3.825A  pdb=" N   TRP A 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 357
      removed outlier: 3.557A  pdb=" N   TYR A 356 " --> pdb=" O   TYR A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 377
      removed outlier: 4.500A  pdb=" N   ASN A 375 " --> pdb=" O   THR A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 395
      removed outlier: 4.333A  pdb=" N   ARG A 395 " --> pdb=" O   GLY A 391 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 391 through 395'
    Processing helix  chain 'A' and resid 403 through 409
    Processing helix  chain 'A' and resid 488 through 491
    Processing helix  chain 'A' and resid 602 through 612
    Processing helix  chain 'A' and resid 719 through 726
    Processing helix  chain 'A' and resid 728 through 736
    Processing helix  chain 'A' and resid 737 through 739
      No H-bonds generated for 'chain 'A' and resid 737 through 739'
    Processing helix  chain 'A' and resid 740 through 765
      removed outlier: 3.514A  pdb=" N   GLU A 755 " --> pdb=" O   GLY A 751 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   GLN A 756 " --> pdb=" O   ILE A 752 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   ASP A 757 " --> pdb=" O   ALA A 753 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 798 through 808
    Processing helix  chain 'A' and resid 848 through 867
      removed outlier: 3.632A  pdb=" N   THR A 865 " --> pdb=" O   SER A 861 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   GLY A 867 " --> pdb=" O   THR A 863 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 868 through 870
      No H-bonds generated for 'chain 'A' and resid 868 through 870'
    Processing helix  chain 'A' and resid 879 through 890
    Processing helix  chain 'A' and resid 895 through 901
      removed outlier: 4.316A  pdb=" N   TYR A 899 " --> pdb=" O   GLN A 895 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 901 through 923
    Processing helix  chain 'A' and resid 927 through 947
    Processing helix  chain 'A' and resid 948 through 950
      No H-bonds generated for 'chain 'A' and resid 948 through 950'
    Processing helix  chain 'A' and resid 959 through 964
    Processing helix  chain 'A' and resid 967 through 1015
    Processing helix  chain 'A' and resid 1122 through 1127
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34
      removed outlier: 7.193A  pdb=" N   ASN A  65 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
      removed outlier: 5.052A  pdb=" N   TYR A 256 " --> pdb=" O   ASN A  65 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   LEU A 194 " --> pdb=" O   LYS A 221 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   LYS A 221 " --> pdb=" O   LEU A 194 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL A 196 " --> pdb=" O   ILE A 219 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 59
      removed outlier: 3.662A  pdb=" N   THR A  51 " --> pdb=" O   TYR A 266 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   THR A 261 " --> pdb=" O   ASP A 277 " (cutoff:3.500A)
      removed outlier: 5.025A  pdb=" N   ASP A 277 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   MET A 263 " --> pdb=" O   ALA A 275 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   ALA A 275 " --> pdb=" O   MET A 263 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   LYS A 265 " --> pdb=" O   THR A 273 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82
      removed outlier: 5.774A  pdb=" N   ARG A  99 " --> pdb=" O   ASN A 118 " (cutoff:3.500A)
      removed outlier: 4.763A  pdb=" N   VAL A 123 " --> pdb=" O   SER A 165 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 137
      removed outlier: 10.608A  pdb=" N   ASN A 135 " --> pdb=" O   PHE A 153 " (cutoff:3.500A)
      removed outlier: 8.623A  pdb=" N   PHE A 153 " --> pdb=" O   ASN A 135 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 615 through 616
      removed outlier: 6.891A  pdb=" N   VAL A 581 " --> pdb=" O   THR A 302 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   ASN A 304 " --> pdb=" O   GLY A 579 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   GLY A 579 " --> pdb=" O   ASN A 304 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 312 through 314
      removed outlier: 5.952A  pdb=" N   ASP A 560 " --> pdb=" O   ILE A 573 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   SER A 561 " --> pdb=" O   GLY A 552 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 345
    Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349
      removed outlier: 6.435A  pdb=" N   CYS A 348 " --> pdb=" O   CYS A 511 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 439 through 441
    Processing sheet with id=AB1, first strand: chain 'A' and resid 640 through 646
      removed outlier: 6.440A  pdb=" N   GLU A 640 " --> pdb=" O   ALA A 676 " (cutoff:3.500A)
      removed outlier: 8.533A  pdb=" N   THR A 678 " --> pdb=" O   GLU A 640 " (cutoff:3.500A)
      removed outlier: 9.034A  pdb=" N   VAL A 642 " --> pdb=" O   THR A 678 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   ILE A 656 " --> pdb=" O   ILE A 652 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 693 through 697
      removed outlier: 3.747A  pdb=" N   THR A1058 " --> pdb=" O   PHE A1079 " (cutoff:3.500A)
      removed outlier: 5.247A  pdb=" N   GLN A1088 " --> pdb=" O   SER A1093 " (cutoff:3.500A)
      removed outlier: 5.723A  pdb=" N   SER A1093 " --> pdb=" O   GLN A1088 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 700 through 710
      removed outlier: 6.062A  pdb=" N   TYR A1049 " --> pdb=" O   HIS A1030 " (cutoff:3.500A)
      removed outlier: 5.580A  pdb=" N   HIS A1030 " --> pdb=" O   TYR A1049 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 715 through 718
      removed outlier: 4.570A  pdb=" N   LYS A 715 " --> pdb=" O   LEU A 843 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 778 through 779
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1102 through 1107
      removed outlier: 4.876A  pdb=" N   ALA A1069 " --> pdb=" O   SER A1105 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 4 through 6
    Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.605A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 104 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'H' and resid 45 through 47
    Processing sheet with id=AC1, first strand: chain 'L' and resid 18 through 23
    Processing sheet with id=AC2, first strand: chain 'L' and resid 57 through 58
      removed outlier: 6.775A  pdb=" N   TRP L  39 " --> pdb=" O   LEU L  51 " (cutoff:3.500A)

    399 hydrogen bonds defined for protein.
    1074 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.00

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.18 -     1.32: 2137
        1.32 -     1.46: 3459
        1.46 -     1.60: 4321
        1.60 -     1.74: 16
        1.74 -     1.88: 66
  Bond restraints: 9999
  Sorted by residual:
  bond pdb=" CA  THR A 332 "
       pdb=" C   THR A 332 "
    ideal  model  delta    sigma   weight residual
    1.524  1.405  0.119 1.29e-02 6.01e+03 8.44e+01
  bond pdb=" NE  ARG A  18 "
       pdb=" CZ  ARG A  18 "
    ideal  model  delta    sigma   weight residual
    1.326  1.400 -0.074 1.10e-02 8.26e+03 4.58e+01
  bond pdb=" CG  LEU A 898 "
       pdb=" CD2 LEU A 898 "
    ideal  model  delta    sigma   weight residual
    1.521  1.341  0.180 3.30e-02 9.18e+02 2.98e+01
  bond pdb=" NE1 TRP H  36 "
       pdb=" CE2 TRP H  36 "
    ideal  model  delta    sigma   weight residual
    1.370  1.311  0.059 1.10e-02 8.26e+03 2.85e+01
  bond pdb=" NE  ARG H  38 "
       pdb=" CZ  ARG H  38 "
    ideal  model  delta    sigma   weight residual
    1.326  1.382 -0.056 1.10e-02 8.26e+03 2.61e+01
  ... (remaining 9994 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 11271
        2.23 -     4.45: 1916
        4.45 -     6.68: 324
        6.68 -     8.91: 64
        8.91 -    11.14: 17
  Bond angle restraints: 13592
  Sorted by residual:
  angle pdb=" N   PHE A 360 "
        pdb=" CA  PHE A 360 "
        pdb=" C   PHE A 360 "
      ideal   model   delta    sigma   weight residual
     114.56  103.42   11.14 1.27e+00 6.20e-01 7.69e+01
  angle pdb=" N   THR A 332 "
        pdb=" CA  THR A 332 "
        pdb=" C   THR A 332 "
      ideal   model   delta    sigma   weight residual
     111.36  101.87    9.49 1.09e+00 8.42e-01 7.57e+01
  angle pdb=" N   GLN L  46 "
        pdb=" CA  GLN L  46 "
        pdb=" C   GLN L  46 "
      ideal   model   delta    sigma   weight residual
     111.71  121.41   -9.70 1.15e+00 7.56e-01 7.12e+01
  angle pdb=" N   SER L  47 "
        pdb=" CA  SER L  47 "
        pdb=" C   SER L  47 "
      ideal   model   delta    sigma   weight residual
     108.25  117.98   -9.73 1.16e+00 7.43e-01 7.04e+01
  angle pdb=" C   GLN L  16 "
        pdb=" N   PRO L  17 "
        pdb=" CA  PRO L  17 "
      ideal   model   delta    sigma   weight residual
     120.03  127.84   -7.81 9.90e-01 1.02e+00 6.22e+01
  ... (remaining 13587 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.70: 5842
       24.70 -    49.40: 84
       49.40 -    74.10: 30
       74.10 -    98.80: 14
       98.80 -   123.50: 14
  Dihedral angle restraints: 5984
    sinusoidal: 2380
      harmonic: 3604
  Sorted by residual:
  dihedral pdb=" CA  ILE H  51 "
           pdb=" C   ILE H  51 "
           pdb=" N   PRO H  52 "
           pdb=" CA  PRO H  52 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -56.50 -123.50     0      5.00e+00 4.00e-02 6.10e+02
  dihedral pdb=" CB  CYS A 278 "
           pdb=" SG  CYS A 278 "
           pdb=" SG  CYS A 288 "
           pdb=" CB  CYS A 288 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -177.34  -89.66     1      1.00e+01 1.00e-02 9.54e+01
  dihedral pdb=" CB  CYS L  22 "
           pdb=" SG  CYS L  22 "
           pdb=" SG  CYS L  92 "
           pdb=" CB  CYS L  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   38.94   54.06     1      1.00e+01 1.00e-02 3.97e+01
  ... (remaining 5981 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.321: 1534
       0.321 -    0.643: 8
       0.643 -    0.964: 0
       0.964 -    1.285: 1
       1.285 -    1.606: 1
  Chirality restraints: 1544
  Sorted by residual:
  chirality pdb=" C1  NAG A1301 "
            pdb=" ND2 ASN A 330 "
            pdb=" C2  NAG A1301 "
            pdb=" O5  NAG A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.79   -1.61 2.00e-01 2.50e+01 6.45e+01
  chirality pdb=" C1  NAG A1305 "
            pdb=" ND2 ASN A  65 "
            pdb=" C2  NAG A1305 "
            pdb=" O5  NAG A1305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.41   -0.99 2.00e-01 2.50e+01 2.47e+01
  chirality pdb=" CA  TYR H  87 "
            pdb=" N   TYR H  87 "
            pdb=" C   TYR H  87 "
            pdb=" CB  TYR H  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.39e+00
  ... (remaining 1541 not shown)

  Planarity restraints: 1748
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A1301 "   -0.304 2.00e-02 2.50e+03   2.62e-01 8.55e+02
        pdb=" C7  NAG A1301 "    0.066 2.00e-02 2.50e+03
        pdb=" C8  NAG A1301 "   -0.006 2.00e-02 2.50e+03
        pdb=" N2  NAG A1301 "    0.450 2.00e-02 2.50e+03
        pdb=" O7  NAG A1301 "   -0.207 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A1305 "   -0.279 2.00e-02 2.50e+03   2.36e-01 6.95e+02
        pdb=" C7  NAG A1305 "    0.071 2.00e-02 2.50e+03
        pdb=" C8  NAG A1305 "   -0.177 2.00e-02 2.50e+03
        pdb=" N2  NAG A1305 "    0.404 2.00e-02 2.50e+03
        pdb=" O7  NAG A1305 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A1304 "   -0.252 2.00e-02 2.50e+03   2.16e-01 5.82e+02
        pdb=" C7  NAG A1304 "    0.056 2.00e-02 2.50e+03
        pdb=" C8  NAG A1304 "    0.024 2.00e-02 2.50e+03
        pdb=" N2  NAG A1304 "    0.361 2.00e-02 2.50e+03
        pdb=" O7  NAG A1304 "   -0.189 2.00e-02 2.50e+03
  ... (remaining 1745 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.29: 2
        2.29 -     2.94: 4790
        2.94 -     3.60: 13241
        3.60 -     4.25: 23009
        4.25 -     4.90: 37001
  Nonbonded interactions: 78043
  Sorted by model distance:
  nonbonded pdb=" CA  GLY A 368 "
            pdb=" CE1 PHE A 416 "
     model   vdw
     1.641 3.740
  nonbonded pdb=" O   TYR A 367 "
            pdb=" CZ  PHE A 416 "
     model   vdw
     2.137 3.340
  nonbonded pdb=" N   GLY A 368 "
            pdb=" CE1 PHE A 416 "
     model   vdw
     2.361 3.420
  nonbonded pdb=" O   TYR A 367 "
            pdb=" CE1 PHE A 416 "
     model   vdw
     2.363 3.340
  nonbonded pdb=" N   TRP H  50 "
            pdb=" O   TRP H  50 "
     model   vdw
     2.376 2.496
  ... (remaining 78038 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             2.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.410
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7123
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      :  0.020   0.180  10019  Z= 1.034
  Angle     :  1.818  11.137  13637  Z= 1.222
  Chirality :  0.108   1.606   1544
  Planarity :  0.013   0.262   1743
  Dihedral  : 12.735 123.499   3623
  Min Nonbonded Distance : 1.641

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.29 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.17 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.69 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.23), residues: 1216
  helix:  0.05 (0.32), residues: 220
  sheet:  0.92 (0.30), residues: 290
  loop : -0.05 (0.22), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 620 
 TYR   0.062   0.009   TYR A 442 
 PHE   0.037   0.006   PHE A 137 
 TRP   0.026   0.007   TRP H  50 
 HIS   0.015   0.003   HIS A 661 

Details of bonding type rmsd
  covalent geometry    : bond        0.01953 ( 9999)
  covalent geometry    : angle       1.80508 (13592)
  SS BOND              : bond        0.02733 (   15)
  SS BOND              : angle       3.31994 (   30)
  hydrogen bonds       : bond        0.17951 (  399)
  hydrogen bonds       : angle       7.89561 ( 1074)
  link_NAG-ASN         : bond        0.01155 (    5)
  link_NAG-ASN         : angle       5.46303 (   15)

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

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

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 291
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 ILE cc_start: 0.8818 (mm) cc_final: 0.8578 (tt)
REVERT: A  411 LYS cc_start: 0.7639 (tptt) cc_final: 0.7348 (tppt)
REVERT: A  427 ASN cc_start: 0.7791 (p0) cc_final: 0.6856 (t0)
REVERT: A  559 THR cc_start: 0.8124 (m) cc_final: 0.7852 (m)
REVERT: A  965 ARG cc_start: 0.6947 (ptt180) cc_final: 0.5144 (tpt90)
REVERT: A 1084 TRP cc_start: 0.7361 (m100) cc_final: 0.7110 (m100)
REVERT: H   62 VAL cc_start: 0.7190 (t) cc_final: 0.6619 (t)
REVERT: L   34 GLN cc_start: 0.4953 (tp-100) cc_final: 0.4496 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 291
  average time/residue: 0.0843
  time to fit residues: 34.2458
Evaluate side-chains
  160 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    0.0870
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 117 optimal weight:    0.9980
   overall best weight:    0.7558

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
A 401 GLN
** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 530 ASN
A 630 GLN
A 901 ASN
H  43 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.184190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.157207 restraints weight = 15432.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.160080 restraints weight = 10343.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.161498 restraints weight = 7251.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.162669 restraints weight = 5993.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.162882 restraints weight = 5662.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6995
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10019  Z= 0.164
  Angle     :  0.759  18.119  13637  Z= 0.389
  Chirality :  0.052   0.579   1544
  Planarity :  0.004   0.080   1743
  Dihedral  :  9.119  88.829   1436
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  3.87 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 10.05 %
    Favored  : 87.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.69 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.23), residues: 1216
  helix:  1.69 (0.35), residues: 213
  sheet:  0.74 (0.30), residues: 281
  loop : -0.36 (0.22), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  58 
 TYR   0.017   0.002   TYR A 252 
 PHE   0.021   0.002   PHE L  75 
 TRP   0.013   0.002   TRP H  50 
 HIS   0.008   0.001   HIS L  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 9999)
  covalent geometry    : angle       0.71592 (13592)
  SS BOND              : bond        0.00352 (   15)
  SS BOND              : angle       1.85494 (   30)
  hydrogen bonds       : bond        0.05943 (  399)
  hydrogen bonds       : angle       6.25327 ( 1074)
  link_NAG-ASN         : bond        0.01614 (    5)
  link_NAG-ASN         : angle       7.24915 (   15)

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

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

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 192
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 ARG cc_start: 0.6847 (ttm-80) cc_final: 0.6308 (ttm-80)
REVERT: A  296 ASP cc_start: 0.7793 (p0) cc_final: 0.7454 (m-30)
REVERT: A  347 ASN cc_start: 0.8278 (m-40) cc_final: 0.7146 (t0)
REVERT: A  367 TYR cc_start: 0.7904 (m-80) cc_final: 0.7696 (m-80)
REVERT: A  411 LYS cc_start: 0.7748 (tptt) cc_final: 0.7237 (tppt)
REVERT: A  427 ASN cc_start: 0.7623 (p0) cc_final: 0.6757 (t0)
REVERT: A  509 THR cc_start: 0.7723 (OUTLIER) cc_final: 0.7182 (t)
REVERT: A  530 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.7697 (p0)
REVERT: A  709 MET cc_start: 0.8344 (ptp) cc_final: 0.8136 (ptp)
REVERT: A  749 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7984 (mt)
REVERT: A  837 PHE cc_start: 0.8239 (m-80) cc_final: 0.7803 (m-80)
REVERT: A  965 ARG cc_start: 0.7083 (ptt180) cc_final: 0.4801 (tpt90)
REVERT: A 1084 TRP cc_start: 0.7299 (m100) cc_final: 0.7069 (m100)
REVERT: H   23 LYS cc_start: 0.8274 (mttt) cc_final: 0.7604 (mtmm)
REVERT: H   73 TYR cc_start: 0.6407 (OUTLIER) cc_final: 0.5627 (m-80)
REVERT: L   34 GLN cc_start: 0.4435 (tp-100) cc_final: 0.4112 (pt0)
REVERT: L  109 GLU cc_start: 0.6142 (mp0) cc_final: 0.5892 (mp0)
  outliers start: 31
  outliers final: 19
  residues processed: 215
  average time/residue: 0.0818
  time to fit residues: 25.0294
Evaluate side-chains
  176 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 153
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  509 THR
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  530 ASN
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  706 THR
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain A residue  863 THR
Chi-restraints excluded: chain A residue  943 THR
Chi-restraints excluded: chain A residue  964 SER
Chi-restraints excluded: chain A residue  979 ILE
Chi-restraints excluded: chain A residue  980 THR
Chi-restraints excluded: chain A residue 1012 SER
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain H residue   73 TYR
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain L residue    6 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 95 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 94 optimal weight:    0.8980
   chunk 122 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 214 ASN
A 550 GLN
A 614 GLN
A 661 HIS
A 759 ASN
A 901 ASN
A 987 GLN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  30 HIS
** L  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  94 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.182401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.155953 restraints weight = 15273.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.159503 restraints weight = 9878.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.161028 restraints weight = 6562.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.161235 restraints weight = 5774.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.161671 restraints weight = 5273.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
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   0.062  10019  Z= 0.144
  Angle     :  0.685  18.636  13637  Z= 0.346
  Chirality :  0.047   0.331   1544
  Planarity :  0.004   0.048   1743
  Dihedral  :  6.317  62.361   1436
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  3.54 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 10.88 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.69 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.23), residues: 1216
  helix:  1.92 (0.34), residues: 217
  sheet:  0.45 (0.27), residues: 325
  loop : -0.65 (0.22), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  58 
 TYR   0.017   0.002   TYR A 252 
 PHE   0.019   0.002   PHE A  89 
 TRP   0.009   0.001   TRP A 340 
 HIS   0.005   0.001   HIS L  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 9999)
  covalent geometry    : angle       0.63724 (13592)
  SS BOND              : bond        0.00359 (   15)
  SS BOND              : angle       2.25529 (   30)
  hydrogen bonds       : bond        0.05050 (  399)
  hydrogen bonds       : angle       6.01547 ( 1074)
  link_NAG-ASN         : bond        0.01452 (    5)
  link_NAG-ASN         : angle       6.93382 (   15)

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

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

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 172
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 ARG cc_start: 0.7042 (ttm-80) cc_final: 0.6514 (ttm-80)
REVERT: A  411 LYS cc_start: 0.7871 (tptt) cc_final: 0.7250 (tppt)
REVERT: A  427 ASN cc_start: 0.7663 (p0) cc_final: 0.6891 (t0)
REVERT: A  747 ARG cc_start: 0.7107 (ptm-80) cc_final: 0.6776 (ptt90)
REVERT: A  965 ARG cc_start: 0.7133 (ptt180) cc_final: 0.5025 (tpt90)
REVERT: H   23 LYS cc_start: 0.8354 (mttt) cc_final: 0.7731 (mtmm)
REVERT: H   73 TYR cc_start: 0.6638 (OUTLIER) cc_final: 0.5714 (m-80)
REVERT: L   34 GLN cc_start: 0.4517 (tp-100) cc_final: 0.4094 (pt0)
REVERT: L   37 PHE cc_start: 0.4026 (m-80) cc_final: 0.2721 (m-80)
  outliers start: 37
  outliers final: 24
  residues processed: 201
  average time/residue: 0.0883
  time to fit residues: 25.6300
Evaluate side-chains
  179 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 154
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  604 THR
Chi-restraints excluded: chain A residue  605 ASP
Chi-restraints excluded: chain A residue  706 THR
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain A residue  798 SER
Chi-restraints excluded: chain A residue  800 ILE
Chi-restraints excluded: chain A residue  943 THR
Chi-restraints excluded: chain A residue  979 ILE
Chi-restraints excluded: chain A residue  980 THR
Chi-restraints excluded: chain A residue 1012 SER
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1097 ILE
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   73 TYR
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain L residue    6 SER
Chi-restraints excluded: chain L residue   30 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 41 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0470
   chunk 94 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.1684

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

Flipped N/Q/H residues before XYZ refinement:
A 786 GLN
A 917 GLN
L  46 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.180546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.152723 restraints weight = 15600.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.155053 restraints weight = 10861.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.156377 restraints weight = 7884.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.157462 restraints weight = 6675.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.157635 restraints weight = 6376.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
moved from start:          0.4277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10019  Z= 0.154
  Angle     :  0.653  18.980  13637  Z= 0.337
  Chirality :  0.047   0.280   1544
  Planarity :  0.004   0.050   1743
  Dihedral  :  5.790  59.628   1436
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  3.87 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 12.84 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.69 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.23), residues: 1216
  helix:  1.81 (0.34), residues: 225
  sheet:  0.29 (0.28), residues: 332
  loop : -0.83 (0.22), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  58 
 TYR   0.016   0.002   TYR A 252 
 PHE   0.018   0.002   PHE A  89 
 TRP   0.017   0.002   TRP A1084 
 HIS   0.020   0.002   HIS L  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 9999)
  covalent geometry    : angle       0.61352 (13592)
  SS BOND              : bond        0.00411 (   15)
  SS BOND              : angle       2.06319 (   30)
  hydrogen bonds       : bond        0.04851 (  399)
  hydrogen bonds       : angle       5.82915 ( 1074)
  link_NAG-ASN         : bond        0.01392 (    5)
  link_NAG-ASN         : angle       6.19680 (   15)

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

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

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 158
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 ARG cc_start: 0.6903 (ttm-80) cc_final: 0.6465 (ttm-80)
REVERT: A  308 VAL cc_start: 0.8592 (t) cc_final: 0.8320 (m)
REVERT: A  411 LYS cc_start: 0.7949 (tptt) cc_final: 0.7425 (tppt)
REVERT: A  427 ASN cc_start: 0.7702 (p0) cc_final: 0.6937 (t0)
REVERT: A  455 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7331 (mt)
REVERT: A  611 HIS cc_start: 0.6594 (m-70) cc_final: 0.6059 (m-70)
REVERT: A  931 GLN cc_start: 0.8449 (tp40) cc_final: 0.8031 (tt0)
REVERT: A  965 ARG cc_start: 0.7295 (ptt180) cc_final: 0.5172 (tpt90)
REVERT: H   23 LYS cc_start: 0.8398 (mttt) cc_final: 0.7741 (mtmm)
REVERT: H   50 TRP cc_start: 0.4140 (t-100) cc_final: 0.3703 (t-100)
REVERT: H   73 TYR cc_start: 0.6775 (OUTLIER) cc_final: 0.5779 (m-80)
REVERT: L   34 GLN cc_start: 0.4789 (tp-100) cc_final: 0.4303 (pt0)
  outliers start: 41
  outliers final: 28
  residues processed: 190
  average time/residue: 0.0862
  time to fit residues: 23.8025
Evaluate side-chains
  178 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 148
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  610 ILE
Chi-restraints excluded: chain A residue  706 THR
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain A residue  770 MET
Chi-restraints excluded: chain A residue  800 ILE
Chi-restraints excluded: chain A residue  863 THR
Chi-restraints excluded: chain A residue  943 THR
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  964 SER
Chi-restraints excluded: chain A residue  979 ILE
Chi-restraints excluded: chain A residue  980 THR
Chi-restraints excluded: chain A residue 1012 SER
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1097 ILE
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   73 TYR
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue   87 TYR
Chi-restraints excluded: chain L residue    6 SER
Chi-restraints excluded: chain L residue   12 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 80 optimal weight:    0.1980
   chunk 102 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 109 optimal weight:    7.9990
   chunk 13 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   chunk 10 optimal weight:    0.4980
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN
A1030 HIS
L  30 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.178341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.149976 restraints weight = 15460.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.153420 restraints weight = 9769.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.155650 restraints weight = 7163.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.157332 restraints weight = 5802.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.158447 restraints weight = 4966.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7157
moved from start:          0.4715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10019  Z= 0.154
  Angle     :  0.639  18.828  13637  Z= 0.327
  Chirality :  0.047   0.264   1544
  Planarity :  0.004   0.050   1743
  Dihedral  :  5.717  57.655   1436
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  3.87 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 13.40 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.69 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.23), residues: 1216
  helix:  1.74 (0.34), residues: 231
  sheet:  0.13 (0.28), residues: 335
  loop : -1.04 (0.23), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  58 
 TYR   0.022   0.002   TYR A1120 
 PHE   0.019   0.002   PHE A  89 
 TRP   0.014   0.002   TRP A 340 
 HIS   0.005   0.001   HIS L  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 9999)
  covalent geometry    : angle       0.60065 (13592)
  SS BOND              : bond        0.00380 (   15)
  SS BOND              : angle       1.86255 (   30)
  hydrogen bonds       : bond        0.04726 (  399)
  hydrogen bonds       : angle       5.77481 ( 1074)
  link_NAG-ASN         : bond        0.01348 (    5)
  link_NAG-ASN         : angle       6.15334 (   15)

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

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

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 169
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 ARG cc_start: 0.6884 (ttm-80) cc_final: 0.6377 (ttm-80)
REVERT: A  411 LYS cc_start: 0.8087 (tptt) cc_final: 0.7474 (tppt)
REVERT: A  427 ASN cc_start: 0.7809 (p0) cc_final: 0.7040 (t0)
REVERT: A  965 ARG cc_start: 0.7288 (ptt180) cc_final: 0.5162 (tpt90)
REVERT: H   23 LYS cc_start: 0.8518 (mttt) cc_final: 0.7805 (mtmm)
REVERT: H   50 TRP cc_start: 0.4174 (t-100) cc_final: 0.3721 (t-100)
REVERT: H   73 TYR cc_start: 0.6761 (OUTLIER) cc_final: 0.5674 (m-80)
REVERT: L   53 TYR cc_start: 0.5641 (OUTLIER) cc_final: 0.5244 (p90)
  outliers start: 44
  outliers final: 32
  residues processed: 198
  average time/residue: 0.0839
  time to fit residues: 23.8531
Evaluate side-chains
  183 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 149
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  605 ASP
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  706 THR
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain A residue  798 SER
Chi-restraints excluded: chain A residue  800 ILE
Chi-restraints excluded: chain A residue  863 THR
Chi-restraints excluded: chain A residue  943 THR
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  979 ILE
Chi-restraints excluded: chain A residue  980 THR
Chi-restraints excluded: chain A residue 1012 SER
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1097 ILE
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   43 GLN
Chi-restraints excluded: chain H residue   73 TYR
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue   87 TYR
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   30 HIS
Chi-restraints excluded: chain L residue   53 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 102 optimal weight:    3.9990
   chunk 55 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 84 optimal weight:    0.2980
   chunk 75 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 109 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN
L  30 HIS
** L  42 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 = 0.4065 r_free = 0.4065 target = 0.180057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.151938 restraints weight = 15522.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.155347 restraints weight = 9794.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.157720 restraints weight = 7173.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.159348 restraints weight = 5768.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.160335 restraints weight = 4941.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7123
moved from start:          0.4940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10019  Z= 0.122
  Angle     :  0.614  18.646  13637  Z= 0.312
  Chirality :  0.045   0.234   1544
  Planarity :  0.004   0.048   1743
  Dihedral  :  5.533  55.234   1436
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.03 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 14.42 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.69 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.23), residues: 1216
  helix:  2.05 (0.35), residues: 227
  sheet:  0.38 (0.29), residues: 310
  loop : -1.02 (0.22), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 449 
 TYR   0.021   0.001   TYR A1120 
 PHE   0.021   0.001   PHE A 329 
 TRP   0.014   0.001   TRP A 340 
 HIS   0.004   0.001   HIS H  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 9999)
  covalent geometry    : angle       0.57455 (13592)
  SS BOND              : bond        0.00325 (   15)
  SS BOND              : angle       1.87803 (   30)
  hydrogen bonds       : bond        0.04334 (  399)
  hydrogen bonds       : angle       5.59701 ( 1074)
  link_NAG-ASN         : bond        0.01254 (    5)
  link_NAG-ASN         : angle       6.04295 (   15)

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

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

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 155
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 ARG cc_start: 0.6659 (ttm-80) cc_final: 0.6178 (ttt90)
REVERT: A  411 LYS cc_start: 0.8047 (tptt) cc_final: 0.7450 (tppt)
REVERT: A  427 ASN cc_start: 0.7748 (p0) cc_final: 0.6985 (t0)
REVERT: A  965 ARG cc_start: 0.7197 (ptt180) cc_final: 0.5052 (tpt90)
REVERT: H   23 LYS cc_start: 0.8539 (mttt) cc_final: 0.7801 (mtmm)
REVERT: H   50 TRP cc_start: 0.4261 (t-100) cc_final: 0.3862 (t-100)
REVERT: H   73 TYR cc_start: 0.6774 (OUTLIER) cc_final: 0.5699 (m-80)
REVERT: L   53 TYR cc_start: 0.5649 (OUTLIER) cc_final: 0.5198 (p90)
REVERT: L   93 MET cc_start: 0.5759 (ppp) cc_final: 0.5469 (ppp)
  outliers start: 41
  outliers final: 28
  residues processed: 186
  average time/residue: 0.0819
  time to fit residues: 21.9334
Evaluate side-chains
  175 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 145
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  360 PHE
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  605 ASP
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  706 THR
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain A residue  863 THR
Chi-restraints excluded: chain A residue  943 THR
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  964 SER
Chi-restraints excluded: chain A residue  979 ILE
Chi-restraints excluded: chain A residue  985 SER
Chi-restraints excluded: chain A residue 1012 SER
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1097 ILE
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain H residue   43 GLN
Chi-restraints excluded: chain H residue   73 TYR
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue   87 TYR
Chi-restraints excluded: chain L residue    6 SER
Chi-restraints excluded: chain L residue   30 HIS
Chi-restraints excluded: chain L residue   53 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 119 optimal weight:    0.2980
   chunk 44 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN
A1117 ASN
H  93 HIS
L  30 HIS
** L  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.180185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.153428 restraints weight = 15435.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.156478 restraints weight = 10427.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.158112 restraints weight = 7152.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.158384 restraints weight = 5938.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.158599 restraints weight = 5796.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
moved from start:          0.5105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10019  Z= 0.123
  Angle     :  0.607  18.452  13637  Z= 0.306
  Chirality :  0.045   0.226   1544
  Planarity :  0.004   0.046   1743
  Dihedral  :  5.456  53.958   1436
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  3.87 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 15.72 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.69 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.10 (0.24), residues: 1216
  helix:  2.10 (0.35), residues: 227
  sheet:  0.29 (0.29), residues: 318
  loop : -1.05 (0.22), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 449 
 TYR   0.018   0.001   TYR A1120 
 PHE   0.018   0.001   PHE A 329 
 TRP   0.018   0.001   TRP A 340 
 HIS   0.003   0.001   HIS L  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 9999)
  covalent geometry    : angle       0.56904 (13592)
  SS BOND              : bond        0.00348 (   15)
  SS BOND              : angle       1.67580 (   30)
  hydrogen bonds       : bond        0.04249 (  399)
  hydrogen bonds       : angle       5.52712 ( 1074)
  link_NAG-ASN         : bond        0.01243 (    5)
  link_NAG-ASN         : angle       5.99927 (   15)

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

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

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 149
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 ARG cc_start: 0.6645 (ttm-80) cc_final: 0.6215 (ttt90)
REVERT: A  411 LYS cc_start: 0.8041 (tptt) cc_final: 0.7460 (tppt)
REVERT: A  427 ASN cc_start: 0.7724 (p0) cc_final: 0.6877 (t0)
REVERT: A  965 ARG cc_start: 0.7341 (ptt180) cc_final: 0.5083 (tpt90)
REVERT: A 1092 PHE cc_start: 0.8015 (t80) cc_final: 0.7568 (t80)
REVERT: H   23 LYS cc_start: 0.8562 (mttt) cc_final: 0.7815 (mtmm)
REVERT: H   73 TYR cc_start: 0.6854 (OUTLIER) cc_final: 0.5781 (m-80)
REVERT: L   34 GLN cc_start: 0.4549 (tp-100) cc_final: 0.4112 (pt0)
  outliers start: 33
  outliers final: 27
  residues processed: 173
  average time/residue: 0.0921
  time to fit residues: 22.4215
Evaluate side-chains
  169 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 141
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  605 ASP
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  706 THR
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain A residue  863 THR
Chi-restraints excluded: chain A residue  943 THR
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  964 SER
Chi-restraints excluded: chain A residue  979 ILE
Chi-restraints excluded: chain A residue  985 SER
Chi-restraints excluded: chain A residue 1012 SER
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain H residue   43 GLN
Chi-restraints excluded: chain H residue   73 TYR
Chi-restraints excluded: chain H residue   75 GLN
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain L residue   30 HIS
Chi-restraints excluded: chain L residue   51 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 85 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 80 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 54 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN
H  93 HIS
** L  42 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 = 0.4038 r_free = 0.4038 target = 0.177632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.151159 restraints weight = 15567.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.152781 restraints weight = 10509.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.154621 restraints weight = 7730.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.154866 restraints weight = 6924.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.155095 restraints weight = 6309.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.5250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10019  Z= 0.157
  Angle     :  0.641  18.167  13637  Z= 0.325
  Chirality :  0.047   0.236   1544
  Planarity :  0.004   0.045   1743
  Dihedral  :  5.612  54.055   1436
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.85 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 15.53 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.69 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.24), residues: 1216
  helix:  1.94 (0.35), residues: 233
  sheet:  0.23 (0.29), residues: 320
  loop : -1.15 (0.22), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  99 
 TYR   0.017   0.002   TYR A1120 
 PHE   0.020   0.002   PHE A  89 
 TRP   0.017   0.002   TRP A 340 
 HIS   0.017   0.002   HIS L  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 9999)
  covalent geometry    : angle       0.60451 (13592)
  SS BOND              : bond        0.00322 (   15)
  SS BOND              : angle       1.73985 (   30)
  hydrogen bonds       : bond        0.04602 (  399)
  hydrogen bonds       : angle       5.63755 ( 1074)
  link_NAG-ASN         : bond        0.01282 (    5)
  link_NAG-ASN         : angle       6.00083 (   15)

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

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

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 151
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 SER cc_start: 0.7685 (t) cc_final: 0.7324 (p)
REVERT: A  232 ARG cc_start: 0.6663 (ttm-80) cc_final: 0.6268 (ttt90)
REVERT: A  411 LYS cc_start: 0.8128 (tptt) cc_final: 0.7488 (tppt)
REVERT: A  427 ASN cc_start: 0.7779 (p0) cc_final: 0.6960 (t0)
REVERT: A  837 PHE cc_start: 0.8686 (m-80) cc_final: 0.8425 (m-80)
REVERT: A  914 SER cc_start: 0.8208 (m) cc_final: 0.7986 (p)
REVERT: A  965 ARG cc_start: 0.7387 (ptt180) cc_final: 0.5134 (tpt90)
REVERT: H   23 LYS cc_start: 0.8594 (mttt) cc_final: 0.7796 (mtmm)
REVERT: H   73 TYR cc_start: 0.6871 (OUTLIER) cc_final: 0.5790 (m-80)
REVERT: L   34 GLN cc_start: 0.4896 (tp-100) cc_final: 0.4379 (pt0)
  outliers start: 40
  outliers final: 33
  residues processed: 186
  average time/residue: 0.0854
  time to fit residues: 22.5790
Evaluate side-chains
  176 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 142
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  605 ASP
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  610 ILE
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  674 ILE
Chi-restraints excluded: chain A residue  706 THR
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain A residue  798 SER
Chi-restraints excluded: chain A residue  863 THR
Chi-restraints excluded: chain A residue  943 THR
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  964 SER
Chi-restraints excluded: chain A residue  979 ILE
Chi-restraints excluded: chain A residue  985 SER
Chi-restraints excluded: chain A residue 1012 SER
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   43 GLN
Chi-restraints excluded: chain H residue   73 TYR
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain L residue    6 SER
Chi-restraints excluded: chain L residue   12 VAL
Chi-restraints excluded: chain L residue   51 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0770
   chunk 117 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 118 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9990
   chunk 61 optimal weight:    0.2980
   chunk 12 optimal weight:    5.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    1.0142

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

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  30 HIS
** L  42 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 = 0.4048 r_free = 0.4048 target = 0.178644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.152418 restraints weight = 15527.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.153603 restraints weight = 10408.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.154778 restraints weight = 7875.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.156062 restraints weight = 6893.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.156206 restraints weight = 6412.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
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      :  0.003   0.047  10019  Z= 0.134
  Angle     :  0.630  18.044  13637  Z= 0.316
  Chirality :  0.046   0.222   1544
  Planarity :  0.004   0.041   1743
  Dihedral  :  5.530  52.789   1436
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  3.95 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 16.47 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.69 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.24), residues: 1216
  helix:  2.01 (0.35), residues: 233
  sheet:  0.23 (0.29), residues: 320
  loop : -1.18 (0.23), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  58 
 TYR   0.029   0.002   TYR H  87 
 PHE   0.018   0.001   PHE A  89 
 TRP   0.016   0.002   TRP A 340 
 HIS   0.007   0.001   HIS L  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 9999)
  covalent geometry    : angle       0.59281 (13592)
  SS BOND              : bond        0.00339 (   15)
  SS BOND              : angle       1.77621 (   30)
  hydrogen bonds       : bond        0.04376 (  399)
  hydrogen bonds       : angle       5.57232 ( 1074)
  link_NAG-ASN         : bond        0.01224 (    5)
  link_NAG-ASN         : angle       5.96597 (   15)

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

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

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 155
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 SER cc_start: 0.7696 (t) cc_final: 0.7327 (p)
REVERT: A  232 ARG cc_start: 0.6614 (ttm-80) cc_final: 0.6241 (ttt90)
REVERT: A  411 LYS cc_start: 0.8068 (tptt) cc_final: 0.7503 (tppt)
REVERT: A  427 ASN cc_start: 0.7764 (p0) cc_final: 0.6797 (t0)
REVERT: A  837 PHE cc_start: 0.8674 (m-80) cc_final: 0.8401 (m-80)
REVERT: A  914 SER cc_start: 0.8143 (m) cc_final: 0.7937 (p)
REVERT: A  965 ARG cc_start: 0.7323 (ptt180) cc_final: 0.5084 (tpt90)
REVERT: A 1092 PHE cc_start: 0.8027 (t80) cc_final: 0.7379 (t80)
REVERT: H   23 LYS cc_start: 0.8585 (mttt) cc_final: 0.7900 (mtmm)
REVERT: H   34 MET cc_start: 0.8704 (mpp) cc_final: 0.8231 (mmt)
REVERT: H   73 TYR cc_start: 0.6810 (OUTLIER) cc_final: 0.5715 (m-80)
REVERT: L   34 GLN cc_start: 0.4933 (tp-100) cc_final: 0.4333 (pt0)
  outliers start: 32
  outliers final: 30
  residues processed: 179
  average time/residue: 0.0959
  time to fit residues: 24.1298
Evaluate side-chains
  172 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 141
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  605 ASP
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  706 THR
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain A residue  798 SER
Chi-restraints excluded: chain A residue  863 THR
Chi-restraints excluded: chain A residue  943 THR
Chi-restraints excluded: chain A residue  955 ILE
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue  964 SER
Chi-restraints excluded: chain A residue  979 ILE
Chi-restraints excluded: chain A residue  985 SER
Chi-restraints excluded: chain A residue 1012 SER
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   43 GLN
Chi-restraints excluded: chain H residue   73 TYR
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue   87 TYR
Chi-restraints excluded: chain L residue    6 SER
Chi-restraints excluded: chain L residue   30 HIS
Chi-restraints excluded: chain L residue   51 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 55 optimal weight:    0.5980
   chunk 78 optimal weight:    2.9990
   chunk 99 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0050
   chunk 91 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0970
   chunk 1 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 101 optimal weight:    0.6980
   overall best weight:    0.3992

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

Flipped N/Q/H residues before XYZ refinement:
A 550 GLN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  93 HIS
L  30 HIS
** L  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.181444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.154714 restraints weight = 15400.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.156956 restraints weight = 10749.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.158197 restraints weight = 7754.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.159118 restraints weight = 6579.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.159247 restraints weight = 6341.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.5587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  10019  Z= 0.110
  Angle     :  0.622  17.816  13637  Z= 0.309
  Chirality :  0.045   0.201   1544
  Planarity :  0.004   0.048   1743
  Dihedral  :  5.333  51.266   1436
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.03 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 18.51 %
    Favored  : 79.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.69 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.06 (0.24), residues: 1216
  helix:  2.06 (0.35), residues: 236
  sheet:  0.29 (0.29), residues: 318
  loop : -1.02 (0.23), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 426 
 TYR   0.027   0.001   TYR H  87 
 PHE   0.018   0.001   PHE A 527 
 TRP   0.014   0.001   TRP A 340 
 HIS   0.005   0.001   HIS L  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 9999)
  covalent geometry    : angle       0.58667 (13592)
  SS BOND              : bond        0.00276 (   15)
  SS BOND              : angle       1.67221 (   30)
  hydrogen bonds       : bond        0.03974 (  399)
  hydrogen bonds       : angle       5.45516 ( 1074)
  link_NAG-ASN         : bond        0.01159 (    5)
  link_NAG-ASN         : angle       5.87998 (   15)

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

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

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 159
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 SER cc_start: 0.7576 (t) cc_final: 0.7263 (p)
REVERT: A  232 ARG cc_start: 0.6520 (ttm-80) cc_final: 0.6159 (ttt90)
REVERT: A  411 LYS cc_start: 0.8048 (tptt) cc_final: 0.7448 (tppt)
REVERT: A  965 ARG cc_start: 0.7266 (ptt180) cc_final: 0.4980 (tpt90)
REVERT: A  980 THR cc_start: 0.8445 (m) cc_final: 0.7892 (p)
REVERT: A 1011 MET cc_start: 0.8116 (tpp) cc_final: 0.7790 (ttm)
REVERT: A 1092 PHE cc_start: 0.7929 (t80) cc_final: 0.7428 (t80)
REVERT: H   23 LYS cc_start: 0.8581 (mttt) cc_final: 0.7844 (mtmm)
REVERT: H   34 MET cc_start: 0.8681 (mpp) cc_final: 0.8246 (mmt)
REVERT: H   73 TYR cc_start: 0.6741 (OUTLIER) cc_final: 0.5701 (m-80)
REVERT: L   34 GLN cc_start: 0.4865 (tp-100) cc_final: 0.4376 (pt0)
  outliers start: 25
  outliers final: 21
  residues processed: 175
  average time/residue: 0.0875
  time to fit residues: 21.7596
Evaluate side-chains
  168 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 146
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  491 TYR
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  605 ASP
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  706 THR
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain A residue  798 SER
Chi-restraints excluded: chain A residue  985 SER
Chi-restraints excluded: chain A residue 1012 SER
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain H residue   43 GLN
Chi-restraints excluded: chain H residue   73 TYR
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue   87 TYR
Chi-restraints excluded: chain L residue    6 SER
Chi-restraints excluded: chain L residue   30 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 92 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0870
   chunk 4 optimal weight:    0.7980
   chunk 79 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 107 optimal weight:    5.9990
   chunk 20 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    1.5764

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

Flipped N/Q/H residues before XYZ refinement:
A 401 GLN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  30 HIS
** L  42 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 = 0.4025 r_free = 0.4025 target = 0.176569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.150416 restraints weight = 15381.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.152536 restraints weight = 10188.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.154338 restraints weight = 7464.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.154529 restraints weight = 6474.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.154762 restraints weight = 6032.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7232
moved from start:          0.5641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  10019  Z= 0.176
  Angle     :  0.687  17.448  13637  Z= 0.347
  Chirality :  0.048   0.224   1544
  Planarity :  0.004   0.042   1743
  Dihedral  :  5.777  53.587   1436
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.10 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 18.42 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.69 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.24), residues: 1216
  helix:  1.87 (0.34), residues: 236
  sheet:  0.09 (0.28), residues: 337
  loop : -1.17 (0.23), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 426 
 TYR   0.025   0.002   TYR H  87 
 PHE   0.022   0.002   PHE A  89 
 TRP   0.021   0.002   TRP A 340 
 HIS   0.005   0.001   HIS A1040 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 9999)
  covalent geometry    : angle       0.65082 (13592)
  SS BOND              : bond        0.00333 (   15)
  SS BOND              : angle       2.26169 (   30)
  hydrogen bonds       : bond        0.04722 (  399)
  hydrogen bonds       : angle       5.64939 ( 1074)
  link_NAG-ASN         : bond        0.01251 (    5)
  link_NAG-ASN         : angle       5.89653 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1661.82 seconds
wall clock time: 29 minutes 23.21 seconds (1763.21 seconds total)