Starting phenix.real_space_refine
on Tue Mar  3 17:27:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7e2g_30956/03_2026/7e2g_30956.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7e2g_30956/03_2026/7e2g_30956.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7e2g_30956/03_2026/7e2g_30956.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7e2g_30956/03_2026/7e2g_30956.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7e2g_30956/03_2026/7e2g_30956.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7e2g_30956/03_2026/7e2g_30956.map"
  }
  resolution = 3.61
  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=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      59      5.16       5
     C    4894      2.51       5
     N    1114      2.21       5
     O    1309      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7376
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "D"
      Number of atoms: 6935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 901, 6935
          Classifications: {'peptide': 901}
          Incomplete info: {'truncation_to_alanine': 56}
          Link IDs: {'PTRANS': 36, 'TRANS': 864}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 232
          Unresolved non-hydrogen angles: 289
          Unresolved non-hydrogen dihedrals: 200
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 6, 'ASN:plan1': 3, 'PHE:plan': 3, 'GLN:plan1': 4, 'ARG:plan': 5, 'ASP:plan': 6, 'HIS:plan': 5}
          Unresolved non-hydrogen planarities: 156
    Chain: "D"
      Number of atoms: 441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 441
          Unusual residues: {'NAG': 4, 'Y01': 11}
          Classifications: {'undetermined': 15}
          Link IDs: {None: 14}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 1.84, per 1000 atoms: 0.25
  Number of scatterers: 7376
  At special positions: 0
  Unit cell: (104.76, 118.8, 114.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      59     16.00
     O    1309      8.00
     N    1114      7.00
     C    4894      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG D1612 " - " ASN D 836 "
      " NAG D1613 " - " ASN D 476 "
      " NAG D1614 " - " ASN D 363 "
      " NAG D1615 " - " ASN D 917 "
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 272.1 milliseconds
  

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1718

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 3 sheets defined
      58.3% alpha, 2.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'D' and resid 181 through 186
      removed outlier: 3.829A  pdb=" N   ILE D 185 " --> pdb=" O   TYR D 181 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 210
      removed outlier: 4.044A  pdb=" N   VAL D 192 " --> pdb=" O   TRP D 188 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 230 through 243
    Processing helix  chain 'D' and resid 315 through 330
    Processing helix  chain 'D' and resid 353 through 361
      removed outlier: 3.913A  pdb=" N   TYR D 357 " --> pdb=" O   THR D 353 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 372 through 386
      removed outlier: 4.079A  pdb=" N   SER D 376 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 387 through 389
      No H-bonds generated for 'chain 'D' and resid 387 through 389'
    Processing helix  chain 'D' and resid 422 through 430
    Processing helix  chain 'D' and resid 464 through 472
      removed outlier: 3.932A  pdb=" N   TYR D 468 " --> pdb=" O   MET D 464 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ASP D 470 " --> pdb=" O   ASN D 466 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   PHE D 472 " --> pdb=" O   TYR D 468 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 495 through 503
      removed outlier: 3.616A  pdb=" N   TYR D 499 " --> pdb=" O   LEU D 495 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 504 through 522
      removed outlier: 3.778A  pdb=" N   ALA D 508 " --> pdb=" O   THR D 504 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 525 through 548
    Processing helix  chain 'D' and resid 557 through 560
    Processing helix  chain 'D' and resid 561 through 587
      removed outlier: 3.803A  pdb=" N   ILE D 565 " --> pdb=" O   THR D 561 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   ALA D 571 " --> pdb=" O   VAL D 567 " (cutoff:3.500A)
      removed outlier: 4.983A  pdb=" N   ASN D 572 " --> pdb=" O   GLY D 568 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   ASN D 573 " --> pdb=" O   ILE D 569 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   ALA D 574 " --> pdb=" O   GLY D 570 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   PHE D 575 " --> pdb=" O   ALA D 571 " (cutoff:3.500A)
      removed outlier: 4.904A  pdb=" N   VAL D 576 " --> pdb=" O   ASN D 572 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 592 through 621
      removed outlier: 5.077A  pdb=" N   LEU D 606 " --> pdb=" O   GLN D 602 " (cutoff:3.500A)
      removed outlier: 5.091A  pdb=" N   SER D 607 " --> pdb=" O   HIS D 603 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   THR D 615 " --> pdb=" O   THR D 611 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 622 through 624
      No H-bonds generated for 'chain 'D' and resid 622 through 624'
    Processing helix  chain 'D' and resid 627 through 659
      removed outlier: 3.671A  pdb=" N   ARG D 631 " --> pdb=" O   ILE D 627 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   LEU D 652 " --> pdb=" O   MET D 648 " (cutoff:3.500A)
      Proline residue:  D 653  - end of helix
    Processing helix  chain 'D' and resid 688 through 708
    Processing helix  chain 'D' and resid 708 through 716
      removed outlier: 3.600A  pdb=" N   CYS D 712 " --> pdb=" O   LYS D 708 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 719 through 738
      removed outlier: 3.515A  pdb=" N   PHE D 723 " --> pdb=" O   TYR D 719 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 748 through 752
      removed outlier: 3.858A  pdb=" N   PHE D 752 " --> pdb=" O   LEU D 749 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 759 through 772
      removed outlier: 3.684A  pdb=" N   ASP D 765 " --> pdb=" O   PHE D 761 " (cutoff:3.500A)
      removed outlier: 4.899A  pdb=" N   LYS D 769 " --> pdb=" O   ASP D 765 " (cutoff:3.500A)
      removed outlier: 5.291A  pdb=" N   LYS D 770 " --> pdb=" O   ALA D 766 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 772 through 777
    Processing helix  chain 'D' and resid 820 through 835
    Processing helix  chain 'D' and resid 851 through 859
      removed outlier: 3.989A  pdb=" N   THR D 855 " --> pdb=" O   CYS D 851 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 885 through 901
      removed outlier: 4.211A  pdb=" N   LYS D 891 " --> pdb=" O   GLU D 887 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ILE D 894 " --> pdb=" O   ILE D 890 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 937 through 953
      removed outlier: 4.308A  pdb=" N   SER D 953 " --> pdb=" O   SER D 949 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 972 through 1004
      removed outlier: 3.873A  pdb=" N   THR D1003 " --> pdb=" O   MET D 999 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   TRP D1004 " --> pdb=" O   LEU D1000 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1005 through 1031
      removed outlier: 3.669A  pdb=" N   TYR D1011 " --> pdb=" O   ILE D1007 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1037 through 1050
      removed outlier: 4.014A  pdb=" N   SER D1043 " --> pdb=" O   SER D1039 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   VAL D1046 " --> pdb=" O   ILE D1042 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   GLY D1047 " --> pdb=" O   SER D1043 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   VAL D1050 " --> pdb=" O   VAL D1046 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1050 through 1059
      removed outlier: 3.853A  pdb=" N   HIS D1055 " --> pdb=" O   ASN D1051 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   TYR D1056 " --> pdb=" O   PHE D1052 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1072 through 1096
      removed outlier: 5.665A  pdb=" N   SER D1081 " --> pdb=" O   SER D1077 " (cutoff:3.500A)
      removed outlier: 5.276A  pdb=" N   ALA D1082 " --> pdb=" O   ARG D1078 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   THR D1090 " --> pdb=" O   ALA D1086 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1102 through 1130
      removed outlier: 3.717A  pdb=" N   THR D1106 " --> pdb=" O   VAL D1102 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 452 through 459
      removed outlier: 4.133A  pdb=" N   SER D 301 " --> pdb=" O   SER D 456 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   GLY D 486 " --> pdb=" O   VAL D 304 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   THR D 306 " --> pdb=" O   ILE D 484 " (cutoff:3.500A)
      removed outlier: 5.166A  pdb=" N   ILE D 484 " --> pdb=" O   THR D 306 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 789 through 790
    Processing sheet with id=AA3, first strand: chain 'D' and resid 913 through 914

    362 hydrogen bonds defined for protein.
    1071 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.03

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1120
        1.32 -     1.44: 2064
        1.44 -     1.56: 4310
        1.56 -     1.69: 0
        1.69 -     1.81: 93
  Bond restraints: 7587
  Sorted by residual:
  bond pdb=" C1  NAG D1612 "
       pdb=" O5  NAG D1612 "
    ideal  model  delta    sigma   weight residual
    1.406  1.500 -0.094 2.00e-02 2.50e+03 2.23e+01
  bond pdb=" CG  ASN D 363 "
       pdb=" ND2 ASN D 363 "
    ideal  model  delta    sigma   weight residual
    1.328  1.375 -0.047 2.10e-02 2.27e+03 5.08e+00
  bond pdb=" C1  NAG D1614 "
       pdb=" O5  NAG D1614 "
    ideal  model  delta    sigma   weight residual
    1.406  1.447 -0.041 2.00e-02 2.50e+03 4.18e+00
  bond pdb=" C   ASN D 739 "
       pdb=" N   PRO D 740 "
    ideal  model  delta    sigma   weight residual
    1.334  1.379 -0.045 2.34e-02 1.83e+03 3.75e+00
  bond pdb=" CG  ASN D 917 "
       pdb=" ND2 ASN D 917 "
    ideal  model  delta    sigma   weight residual
    1.328  1.365 -0.037 2.10e-02 2.27e+03 3.05e+00
  ... (remaining 7582 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 9916
        1.51 -     3.01: 389
        3.01 -     4.52: 72
        4.52 -     6.02: 10
        6.02 -     7.53: 9
  Bond angle restraints: 10396
  Sorted by residual:
  angle pdb=" N   LYS D 805 "
        pdb=" CA  LYS D 805 "
        pdb=" C   LYS D 805 "
      ideal   model   delta    sigma   weight residual
     113.19  108.39    4.80 1.19e+00 7.06e-01 1.62e+01
  angle pdb=" C   ASP D 906 "
        pdb=" N   SER D 907 "
        pdb=" CA  SER D 907 "
      ideal   model   delta    sigma   weight residual
     121.54  128.85   -7.31 1.91e+00 2.74e-01 1.47e+01
  angle pdb=" C   ALA D 186 "
        pdb=" N   ASP D 187 "
        pdb=" CA  ASP D 187 "
      ideal   model   delta    sigma   weight residual
     121.54  128.25   -6.71 1.91e+00 2.74e-01 1.23e+01
  angle pdb=" C   THR D 228 "
        pdb=" N   ALA D 229 "
        pdb=" CA  ALA D 229 "
      ideal   model   delta    sigma   weight residual
     121.54  127.98   -6.44 1.91e+00 2.74e-01 1.14e+01
  angle pdb=" C   MET D 437 "
        pdb=" N   THR D 438 "
        pdb=" CA  THR D 438 "
      ideal   model   delta    sigma   weight residual
     122.28  118.89    3.39 1.02e+00 9.61e-01 1.10e+01
  ... (remaining 10391 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.08: 4703
       22.08 -    44.16: 271
       44.16 -    66.24: 40
       66.24 -    88.32: 3
       88.32 -   110.40: 4
  Dihedral angle restraints: 5021
    sinusoidal: 2372
      harmonic: 2649
  Sorted by residual:
  dihedral pdb=" CA  ASN D 739 "
           pdb=" C   ASN D 739 "
           pdb=" N   PRO D 740 "
           pdb=" CA  PRO D 740 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.45  -25.55     0      5.00e+00 4.00e-02 2.61e+01
  dihedral pdb=" CA  LYS D 256 "
           pdb=" C   LYS D 256 "
           pdb=" N   TYR D 257 "
           pdb=" CA  TYR D 257 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.71  -25.29     0      5.00e+00 4.00e-02 2.56e+01
  dihedral pdb=" CA  ASP D 918 "
           pdb=" C   ASP D 918 "
           pdb=" N   THR D 919 "
           pdb=" CA  THR D 919 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.37   21.63     0      5.00e+00 4.00e-02 1.87e+01
  ... (remaining 5018 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.241: 1230
       0.241 -    0.482: 0
       0.482 -    0.723: 3
       0.723 -    0.964: 0
       0.964 -    1.205: 1
  Chirality restraints: 1234
  Sorted by residual:
  chirality pdb=" C1  NAG D1615 "
            pdb=" ND2 ASN D 917 "
            pdb=" C2  NAG D1615 "
            pdb=" O5  NAG D1615 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.20   -1.20 2.00e-01 2.50e+01 3.63e+01
  chirality pdb=" C1  NAG D1614 "
            pdb=" ND2 ASN D 363 "
            pdb=" C2  NAG D1614 "
            pdb=" O5  NAG D1614 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.70   -0.70 2.00e-01 2.50e+01 1.23e+01
  chirality pdb=" C1  NAG D1613 "
            pdb=" ND2 ASN D 476 "
            pdb=" C2  NAG D1613 "
            pdb=" O5  NAG D1613 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.71   -0.69 2.00e-01 2.50e+01 1.19e+01
  ... (remaining 1231 not shown)

  Planarity restraints: 1235
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE D 557 "   -0.012 2.00e-02 2.50e+03   2.33e-02 5.41e+00
        pdb=" C   PHE D 557 "    0.040 2.00e-02 2.50e+03
        pdb=" O   PHE D 557 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   MET D 558 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN D 739 "    0.038 5.00e-02 4.00e+02   5.82e-02 5.41e+00
        pdb=" N   PRO D 740 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO D 740 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO D 740 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN D 883 "    0.011 2.00e-02 2.50e+03   2.22e-02 4.93e+00
        pdb=" C   GLN D 883 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   GLN D 883 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLU D 884 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1232 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 136
        2.69 -     3.24: 7644
        3.24 -     3.79: 10657
        3.79 -     4.35: 13430
        4.35 -     4.90: 22539
  Nonbonded interactions: 54406
  Sorted by model distance:
  nonbonded pdb=" CAI Y01 D1610 "
            pdb=" CAR Y01 D1611 "
     model   vdw
     2.132 3.740
  nonbonded pdb=" OH  TYR D 357 "
            pdb=" OE1 GLN D 426 "
     model   vdw
     2.165 3.040
  nonbonded pdb=" CAK Y01 D1610 "
            pdb=" CAT Y01 D1611 "
     model   vdw
     2.196 3.840
  nonbonded pdb=" O   ASP D 948 "
            pdb=" OG  SER D 952 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" NZ  LYS D 741 "
            pdb=" OAG Y01 D1607 "
     model   vdw
     2.236 3.120
  ... (remaining 54401 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             0.400
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.090
  Find NCS groups from input model:        0.030
  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:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
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      :  0.005   0.094   7591  Z= 0.220
  Angle     :  0.799  22.880  10408  Z= 0.399
  Chirality :  0.063   1.205   1234
  Planarity :  0.004   0.058   1231
  Dihedral  : 13.567 110.396   3303
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.76 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  5.99 %
    Favored  : 93.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.91 (0.25), residues: 891
  helix: -0.61 (0.23), residues: 474
  sheet: -2.20 (0.87), residues: 24
  loop : -3.71 (0.25), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 661 
 TYR   0.009   0.001   TYR D 636 
 PHE   0.020   0.001   PHE D 552 
 TRP   0.015   0.002   TRP D 651 
 HIS   0.002   0.001   HIS D 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 7587)
  covalent geometry    : angle       0.71674 (10396)
  hydrogen bonds       : bond        0.11749 (  362)
  hydrogen bonds       : angle       5.63765 ( 1071)
  link_NAG-ASN         : bond        0.03089 (    4)
  link_NAG-ASN         : angle      10.42505 (   12)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 131
  time to evaluate  : 0.292 
Fit side-chains
REVERT: D  431 LEU cc_start: 0.8989 (mp) cc_final: 0.8777 (mp)
REVERT: D  595 GLU cc_start: 0.8169 (pt0) cc_final: 0.7954 (pt0)
REVERT: D  700 GLU cc_start: 0.7949 (pt0) cc_final: 0.7439 (pt0)
REVERT: D  738 ILE cc_start: 0.8156 (mm) cc_final: 0.7946 (mt)
REVERT: D  926 GLU cc_start: 0.7668 (pp20) cc_final: 0.7266 (pp20)
REVERT: D  960 GLU cc_start: 0.8745 (pp20) cc_final: 0.8291 (pp20)
  outliers start: 1
  outliers final: 1
  residues processed: 132
  average time/residue: 0.0559
  time to fit residues: 11.4713
Evaluate side-chains
  102 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  557 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    9.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
D 232 GLN
D 356 ASN
D 422 ASN
D 497 GLN
D 622 ASN
D 644 ASN
** D 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 784 HIS
** D1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1107 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.133657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.099738 restraints weight = 12912.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.101787 restraints weight = 7334.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.102949 restraints weight = 5345.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.103290 restraints weight = 4270.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.103425 restraints weight = 4292.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.1076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7591  Z= 0.171
  Angle     :  0.745  19.271  10408  Z= 0.351
  Chirality :  0.044   0.389   1234
  Planarity :  0.004   0.043   1231
  Dihedral  :  9.760  78.217   1823
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 12.24 %
    Favored  : 85.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.27), residues: 891
  helix:  0.77 (0.24), residues: 473
  sheet: -1.64 (0.91), residues: 24
  loop : -3.28 (0.27), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 661 
 TYR   0.013   0.001   TYR D 430 
 PHE   0.021   0.002   PHE D 552 
 TRP   0.017   0.001   TRP D 651 
 HIS   0.003   0.001   HIS D 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 7587)
  covalent geometry    : angle       0.68270 (10396)
  hydrogen bonds       : bond        0.05486 (  362)
  hydrogen bonds       : angle       4.18649 ( 1071)
  link_NAG-ASN         : bond        0.00934 (    4)
  link_NAG-ASN         : angle       8.78144 (   12)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.261 
Fit side-chains
REVERT: D  205 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8001 (mp)
REVERT: D  431 LEU cc_start: 0.9040 (mp) cc_final: 0.8839 (mp)
REVERT: D  700 GLU cc_start: 0.7929 (pt0) cc_final: 0.7462 (pt0)
REVERT: D  768 TYR cc_start: 0.9109 (m-10) cc_final: 0.8658 (m-10)
REVERT: D  877 TRP cc_start: 0.8542 (m100) cc_final: 0.8220 (m100)
REVERT: D  940 MET cc_start: 0.8950 (mmm) cc_final: 0.8544 (mmp)
REVERT: D  960 GLU cc_start: 0.8556 (pp20) cc_final: 0.7628 (pp20)
  outliers start: 14
  outliers final: 10
  residues processed: 110
  average time/residue: 0.0552
  time to fit residues: 9.5027
Evaluate side-chains
  107 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  361 LEU
Chi-restraints excluded: chain D residue  557 PHE
Chi-restraints excluded: chain D residue  590 HIS
Chi-restraints excluded: chain D residue  649 VAL
Chi-restraints excluded: chain D residue  692 HIS
Chi-restraints excluded: chain D residue  709 VAL
Chi-restraints excluded: chain D residue  728 LEU
Chi-restraints excluded: chain D residue 1020 ILE
Chi-restraints excluded: chain D residue 1030 LEU
Chi-restraints excluded: chain D residue 1112 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 11 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 83 optimal weight:    0.4980
   chunk 37 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0870
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.6960

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

Flipped N/Q/H residues before XYZ refinement:
D 232 GLN
** D1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.135999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.102789 restraints weight = 12868.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.105120 restraints weight = 7171.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.106084 restraints weight = 5220.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.106833 restraints weight = 4135.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.106803 restraints weight = 3821.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.1437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   7591  Z= 0.120
  Angle     :  0.694  18.701  10408  Z= 0.322
  Chirality :  0.041   0.350   1234
  Planarity :  0.004   0.035   1231
  Dihedral  :  8.981  58.932   1823
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 11.84 %
    Favored  : 85.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.29), residues: 891
  helix:  1.45 (0.24), residues: 474
  sheet: -1.31 (0.94), residues: 24
  loop : -3.06 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 835 
 TYR   0.011   0.001   TYR D 430 
 PHE   0.023   0.001   PHE D 856 
 TRP   0.016   0.001   TRP D 651 
 HIS   0.002   0.001   HIS D 659 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 7587)
  covalent geometry    : angle       0.62556 (10396)
  hydrogen bonds       : bond        0.04486 (  362)
  hydrogen bonds       : angle       3.92473 ( 1071)
  link_NAG-ASN         : bond        0.01105 (    4)
  link_NAG-ASN         : angle       8.87517 (   12)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.266 
Fit side-chains
REVERT: D  205 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8020 (mp)
REVERT: D  349 CYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7644 (m)
REVERT: D  437 MET cc_start: 0.3750 (mmt) cc_final: 0.3466 (tpp)
REVERT: D  700 GLU cc_start: 0.7822 (pt0) cc_final: 0.7388 (pt0)
REVERT: D  768 TYR cc_start: 0.8973 (m-10) cc_final: 0.8626 (m-10)
REVERT: D  940 MET cc_start: 0.8889 (mmm) cc_final: 0.8561 (mmp)
REVERT: D  960 GLU cc_start: 0.8345 (pp20) cc_final: 0.7563 (pp20)
  outliers start: 21
  outliers final: 8
  residues processed: 121
  average time/residue: 0.0561
  time to fit residues: 10.4317
Evaluate side-chains
  114 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  349 CYS
Chi-restraints excluded: chain D residue  557 PHE
Chi-restraints excluded: chain D residue  649 VAL
Chi-restraints excluded: chain D residue  692 HIS
Chi-restraints excluded: chain D residue  709 VAL
Chi-restraints excluded: chain D residue  728 LEU
Chi-restraints excluded: chain D residue  966 TRP
Chi-restraints excluded: chain D residue 1020 ILE
Chi-restraints excluded: chain D residue 1073 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0870
   chunk 28 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 23 optimal weight:   30.0000
   chunk 79 optimal weight:    0.6980
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
D 232 GLN
** D1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.137435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.104555 restraints weight = 13020.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.106753 restraints weight = 7489.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.107646 restraints weight = 5571.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.108363 restraints weight = 4362.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.108354 restraints weight = 4055.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7591  Z= 0.118
  Angle     :  0.657  18.014  10408  Z= 0.308
  Chirality :  0.040   0.322   1234
  Planarity :  0.003   0.034   1231
  Dihedral  :  8.722  59.174   1823
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 14.56 %
    Favored  : 82.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.29), residues: 891
  helix:  1.79 (0.24), residues: 474
  sheet: -0.99 (0.96), residues: 24
  loop : -2.98 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 835 
 TYR   0.008   0.001   TYR D 257 
 PHE   0.024   0.001   PHE D 856 
 TRP   0.015   0.001   TRP D 651 
 HIS   0.002   0.000   HIS D 659 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 7587)
  covalent geometry    : angle       0.59073 (10396)
  hydrogen bonds       : bond        0.04063 (  362)
  hydrogen bonds       : angle       3.81423 ( 1071)
  link_NAG-ASN         : bond        0.01122 (    4)
  link_NAG-ASN         : angle       8.51896 (   12)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.277 
Fit side-chains
REVERT: D  205 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8015 (mp)
REVERT: D  437 MET cc_start: 0.3597 (mmt) cc_final: 0.3356 (tpp)
REVERT: D  700 GLU cc_start: 0.7818 (pt0) cc_final: 0.7335 (pt0)
REVERT: D  768 TYR cc_start: 0.8899 (m-10) cc_final: 0.8590 (m-10)
REVERT: D  785 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8721 (ttp)
REVERT: D  940 MET cc_start: 0.8799 (mmm) cc_final: 0.8573 (mmt)
REVERT: D  960 GLU cc_start: 0.8234 (pp20) cc_final: 0.7569 (pp20)
REVERT: D 1116 MET cc_start: 0.8516 (mmt) cc_final: 0.8281 (mmt)
  outliers start: 18
  outliers final: 9
  residues processed: 126
  average time/residue: 0.0572
  time to fit residues: 10.9886
Evaluate side-chains
  118 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  361 LEU
Chi-restraints excluded: chain D residue  446 THR
Chi-restraints excluded: chain D residue  458 THR
Chi-restraints excluded: chain D residue  557 PHE
Chi-restraints excluded: chain D residue  649 VAL
Chi-restraints excluded: chain D residue  692 HIS
Chi-restraints excluded: chain D residue  709 VAL
Chi-restraints excluded: chain D residue  728 LEU
Chi-restraints excluded: chain D residue  785 MET
Chi-restraints excluded: chain D residue 1073 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 17 optimal weight:   20.0000
   chunk 13 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
D 232 GLN
** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.136857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.103853 restraints weight = 12891.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.106196 restraints weight = 7474.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.107127 restraints weight = 5394.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.107578 restraints weight = 4270.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.107671 restraints weight = 4033.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7591  Z= 0.122
  Angle     :  0.651  17.596  10408  Z= 0.304
  Chirality :  0.040   0.313   1234
  Planarity :  0.003   0.033   1231
  Dihedral  :  8.631  59.500   1823
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 15.65 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.29), residues: 891
  helix:  1.86 (0.24), residues: 474
  sheet: -0.81 (0.98), residues: 24
  loop : -2.92 (0.28), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 373 
 TYR   0.007   0.001   TYR D 645 
 PHE   0.024   0.001   PHE D 856 
 TRP   0.015   0.001   TRP D 651 
 HIS   0.001   0.000   HIS D 659 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 7587)
  covalent geometry    : angle       0.58929 (10396)
  hydrogen bonds       : bond        0.04202 (  362)
  hydrogen bonds       : angle       3.77407 ( 1071)
  link_NAG-ASN         : bond        0.01165 (    4)
  link_NAG-ASN         : angle       8.13475 (   12)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.290 
Fit side-chains
REVERT: D  205 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8015 (mp)
REVERT: D  349 CYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7570 (m)
REVERT: D  428 LEU cc_start: 0.9411 (mp) cc_final: 0.9020 (mp)
REVERT: D  437 MET cc_start: 0.3493 (mmt) cc_final: 0.3274 (tpp)
REVERT: D  700 GLU cc_start: 0.7815 (pt0) cc_final: 0.7341 (pt0)
REVERT: D  920 ILE cc_start: 0.8979 (mm) cc_final: 0.8663 (tp)
REVERT: D  940 MET cc_start: 0.8797 (mmm) cc_final: 0.8596 (mmt)
REVERT: D  960 GLU cc_start: 0.8228 (pp20) cc_final: 0.7587 (pp20)
  outliers start: 21
  outliers final: 12
  residues processed: 124
  average time/residue: 0.0562
  time to fit residues: 10.6843
Evaluate side-chains
  122 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  349 CYS
Chi-restraints excluded: chain D residue  361 LEU
Chi-restraints excluded: chain D residue  446 THR
Chi-restraints excluded: chain D residue  458 THR
Chi-restraints excluded: chain D residue  557 PHE
Chi-restraints excluded: chain D residue  649 VAL
Chi-restraints excluded: chain D residue  692 HIS
Chi-restraints excluded: chain D residue  709 VAL
Chi-restraints excluded: chain D residue  728 LEU
Chi-restraints excluded: chain D residue  966 TRP
Chi-restraints excluded: chain D residue 1020 ILE
Chi-restraints excluded: chain D residue 1041 THR
Chi-restraints excluded: chain D residue 1073 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 19 optimal weight:   20.0000
   chunk 73 optimal weight:    0.9990
   chunk 37 optimal weight:    6.9990
   chunk 85 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 38 optimal weight:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0570
   overall best weight:    0.7502

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

Flipped N/Q/H residues before XYZ refinement:
** D1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.138551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.105543 restraints weight = 12797.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.107507 restraints weight = 7411.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.108583 restraints weight = 5510.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.109106 restraints weight = 4340.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.109215 restraints weight = 4111.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   7591  Z= 0.112
  Angle     :  0.633  17.024  10408  Z= 0.297
  Chirality :  0.039   0.303   1234
  Planarity :  0.003   0.034   1231
  Dihedral  :  8.535  58.157   1823
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 16.05 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.29), residues: 891
  helix:  1.98 (0.24), residues: 474
  sheet: -0.60 (1.00), residues: 24
  loop : -2.88 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 373 
 TYR   0.007   0.001   TYR D 257 
 PHE   0.027   0.001   PHE D 856 
 TRP   0.014   0.001   TRP D 651 
 HIS   0.002   0.000   HIS D 659 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 7587)
  covalent geometry    : angle       0.57553 (10396)
  hydrogen bonds       : bond        0.03914 (  362)
  hydrogen bonds       : angle       3.73492 ( 1071)
  link_NAG-ASN         : bond        0.01164 (    4)
  link_NAG-ASN         : angle       7.78537 (   12)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.205 
Fit side-chains
REVERT: D  205 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8007 (mp)
REVERT: D  349 CYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7467 (m)
REVERT: D  352 TRP cc_start: 0.8304 (OUTLIER) cc_final: 0.7941 (t-100)
REVERT: D  437 MET cc_start: 0.3359 (mmt) cc_final: 0.2480 (tpp)
REVERT: D  700 GLU cc_start: 0.7828 (pt0) cc_final: 0.7404 (pt0)
REVERT: D  940 MET cc_start: 0.8752 (mmm) cc_final: 0.8499 (mmt)
REVERT: D  960 GLU cc_start: 0.8170 (pp20) cc_final: 0.7562 (pp20)
  outliers start: 24
  outliers final: 13
  residues processed: 126
  average time/residue: 0.0601
  time to fit residues: 11.5113
Evaluate side-chains
  124 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  349 CYS
Chi-restraints excluded: chain D residue  352 TRP
Chi-restraints excluded: chain D residue  361 LEU
Chi-restraints excluded: chain D residue  446 THR
Chi-restraints excluded: chain D residue  458 THR
Chi-restraints excluded: chain D residue  557 PHE
Chi-restraints excluded: chain D residue  649 VAL
Chi-restraints excluded: chain D residue  692 HIS
Chi-restraints excluded: chain D residue  709 VAL
Chi-restraints excluded: chain D residue  728 LEU
Chi-restraints excluded: chain D residue  785 MET
Chi-restraints excluded: chain D residue  855 THR
Chi-restraints excluded: chain D residue  909 THR
Chi-restraints excluded: chain D residue 1041 THR
Chi-restraints excluded: chain D residue 1073 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 81 optimal weight:    7.9990
   chunk 59 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0970
   chunk 64 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   chunk 50 optimal weight:    8.9990
   chunk 60 optimal weight:    8.9990
   chunk 43 optimal weight:    0.9980
   chunk 84 optimal weight:    0.6980
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.138676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.105580 restraints weight = 12744.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.107032 restraints weight = 7273.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.107921 restraints weight = 5145.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.108237 restraints weight = 4418.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.108626 restraints weight = 4214.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7591  Z= 0.114
  Angle     :  0.636  16.579  10408  Z= 0.297
  Chirality :  0.040   0.300   1234
  Planarity :  0.004   0.041   1231
  Dihedral  :  8.474  58.942   1823
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 16.73 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.29), residues: 891
  helix:  2.04 (0.24), residues: 474
  sheet: -0.59 (1.01), residues: 24
  loop : -2.84 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 373 
 TYR   0.007   0.001   TYR D 645 
 PHE   0.024   0.001   PHE D 856 
 TRP   0.014   0.001   TRP D 651 
 HIS   0.002   0.000   HIS D 659 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 7587)
  covalent geometry    : angle       0.58139 (10396)
  hydrogen bonds       : bond        0.04046 (  362)
  hydrogen bonds       : angle       3.74550 ( 1071)
  link_NAG-ASN         : bond        0.01115 (    4)
  link_NAG-ASN         : angle       7.58973 (   12)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.212 
Fit side-chains
REVERT: D  205 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8022 (mp)
REVERT: D  349 CYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7502 (m)
REVERT: D  352 TRP cc_start: 0.8349 (OUTLIER) cc_final: 0.8035 (t-100)
REVERT: D  428 LEU cc_start: 0.9355 (mp) cc_final: 0.9000 (mp)
REVERT: D  453 MET cc_start: 0.8957 (ttm) cc_final: 0.8401 (ttt)
REVERT: D  700 GLU cc_start: 0.7843 (pt0) cc_final: 0.7419 (pt0)
REVERT: D  723 PHE cc_start: 0.7837 (t80) cc_final: 0.7338 (t80)
REVERT: D  940 MET cc_start: 0.8738 (mmm) cc_final: 0.8481 (mmt)
REVERT: D  960 GLU cc_start: 0.8136 (pp20) cc_final: 0.7555 (pp20)
  outliers start: 23
  outliers final: 16
  residues processed: 128
  average time/residue: 0.0589
  time to fit residues: 11.6055
Evaluate side-chains
  124 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  349 CYS
Chi-restraints excluded: chain D residue  352 TRP
Chi-restraints excluded: chain D residue  361 LEU
Chi-restraints excluded: chain D residue  446 THR
Chi-restraints excluded: chain D residue  458 THR
Chi-restraints excluded: chain D residue  549 VAL
Chi-restraints excluded: chain D residue  557 PHE
Chi-restraints excluded: chain D residue  649 VAL
Chi-restraints excluded: chain D residue  692 HIS
Chi-restraints excluded: chain D residue  709 VAL
Chi-restraints excluded: chain D residue  728 LEU
Chi-restraints excluded: chain D residue  785 MET
Chi-restraints excluded: chain D residue  966 TRP
Chi-restraints excluded: chain D residue 1020 ILE
Chi-restraints excluded: chain D residue 1041 THR
Chi-restraints excluded: chain D residue 1042 ILE
Chi-restraints excluded: chain D residue 1073 ILE
Chi-restraints excluded: chain D residue 1122 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 80 optimal weight:    0.1980
   chunk 73 optimal weight:    0.9990
   chunk 69 optimal weight:    6.9990
   chunk 32 optimal weight:    0.8980
   chunk 22 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.139075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.105395 restraints weight = 12901.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.106863 restraints weight = 7235.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.107741 restraints weight = 5156.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.108596 restraints weight = 4370.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.108714 restraints weight = 4089.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   7591  Z= 0.113
  Angle     :  0.640  16.202  10408  Z= 0.297
  Chirality :  0.040   0.330   1234
  Planarity :  0.004   0.034   1231
  Dihedral  :  8.440  57.987   1823
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 17.01 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.29), residues: 891
  helix:  2.07 (0.24), residues: 474
  sheet: -0.58 (1.02), residues: 24
  loop : -2.82 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 373 
 TYR   0.007   0.001   TYR D 645 
 PHE   0.024   0.001   PHE D 856 
 TRP   0.014   0.001   TRP D 651 
 HIS   0.001   0.000   HIS D 659 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 7587)
  covalent geometry    : angle       0.58871 (10396)
  hydrogen bonds       : bond        0.03893 (  362)
  hydrogen bonds       : angle       3.73612 ( 1071)
  link_NAG-ASN         : bond        0.01106 (    4)
  link_NAG-ASN         : angle       7.41111 (   12)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.266 
Fit side-chains
REVERT: D  205 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8053 (mp)
REVERT: D  349 CYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7502 (m)
REVERT: D  352 TRP cc_start: 0.8271 (OUTLIER) cc_final: 0.7996 (t-100)
REVERT: D  428 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8969 (mp)
REVERT: D  453 MET cc_start: 0.8922 (ttm) cc_final: 0.8358 (ttt)
REVERT: D  700 GLU cc_start: 0.7899 (pt0) cc_final: 0.7593 (pt0)
REVERT: D  723 PHE cc_start: 0.7860 (t80) cc_final: 0.7315 (t80)
REVERT: D  940 MET cc_start: 0.8785 (mmm) cc_final: 0.8515 (mmt)
REVERT: D  960 GLU cc_start: 0.8138 (pp20) cc_final: 0.7542 (pp20)
  outliers start: 24
  outliers final: 18
  residues processed: 123
  average time/residue: 0.0579
  time to fit residues: 10.9778
Evaluate side-chains
  129 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  349 CYS
Chi-restraints excluded: chain D residue  352 TRP
Chi-restraints excluded: chain D residue  361 LEU
Chi-restraints excluded: chain D residue  428 LEU
Chi-restraints excluded: chain D residue  446 THR
Chi-restraints excluded: chain D residue  458 THR
Chi-restraints excluded: chain D residue  549 VAL
Chi-restraints excluded: chain D residue  557 PHE
Chi-restraints excluded: chain D residue  647 LEU
Chi-restraints excluded: chain D residue  649 VAL
Chi-restraints excluded: chain D residue  692 HIS
Chi-restraints excluded: chain D residue  709 VAL
Chi-restraints excluded: chain D residue  728 LEU
Chi-restraints excluded: chain D residue  785 MET
Chi-restraints excluded: chain D residue  855 THR
Chi-restraints excluded: chain D residue  909 THR
Chi-restraints excluded: chain D residue  968 VAL
Chi-restraints excluded: chain D residue 1020 ILE
Chi-restraints excluded: chain D residue 1041 THR
Chi-restraints excluded: chain D residue 1073 ILE
Chi-restraints excluded: chain D residue 1122 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 23 optimal weight:   20.0000
   chunk 0 optimal weight:    9.9990
   chunk 60 optimal weight:    0.0030
   chunk 68 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 22 optimal weight:    0.1980
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.6396

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.137033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.103323 restraints weight = 12811.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.104384 restraints weight = 7409.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.105755 restraints weight = 5327.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.106296 restraints weight = 4346.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.106463 restraints weight = 4071.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7591  Z= 0.136
  Angle     :  0.652  15.950  10408  Z= 0.305
  Chirality :  0.041   0.339   1234
  Planarity :  0.004   0.035   1231
  Dihedral  :  8.485  59.996   1823
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 17.14 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.29), residues: 891
  helix:  2.10 (0.24), residues: 474
  sheet: -0.74 (1.01), residues: 24
  loop : -2.78 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 373 
 TYR   0.009   0.001   TYR D 546 
 PHE   0.022   0.001   PHE D 856 
 TRP   0.014   0.001   TRP D 651 
 HIS   0.001   0.000   HIS D 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7587)
  covalent geometry    : angle       0.60348 (10396)
  hydrogen bonds       : bond        0.04410 (  362)
  hydrogen bonds       : angle       3.77425 ( 1071)
  link_NAG-ASN         : bond        0.01061 (    4)
  link_NAG-ASN         : angle       7.28971 (   12)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.246 
Fit side-chains
REVERT: D  205 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8079 (mp)
REVERT: D  349 CYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7511 (m)
REVERT: D  352 TRP cc_start: 0.8347 (OUTLIER) cc_final: 0.8014 (t-100)
REVERT: D  428 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.8986 (mp)
REVERT: D  453 MET cc_start: 0.8996 (ttm) cc_final: 0.8453 (ttt)
REVERT: D  700 GLU cc_start: 0.7947 (pt0) cc_final: 0.7491 (pt0)
REVERT: D  723 PHE cc_start: 0.7901 (t80) cc_final: 0.7334 (t80)
REVERT: D  940 MET cc_start: 0.8807 (mmm) cc_final: 0.8512 (mmt)
REVERT: D  960 GLU cc_start: 0.8230 (pp20) cc_final: 0.7640 (pp20)
  outliers start: 23
  outliers final: 15
  residues processed: 122
  average time/residue: 0.0555
  time to fit residues: 10.2607
Evaluate side-chains
  125 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  349 CYS
Chi-restraints excluded: chain D residue  352 TRP
Chi-restraints excluded: chain D residue  361 LEU
Chi-restraints excluded: chain D residue  428 LEU
Chi-restraints excluded: chain D residue  446 THR
Chi-restraints excluded: chain D residue  458 THR
Chi-restraints excluded: chain D residue  549 VAL
Chi-restraints excluded: chain D residue  557 PHE
Chi-restraints excluded: chain D residue  649 VAL
Chi-restraints excluded: chain D residue  692 HIS
Chi-restraints excluded: chain D residue  709 VAL
Chi-restraints excluded: chain D residue  728 LEU
Chi-restraints excluded: chain D residue  785 MET
Chi-restraints excluded: chain D residue  909 THR
Chi-restraints excluded: chain D residue 1020 ILE
Chi-restraints excluded: chain D residue 1041 THR
Chi-restraints excluded: chain D residue 1073 ILE
Chi-restraints excluded: chain D residue 1122 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 69 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 19 optimal weight:   30.0000
   chunk 26 optimal weight:    0.9990
   chunk 17 optimal weight:   20.0000
   overall best weight:    1.3586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.137330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.104335 restraints weight = 12764.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.105192 restraints weight = 7463.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.106645 restraints weight = 5575.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.107291 restraints weight = 4493.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.107394 restraints weight = 4264.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7591  Z= 0.125
  Angle     :  0.651  15.653  10408  Z= 0.303
  Chirality :  0.041   0.359   1234
  Planarity :  0.004   0.036   1231
  Dihedral  :  8.518  58.645   1823
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 16.87 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.29), residues: 891
  helix:  2.10 (0.24), residues: 475
  sheet: -0.49 (1.01), residues: 24
  loop : -2.75 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 373 
 TYR   0.008   0.001   TYR D 546 
 PHE   0.023   0.001   PHE D 856 
 TRP   0.015   0.001   TRP D 651 
 HIS   0.001   0.000   HIS D 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7587)
  covalent geometry    : angle       0.60388 (10396)
  hydrogen bonds       : bond        0.04283 (  362)
  hydrogen bonds       : angle       3.73539 ( 1071)
  link_NAG-ASN         : bond        0.01076 (    4)
  link_NAG-ASN         : angle       7.14817 (   12)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 107
  time to evaluate  : 0.276 
Fit side-chains
REVERT: D  205 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8086 (mp)
REVERT: D  349 CYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7521 (m)
REVERT: D  428 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9010 (mp)
REVERT: D  453 MET cc_start: 0.9017 (ttm) cc_final: 0.8534 (ttt)
REVERT: D  700 GLU cc_start: 0.7888 (pt0) cc_final: 0.7581 (pt0)
REVERT: D  723 PHE cc_start: 0.7803 (t80) cc_final: 0.7302 (t80)
REVERT: D  940 MET cc_start: 0.8763 (mmm) cc_final: 0.8488 (mmt)
REVERT: D  960 GLU cc_start: 0.8264 (pp20) cc_final: 0.7709 (pp20)
  outliers start: 25
  outliers final: 17
  residues processed: 123
  average time/residue: 0.0590
  time to fit residues: 11.1188
Evaluate side-chains
  125 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  205 LEU
Chi-restraints excluded: chain D residue  349 CYS
Chi-restraints excluded: chain D residue  361 LEU
Chi-restraints excluded: chain D residue  428 LEU
Chi-restraints excluded: chain D residue  446 THR
Chi-restraints excluded: chain D residue  458 THR
Chi-restraints excluded: chain D residue  549 VAL
Chi-restraints excluded: chain D residue  557 PHE
Chi-restraints excluded: chain D residue  611 THR
Chi-restraints excluded: chain D residue  649 VAL
Chi-restraints excluded: chain D residue  692 HIS
Chi-restraints excluded: chain D residue  709 VAL
Chi-restraints excluded: chain D residue  728 LEU
Chi-restraints excluded: chain D residue  785 MET
Chi-restraints excluded: chain D residue  855 THR
Chi-restraints excluded: chain D residue  909 THR
Chi-restraints excluded: chain D residue 1020 ILE
Chi-restraints excluded: chain D residue 1041 THR
Chi-restraints excluded: chain D residue 1073 ILE
Chi-restraints excluded: chain D residue 1122 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   chunk 50 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9990
   chunk 6 optimal weight:    0.4980
   chunk 75 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 67 optimal weight:    7.9990
   chunk 36 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0870
   chunk 22 optimal weight:    0.0050
   overall best weight:    0.5176

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.139916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.107093 restraints weight = 12734.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.107588 restraints weight = 7770.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.108571 restraints weight = 5935.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.109330 restraints weight = 4991.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.109527 restraints weight = 4583.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   7591  Z= 0.110
  Angle     :  0.652  15.159  10408  Z= 0.301
  Chirality :  0.040   0.366   1234
  Planarity :  0.003   0.034   1231
  Dihedral  :  8.472  58.219   1823
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 18.23 %
    Favored  : 79.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.29), residues: 891
  helix:  2.13 (0.24), residues: 475
  sheet:  0.01 (1.08), residues: 24
  loop : -2.74 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D1132 
 TYR   0.006   0.001   TYR D 645 
 PHE   0.022   0.001   PHE D 856 
 TRP   0.015   0.001   TRP D 651 
 HIS   0.001   0.000   HIS D 941 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 7587)
  covalent geometry    : angle       0.60786 (10396)
  hydrogen bonds       : bond        0.03764 (  362)
  hydrogen bonds       : angle       3.75567 ( 1071)
  link_NAG-ASN         : bond        0.01111 (    4)
  link_NAG-ASN         : angle       6.99867 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1219.29 seconds
wall clock time: 21 minutes 41.40 seconds (1301.40 seconds total)