Starting phenix.real_space_refine
on Wed Mar  4 01:07:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7e2i_30958/03_2026/7e2i_30958.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7e2i_30958/03_2026/7e2i_30958.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7e2i_30958/03_2026/7e2i_30958.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7e2i_30958/03_2026/7e2i_30958.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7e2i_30958/03_2026/7e2i_30958.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7e2i_30958/03_2026/7e2i_30958.map"
  }
  resolution = 4.07
  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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1208 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      67      5.16       5
     C    5595      2.51       5
     N    1354      2.21       5
     O    1552      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 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: 8569
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "G"
      Number of atoms: 1209
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 1209
          Classifications: {'peptide': 151}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 145}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "D"
      Number of atoms: 7058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 907, 7058
          Classifications: {'peptide': 907}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 37, 'TRANS': 869}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 155
          Unresolved non-hydrogen angles: 191
          Unresolved non-hydrogen dihedrals: 132
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 3, 'HIS:plan': 1, 'ARG:plan': 5, 'ASP:plan': 5, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 92
    Chain: "G"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 301
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 301
          Unusual residues: {'NAG': 4, 'Y01': 7}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 2.30, per 1000 atoms: 0.27
  Number of scatterers: 8569
  At special positions: 0
  Unit cell: (109.172, 115.856, 115.856, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      67     16.00
     O    1552      8.00
     N    1354      7.00
     C    5595      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 D1608 " - " ASN D 476 "
      " NAG D1610 " - " ASN D 917 "
      " NAG D1611 " - " ASN D 836 "
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 331.4 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN G 501 "
        pdb="ZN    ZN G 501 " - pdb=" NE2 HIS G 140 "
        pdb="ZN    ZN G 501 " - pdb=" ND1 HIS G 182 "


  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2012

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 5 sheets defined
      55.0% alpha, 4.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'G' and resid 71 through 74
    Processing helix  chain 'G' and resid 100 through 117
      removed outlier: 3.604A  pdb=" N   LYS G 105 " --> pdb=" O   ARG G 101 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 138 through 143
      removed outlier: 3.754A  pdb=" N   GLU G 142 " --> pdb=" O   SER G 138 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 155 through 168
      removed outlier: 3.592A  pdb=" N   GLY G 159 " --> pdb=" O   ARG G 155 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ARG G 163 " --> pdb=" O   GLY G 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 182 through 186
      removed outlier: 4.083A  pdb=" N   ALA D 186 " --> pdb=" O   ALA D 182 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 182 through 186'
    Processing helix  chain 'D' and resid 189 through 210
    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 363
    Processing helix  chain 'D' and resid 372 through 388
      removed outlier: 3.505A  pdb=" N   SER D 376 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   HIS D 388 " --> pdb=" O   THR D 384 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 423 through 430
    Processing helix  chain 'D' and resid 463 through 472
      removed outlier: 4.479A  pdb=" N   ILE D 467 " --> pdb=" O   SER D 463 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 492 through 503
      removed outlier: 4.366A  pdb=" N   GLN D 497 " --> pdb=" O   HIS D 493 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   ASP D 498 " --> pdb=" O   SER D 494 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 504 through 522
      removed outlier: 3.518A  pdb=" N   ALA D 508 " --> pdb=" O   THR D 504 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 524 through 548
    Processing helix  chain 'D' and resid 558 through 587
      removed outlier: 3.834A  pdb=" N   LEU D 563 " --> pdb=" O   ASN D 559 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ILE D 564 " --> pdb=" O   LEU D 560 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   ILE D 565 " --> pdb=" O   THR D 561 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   VAL D 576 " --> pdb=" O   ASN D 572 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LEU D 577 " --> pdb=" O   ASN D 573 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ASP D 587 " --> pdb=" O   TYR D 583 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 592 through 623
      removed outlier: 5.132A  pdb=" N   LEU D 606 " --> pdb=" O   GLN D 602 " (cutoff:3.500A)
      removed outlier: 5.185A  pdb=" N   SER D 607 " --> pdb=" O   HIS D 603 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   THR D 615 " --> pdb=" O   THR D 611 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 627 through 659
      removed outlier: 4.537A  pdb=" N   PHE D 633 " --> pdb=" O   ALA D 629 " (cutoff:3.500A)
      Proline residue:  D 653  - end of helix
    Processing helix  chain 'D' and resid 688 through 718
      removed outlier: 5.084A  pdb=" N   LEU D 710 " --> pdb=" O   PHE D 706 " (cutoff:3.500A)
      Proline residue:  D 711  - end of helix
    Processing helix  chain 'D' and resid 719 through 738
    Processing helix  chain 'D' and resid 748 through 752
      removed outlier: 3.676A  pdb=" N   PHE D 752 " --> pdb=" O   LEU D 749 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 759 through 765
      removed outlier: 4.261A  pdb=" N   ASP D 765 " --> pdb=" O   PHE D 761 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 768 through 771
    Processing helix  chain 'D' and resid 772 through 779
    Processing helix  chain 'D' and resid 820 through 835
    Processing helix  chain 'D' and resid 851 through 860
      removed outlier: 4.006A  pdb=" N   THR D 855 " --> pdb=" O   CYS D 851 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 883 through 902
      removed outlier: 4.347A  pdb=" N   LYS D 891 " --> pdb=" O   GLU D 887 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ARG D 892 " --> pdb=" O   LEU D 888 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 936 through 953
      removed outlier: 3.965A  pdb=" N   MET D 940 " --> pdb=" O   ALA D 936 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   SER D 953 " --> pdb=" O   SER D 949 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 971 through 1004
    Processing helix  chain 'D' and resid 1005 through 1030
    Processing helix  chain 'D' and resid 1036 through 1059
      removed outlier: 4.479A  pdb=" N   VAL D1040 " --> pdb=" O   VAL D1036 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   THR D1041 " --> pdb=" O   LEU D1037 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ILE D1042 " --> pdb=" O   GLU D1038 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   SER D1043 " --> pdb=" O   SER D1039 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   VAL D1046 " --> pdb=" O   ILE D1042 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLY D1047 " --> pdb=" O   SER D1043 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ASN D1051 " --> pdb=" O   GLY D1047 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   PHE D1052 " --> pdb=" O   LEU D1048 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ALA D1053 " --> pdb=" O   SER D1049 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   HIS D1055 " --> pdb=" O   ASN D1051 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1068 through 1098
      removed outlier: 3.520A  pdb=" N   VAL D1072 " --> pdb=" O   ARG D1068 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILE D1073 " --> pdb=" O   GLU D1069 " (cutoff:3.500A)
      removed outlier: 5.569A  pdb=" N   SER D1081 " --> pdb=" O   SER D1077 " (cutoff:3.500A)
      removed outlier: 5.564A  pdb=" N   ALA D1082 " --> pdb=" O   ARG D1078 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   THR D1090 " --> pdb=" O   ALA D1086 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1102 through 1133
      removed outlier: 3.792A  pdb=" N   THR D1106 " --> pdb=" O   VAL D1102 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   CYS D1131 " --> pdb=" O   PHE D1127 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'G' and resid 76 through 78
    Processing sheet with id=AA2, first strand: chain 'G' and resid 85 through 86
      removed outlier: 7.775A  pdb=" N   ILE G  85 " --> pdb=" O   VAL G 124 " (cutoff:3.500A)
      removed outlier: 8.935A  pdb=" N   GLU G 126 " --> pdb=" O   ILE G  85 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   ASP G 147 " --> pdb=" O   THR G 125 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 451 through 459
      removed outlier: 4.668A  pdb=" N   SER D 301 " --> pdb=" O   SER D 456 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   ARG D 302 " --> pdb=" O   ILE D 487 " (cutoff:3.500A)
      removed outlier: 5.473A  pdb=" N   ILE D 487 " --> pdb=" O   ARG D 302 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   VAL D 304 " --> pdb=" O   THR D 485 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 788 through 789
    Processing sheet with id=AA5, first strand: chain 'D' and resid 913 through 914
      removed outlier: 6.290A  pdb=" N   ARG D 913 " --> pdb=" O   ARG D 921 " (cutoff:3.500A)

    425 hydrogen bonds defined for protein.
    1254 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: 1.19

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1356
        1.32 -     1.44: 2434
        1.44 -     1.57: 4908
        1.57 -     1.69: 0
        1.69 -     1.81: 103
  Bond restraints: 8801
  Sorted by residual:
  bond pdb=" CB  TRP D 966 "
       pdb=" CG  TRP D 966 "
    ideal  model  delta    sigma   weight residual
    1.498  1.414  0.084 3.10e-02 1.04e+03 7.31e+00
  bond pdb=" C   MET D 785 "
       pdb=" N   PRO D 786 "
    ideal  model  delta    sigma   weight residual
    1.333  1.307  0.026 1.20e-02 6.94e+03 4.85e+00
  bond pdb=" C   SER D 758 "
       pdb=" N   HIS D 759 "
    ideal  model  delta    sigma   weight residual
    1.331  1.287  0.044 2.07e-02 2.33e+03 4.57e+00
  bond pdb=" CG  ASN D 476 "
       pdb=" ND2 ASN D 476 "
    ideal  model  delta    sigma   weight residual
    1.328  1.369 -0.041 2.10e-02 2.27e+03 3.90e+00
  bond pdb=" C   LEU D 749 "
       pdb=" N   SER D 750 "
    ideal  model  delta    sigma   weight residual
    1.331  1.301  0.031 1.62e-02 3.81e+03 3.57e+00
  ... (remaining 8796 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 11391
        1.63 -     3.26: 511
        3.26 -     4.88: 75
        4.88 -     6.51: 19
        6.51 -     8.14: 9
  Bond angle restraints: 12005
  Sorted by residual:
  angle pdb=" N   PHE D 255 "
        pdb=" CA  PHE D 255 "
        pdb=" C   PHE D 255 "
      ideal   model   delta    sigma   weight residual
     108.19  116.33   -8.14 1.29e+00 6.01e-01 3.98e+01
  angle pdb=" N   PRO D 254 "
        pdb=" CA  PRO D 254 "
        pdb=" C   PRO D 254 "
      ideal   model   delta    sigma   weight residual
     112.47  120.58   -8.11 2.06e+00 2.36e-01 1.55e+01
  angle pdb=" C   PRO D 254 "
        pdb=" N   PHE D 255 "
        pdb=" CA  PHE D 255 "
      ideal   model   delta    sigma   weight residual
     122.08  115.53    6.55 1.84e+00 2.95e-01 1.27e+01
  angle pdb=" C   LEU D 749 "
        pdb=" N   SER D 750 "
        pdb=" CA  SER D 750 "
      ideal   model   delta    sigma   weight residual
     122.31  115.38    6.93 2.00e+00 2.50e-01 1.20e+01
  angle pdb=" C   PHE D 554 "
        pdb=" N   PHE D 555 "
        pdb=" CA  PHE D 555 "
      ideal   model   delta    sigma   weight residual
     121.80  113.75    8.05 2.44e+00 1.68e-01 1.09e+01
  ... (remaining 12000 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.97: 4962
       16.97 -    33.95: 491
       33.95 -    50.92: 77
       50.92 -    67.90: 23
       67.90 -    84.87: 5
  Dihedral angle restraints: 5558
    sinusoidal: 2452
      harmonic: 3106
  Sorted by residual:
  dihedral pdb=" CA  SER D 290 "
           pdb=" C   SER D 290 "
           pdb=" N   PHE D 291 "
           pdb=" CA  PHE D 291 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.86  -24.14     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" CA  TYR D 253 "
           pdb=" C   TYR D 253 "
           pdb=" N   PRO D 254 "
           pdb=" CA  PRO D 254 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.84  -23.16     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  PHE D1127 "
           pdb=" C   PHE D1127 "
           pdb=" N   GLN D1128 "
           pdb=" CA  GLN D1128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.63   22.37     0      5.00e+00 4.00e-02 2.00e+01
  ... (remaining 5555 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.132: 1367
       0.132 -    0.264: 14
       0.264 -    0.396: 0
       0.396 -    0.529: 1
       0.529 -    0.661: 1
  Chirality restraints: 1383
  Sorted by residual:
  chirality pdb=" C1  NAG D1610 "
            pdb=" ND2 ASN D 917 "
            pdb=" C2  NAG D1610 "
            pdb=" O5  NAG D1610 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.74   -0.66 2.00e-01 2.50e+01 1.09e+01
  chirality pdb=" C1  NAG D1611 "
            pdb=" ND2 ASN D 836 "
            pdb=" C2  NAG D1611 "
            pdb=" O5  NAG D1611 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.93   -0.47 2.00e-01 2.50e+01 5.45e+00
  chirality pdb=" CA  PRO D 254 "
            pdb=" N   PRO D 254 "
            pdb=" C   PRO D 254 "
            pdb=" CB  PRO D 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 1380 not shown)

  Planarity restraints: 1468
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN D 883 "    0.012 2.00e-02 2.50e+03   2.37e-02 5.61e+00
        pdb=" C   GLN D 883 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   GLN D 883 "    0.015 2.00e-02 2.50e+03
        pdb=" N   GLU D 884 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D 456 "   -0.031 5.00e-02 4.00e+02   4.65e-02 3.46e+00
        pdb=" N   PRO D 457 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO D 457 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO D 457 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 291 "    0.004 2.00e-02 2.50e+03   1.26e-02 2.79e+00
        pdb=" CG  PHE D 291 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 291 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 291 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 291 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 291 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 291 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1465 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 166
        2.63 -     3.19: 9307
        3.19 -     3.76: 13529
        3.76 -     4.33: 17745
        4.33 -     4.90: 26852
  Nonbonded interactions: 67599
  Sorted by model distance:
  nonbonded pdb=" O   PRO D 350 "
            pdb=" ND2 ASN D 356 "
     model   vdw
     2.056 3.120
  nonbonded pdb=" OD1 ASP G 147 "
            pdb="ZN    ZN G 501 "
     model   vdw
     2.074 2.230
  nonbonded pdb=" OE1 GLU G 176 "
            pdb="ZN    ZN G 501 "
     model   vdw
     2.094 2.230
  nonbonded pdb=" O   ALA D1059 "
            pdb=" OG  SER D1075 "
     model   vdw
     2.105 3.040
  nonbonded pdb=" O   GLU G  53 "
            pdb=" OG  SER G  59 "
     model   vdw
     2.106 3.040
  ... (remaining 67594 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.080
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
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      :  0.007   0.242   8806  Z= 0.309
  Angle     :  0.839  12.751  12014  Z= 0.443
  Chirality :  0.051   0.661   1383
  Planarity :  0.005   0.047   1465
  Dihedral  : 13.723  84.873   3546
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 20.89
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 11.66 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  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: -4.32 (0.21), residues: 1046
  helix: -2.23 (0.18), residues: 534
  sheet: -3.19 (0.67), residues: 52
  loop : -3.60 (0.26), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D 329 
 TYR   0.017   0.002   TYR D1060 
 PHE   0.024   0.002   PHE D 967 
 TRP   0.022   0.002   TRP D1120 
 HIS   0.005   0.001   HIS D 778 

Details of bonding type rmsd
  covalent geometry    : bond        0.00608 ( 8801)
  covalent geometry    : angle       0.82031 (12005)
  hydrogen bonds       : bond        0.13384 (  425)
  hydrogen bonds       : angle       6.73104 ( 1254)
  metal coordination   : bond        0.21484 (    2)
  link_NAG-ASN         : bond        0.02200 (    3)
  link_NAG-ASN         : angle       6.50268 (    9)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   81 ASN cc_start: 0.8670 (t0) cc_final: 0.8455 (t0)
REVERT: G   98 MET cc_start: 0.8708 (ptm) cc_final: 0.8233 (ptp)
REVERT: G  102 CYS cc_start: 0.9143 (t) cc_final: 0.8353 (t)
REVERT: G  141 TYR cc_start: 0.8299 (m-10) cc_final: 0.7834 (m-10)
REVERT: G  154 ASP cc_start: 0.8478 (m-30) cc_final: 0.8256 (m-30)
REVERT: G  175 TYR cc_start: 0.7553 (t80) cc_final: 0.6516 (t80)
REVERT: G  186 LYS cc_start: 0.8525 (ttmt) cc_final: 0.8247 (ttmt)
REVERT: G  188 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8219 (mm-30)
REVERT: D  343 THR cc_start: 0.7712 (t) cc_final: 0.7454 (m)
REVERT: D  460 LYS cc_start: 0.9241 (pttm) cc_final: 0.8865 (pttm)
REVERT: D  502 MET cc_start: 0.8768 (tmm) cc_final: 0.8526 (tmm)
REVERT: D  530 MET cc_start: 0.8998 (tpp) cc_final: 0.8459 (tpp)
REVERT: D  595 GLU cc_start: 0.8961 (mp0) cc_final: 0.8512 (mp0)
REVERT: D  641 ILE cc_start: 0.9617 (tp) cc_final: 0.9379 (tp)
REVERT: D  753 GLN cc_start: 0.8912 (pt0) cc_final: 0.8634 (pt0)
REVERT: D  796 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8031 (tm-30)
REVERT: D  896 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8030 (mt-10)
REVERT: D  926 GLU cc_start: 0.8271 (pm20) cc_final: 0.8006 (pm20)
REVERT: D 1011 TYR cc_start: 0.9243 (m-80) cc_final: 0.8795 (m-80)
REVERT: D 1097 MET cc_start: 0.9178 (ttm) cc_final: 0.8868 (tmm)
REVERT: D 1126 PHE cc_start: 0.8840 (t80) cc_final: 0.8417 (t80)
REVERT: D 1128 GLN cc_start: 0.9315 (mp10) cc_final: 0.9031 (mp10)
REVERT: D 1129 CYS cc_start: 0.9471 (t) cc_final: 0.9000 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 261
  average time/residue: 0.0853
  time to fit residues: 31.3517
Evaluate side-chains
  202 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:   30.0000
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    0.0060
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    6.9990
   chunk 38 optimal weight:    0.0870
   chunk 61 optimal weight:    6.9990
   overall best weight:    2.3978

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

Flipped N/Q/H residues before XYZ refinement:
D 252 ASN
D 327 ASN
D 356 ASN
D 362 ASN
D 363 ASN
** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 622 ASN
D 659 HIS
** D 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 842 GLN
D 964 ASN
D 977 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.112794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.087031 restraints weight = 22958.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.088525 restraints weight = 12483.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.089562 restraints weight = 8498.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.089902 restraints weight = 7164.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.090120 restraints weight = 6501.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.1741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8806  Z= 0.170
  Angle     :  0.712   9.486  12014  Z= 0.366
  Chirality :  0.043   0.259   1383
  Planarity :  0.005   0.042   1465
  Dihedral  :  7.400  54.323   1710
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.46 %
    Favored  : 90.54 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  6.86 %
    Favored  : 92.91 %
  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: -2.57 (0.25), residues: 1046
  helix: -0.56 (0.21), residues: 539
  sheet: -3.11 (0.64), residues: 56
  loop : -2.99 (0.28), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  61 
 TYR   0.014   0.001   TYR G  80 
 PHE   0.025   0.002   PHE D 291 
 TRP   0.018   0.001   TRP D1120 
 HIS   0.003   0.001   HIS D 692 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 8801)
  covalent geometry    : angle       0.70628 (12005)
  hydrogen bonds       : bond        0.04850 (  425)
  hydrogen bonds       : angle       5.31411 ( 1254)
  metal coordination   : bond        0.00434 (    2)
  link_NAG-ASN         : bond        0.00621 (    3)
  link_NAG-ASN         : angle       3.46782 (    9)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 243
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   98 MET cc_start: 0.8452 (ptm) cc_final: 0.8200 (ptp)
REVERT: G  106 LEU cc_start: 0.9451 (tt) cc_final: 0.9177 (pp)
REVERT: G  141 TYR cc_start: 0.8278 (m-10) cc_final: 0.7896 (m-10)
REVERT: G  154 ASP cc_start: 0.8381 (m-30) cc_final: 0.8164 (m-30)
REVERT: G  175 TYR cc_start: 0.7358 (t80) cc_final: 0.7151 (t80)
REVERT: G  184 SER cc_start: 0.8628 (p) cc_final: 0.7886 (p)
REVERT: G  186 LYS cc_start: 0.8466 (ttmt) cc_final: 0.8219 (ttmt)
REVERT: D  373 ARG cc_start: 0.9346 (mmt-90) cc_final: 0.8786 (mmp80)
REVERT: D  453 MET cc_start: 0.9054 (tmm) cc_final: 0.8011 (tmm)
REVERT: D  454 LEU cc_start: 0.8515 (tp) cc_final: 0.7835 (tp)
REVERT: D  460 LYS cc_start: 0.9232 (pttp) cc_final: 0.8984 (pttm)
REVERT: D  502 MET cc_start: 0.8529 (tmm) cc_final: 0.8093 (tpp)
REVERT: D  518 MET cc_start: 0.8808 (mtm) cc_final: 0.8567 (mtm)
REVERT: D  530 MET cc_start: 0.9122 (tpp) cc_final: 0.8415 (tpp)
REVERT: D  554 PHE cc_start: 0.8547 (t80) cc_final: 0.8227 (t80)
REVERT: D  575 PHE cc_start: 0.8885 (m-10) cc_final: 0.8112 (m-80)
REVERT: D  579 ASP cc_start: 0.8879 (m-30) cc_final: 0.8635 (m-30)
REVERT: D  753 GLN cc_start: 0.8785 (pt0) cc_final: 0.8504 (pt0)
REVERT: D  796 GLU cc_start: 0.8969 (mt-10) cc_final: 0.7970 (tm-30)
REVERT: D  926 GLU cc_start: 0.8054 (pm20) cc_final: 0.7696 (pm20)
REVERT: D  996 PHE cc_start: 0.8712 (t80) cc_final: 0.8478 (t80)
REVERT: D 1011 TYR cc_start: 0.9002 (m-80) cc_final: 0.8627 (m-80)
REVERT: D 1055 HIS cc_start: 0.9433 (m-70) cc_final: 0.9188 (m-70)
REVERT: D 1085 MET cc_start: 0.8877 (tpp) cc_final: 0.8470 (tpp)
REVERT: D 1126 PHE cc_start: 0.8727 (t80) cc_final: 0.8313 (t80)
  outliers start: 2
  outliers final: 1
  residues processed: 245
  average time/residue: 0.0783
  time to fit residues: 27.6677
Evaluate side-chains
  209 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 208
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 96 optimal weight:    2.9990
   chunk 24 optimal weight:    7.9990
   chunk 83 optimal weight:    2.9990
   chunk 94 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 11 optimal weight:   30.0000
   chunk 15 optimal weight:    9.9990
   chunk 53 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 63 optimal weight:    9.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
D 362 ASN
D 572 ASN
D 842 GLN
D1055 HIS
D1107 GLN
D1128 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.112627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.087069 restraints weight = 22867.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.088530 restraints weight = 12581.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.089444 restraints weight = 8725.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.089916 restraints weight = 7276.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.090175 restraints weight = 6538.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8806  Z= 0.187
  Angle     :  0.710   9.435  12014  Z= 0.362
  Chirality :  0.043   0.243   1383
  Planarity :  0.004   0.044   1465
  Dihedral  :  7.296  55.029   1710
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 14.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.89 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  6.19 %
    Favored  : 93.59 %
  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: -1.98 (0.26), residues: 1046
  helix:  0.05 (0.22), residues: 535
  sheet: -3.38 (0.59), residues: 59
  loop : -2.77 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG G  61 
 TYR   0.014   0.001   TYR D 468 
 PHE   0.020   0.002   PHE D 533 
 TRP   0.013   0.001   TRP D 651 
 HIS   0.003   0.001   HIS D 778 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 8801)
  covalent geometry    : angle       0.70286 (12005)
  hydrogen bonds       : bond        0.04680 (  425)
  hydrogen bonds       : angle       5.14662 ( 1254)
  metal coordination   : bond        0.00174 (    2)
  link_NAG-ASN         : bond        0.00714 (    3)
  link_NAG-ASN         : angle       3.69005 (    9)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 251
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   80 TYR cc_start: 0.9230 (m-10) cc_final: 0.8847 (m-80)
REVERT: G  141 TYR cc_start: 0.8329 (m-10) cc_final: 0.7909 (m-10)
REVERT: G  150 THR cc_start: 0.7724 (t) cc_final: 0.7487 (t)
REVERT: G  157 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7908 (tptt)
REVERT: G  184 SER cc_start: 0.8749 (p) cc_final: 0.8472 (p)
REVERT: G  186 LYS cc_start: 0.8459 (ttmt) cc_final: 0.8117 (tmtt)
REVERT: D  453 MET cc_start: 0.9099 (tmm) cc_final: 0.8180 (tmm)
REVERT: D  454 LEU cc_start: 0.8576 (tp) cc_final: 0.7937 (tp)
REVERT: D  460 LYS cc_start: 0.9150 (pttp) cc_final: 0.8849 (pttm)
REVERT: D  465 MET cc_start: 0.8711 (ttt) cc_final: 0.8484 (tpp)
REVERT: D  467 ILE cc_start: 0.9302 (mp) cc_final: 0.9008 (mp)
REVERT: D  502 MET cc_start: 0.8397 (tmm) cc_final: 0.8035 (tpp)
REVERT: D  518 MET cc_start: 0.8847 (mtm) cc_final: 0.8602 (mtm)
REVERT: D  530 MET cc_start: 0.9103 (tpp) cc_final: 0.8227 (tpp)
REVERT: D  554 PHE cc_start: 0.8333 (t80) cc_final: 0.8069 (t80)
REVERT: D  575 PHE cc_start: 0.8881 (m-10) cc_final: 0.8155 (m-80)
REVERT: D  579 ASP cc_start: 0.8813 (m-30) cc_final: 0.8591 (m-30)
REVERT: D  722 LEU cc_start: 0.9175 (tt) cc_final: 0.8925 (tt)
REVERT: D  753 GLN cc_start: 0.8707 (pt0) cc_final: 0.8403 (pt0)
REVERT: D  796 GLU cc_start: 0.8971 (mt-10) cc_final: 0.7965 (tm-30)
REVERT: D  805 LYS cc_start: 0.9176 (pttm) cc_final: 0.8930 (pttm)
REVERT: D  926 GLU cc_start: 0.8064 (pm20) cc_final: 0.7701 (pm20)
REVERT: D  966 TRP cc_start: 0.7832 (m100) cc_final: 0.7038 (m100)
REVERT: D 1011 TYR cc_start: 0.8930 (m-10) cc_final: 0.8670 (m-80)
REVERT: D 1085 MET cc_start: 0.8952 (tpp) cc_final: 0.8596 (tpp)
REVERT: D 1126 PHE cc_start: 0.8781 (t80) cc_final: 0.8352 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 252
  average time/residue: 0.0829
  time to fit residues: 29.7332
Evaluate side-chains
  211 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 78 optimal weight:    9.9990
   chunk 41 optimal weight:    9.9990
   chunk 61 optimal weight:    9.9990
   chunk 102 optimal weight:    3.9990
   chunk 17 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   chunk 84 optimal weight:   10.0000
   chunk 72 optimal weight:    9.9990
   chunk 24 optimal weight:    0.2980
   chunk 63 optimal weight:    8.9990
   overall best weight:    3.6588

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

Flipped N/Q/H residues before XYZ refinement:
D 362 ASN
D 363 ASN
** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 842 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.112962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.087193 restraints weight = 22998.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.088315 restraints weight = 12541.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.089217 restraints weight = 8833.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.089638 restraints weight = 7381.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.089925 restraints weight = 6680.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8806  Z= 0.201
  Angle     :  0.716   9.891  12014  Z= 0.365
  Chirality :  0.043   0.230   1383
  Planarity :  0.005   0.047   1465
  Dihedral  :  7.346  54.768   1710
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  4.95 %
    Favored  : 94.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.74 (0.26), residues: 1046
  helix:  0.23 (0.22), residues: 534
  sheet: -3.14 (0.66), residues: 51
  loop : -2.65 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG G  61 
 TYR   0.018   0.002   TYR D 499 
 PHE   0.020   0.002   PHE D 455 
 TRP   0.016   0.001   TRP D 651 
 HIS   0.004   0.001   HIS D 941 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 8801)
  covalent geometry    : angle       0.70926 (12005)
  hydrogen bonds       : bond        0.04649 (  425)
  hydrogen bonds       : angle       5.08278 ( 1254)
  metal coordination   : bond        0.00310 (    2)
  link_NAG-ASN         : bond        0.00769 (    3)
  link_NAG-ASN         : angle       3.72493 (    9)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 242
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   80 TYR cc_start: 0.9289 (m-10) cc_final: 0.8812 (m-80)
REVERT: G  141 TYR cc_start: 0.8205 (m-10) cc_final: 0.7829 (m-10)
REVERT: G  150 THR cc_start: 0.7914 (t) cc_final: 0.7619 (t)
REVERT: G  175 TYR cc_start: 0.7351 (t80) cc_final: 0.7043 (t80)
REVERT: G  186 LYS cc_start: 0.8364 (ttmt) cc_final: 0.8085 (tmtt)
REVERT: D  195 MET cc_start: 0.8442 (mmt) cc_final: 0.8229 (mmp)
REVERT: D  460 LYS cc_start: 0.9158 (pttp) cc_final: 0.8835 (pttm)
REVERT: D  502 MET cc_start: 0.8259 (tmm) cc_final: 0.7857 (tmm)
REVERT: D  530 MET cc_start: 0.9069 (tpp) cc_final: 0.8243 (tpp)
REVERT: D  554 PHE cc_start: 0.8421 (t80) cc_final: 0.8087 (t80)
REVERT: D  575 PHE cc_start: 0.8903 (m-10) cc_final: 0.8189 (m-80)
REVERT: D  579 ASP cc_start: 0.8749 (m-30) cc_final: 0.8532 (m-30)
REVERT: D  595 GLU cc_start: 0.9040 (mp0) cc_final: 0.8534 (mp0)
REVERT: D  728 LEU cc_start: 0.9059 (mm) cc_final: 0.8859 (mt)
REVERT: D  753 GLN cc_start: 0.8670 (pt0) cc_final: 0.8363 (pt0)
REVERT: D  796 GLU cc_start: 0.8969 (mt-10) cc_final: 0.7944 (tm-30)
REVERT: D  805 LYS cc_start: 0.9161 (pttm) cc_final: 0.8842 (pttm)
REVERT: D  926 GLU cc_start: 0.8033 (pm20) cc_final: 0.7662 (pm20)
REVERT: D 1011 TYR cc_start: 0.9005 (m-10) cc_final: 0.8630 (m-80)
REVERT: D 1085 MET cc_start: 0.8960 (tpp) cc_final: 0.8681 (tpp)
REVERT: D 1126 PHE cc_start: 0.8772 (t80) cc_final: 0.8389 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 242
  average time/residue: 0.0869
  time to fit residues: 29.6746
Evaluate side-chains
  203 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   chunk 17 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 71 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9980
   chunk 80 optimal weight:    6.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
D 362 ASN
D 363 ASN
D 572 ASN
D1128 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.113537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.085726 restraints weight = 22994.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.088433 restraints weight = 12783.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.090227 restraints weight = 8692.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.091347 restraints weight = 6744.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.092075 restraints weight = 5737.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.2755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8806  Z= 0.176
  Angle     :  0.707  11.070  12014  Z= 0.359
  Chirality :  0.042   0.235   1383
  Planarity :  0.004   0.045   1465
  Dihedral  :  7.234  54.667   1710
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.56 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  4.27 %
    Favored  : 95.50 %
  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: -1.57 (0.26), residues: 1046
  helix:  0.33 (0.23), residues: 537
  sheet: -3.11 (0.64), residues: 51
  loop : -2.53 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  61 
 TYR   0.010   0.001   TYR D 468 
 PHE   0.033   0.002   PHE D 996 
 TRP   0.015   0.001   TRP D 651 
 HIS   0.003   0.001   HIS D 778 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 8801)
  covalent geometry    : angle       0.69880 (12005)
  hydrogen bonds       : bond        0.04509 (  425)
  hydrogen bonds       : angle       5.00314 ( 1254)
  metal coordination   : bond        0.00306 (    2)
  link_NAG-ASN         : bond        0.00762 (    3)
  link_NAG-ASN         : angle       4.02527 (    9)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 249
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   45 LYS cc_start: 0.8526 (mmtm) cc_final: 0.8289 (mmmt)
REVERT: G   65 LYS cc_start: 0.8470 (mmmt) cc_final: 0.8111 (mmmt)
REVERT: G   80 TYR cc_start: 0.9271 (m-10) cc_final: 0.9010 (m-10)
REVERT: G   98 MET cc_start: 0.8991 (ptt) cc_final: 0.8604 (ptt)
REVERT: G  102 CYS cc_start: 0.8987 (t) cc_final: 0.8010 (t)
REVERT: G  141 TYR cc_start: 0.8243 (m-10) cc_final: 0.7664 (m-10)
REVERT: G  150 THR cc_start: 0.7925 (t) cc_final: 0.7604 (t)
REVERT: G  175 TYR cc_start: 0.7752 (t80) cc_final: 0.7169 (t80)
REVERT: D  218 ASP cc_start: 0.8577 (m-30) cc_final: 0.8347 (m-30)
REVERT: D  426 GLN cc_start: 0.9527 (mm-40) cc_final: 0.9262 (mp10)
REVERT: D  460 LYS cc_start: 0.9158 (pttp) cc_final: 0.8856 (pttm)
REVERT: D  502 MET cc_start: 0.8205 (tmm) cc_final: 0.7744 (tpp)
REVERT: D  530 MET cc_start: 0.9121 (tpp) cc_final: 0.8284 (tpp)
REVERT: D  554 PHE cc_start: 0.8354 (t80) cc_final: 0.7992 (t80)
REVERT: D  575 PHE cc_start: 0.8874 (m-10) cc_final: 0.8193 (m-80)
REVERT: D  595 GLU cc_start: 0.9018 (mp0) cc_final: 0.8428 (mp0)
REVERT: D  722 LEU cc_start: 0.9169 (tt) cc_final: 0.8941 (tt)
REVERT: D  796 GLU cc_start: 0.8891 (mt-10) cc_final: 0.7966 (tm-30)
REVERT: D  805 LYS cc_start: 0.9112 (pttm) cc_final: 0.8816 (pttm)
REVERT: D  926 GLU cc_start: 0.8023 (pm20) cc_final: 0.7657 (pm20)
REVERT: D  966 TRP cc_start: 0.7898 (m100) cc_final: 0.7145 (m100)
REVERT: D 1011 TYR cc_start: 0.9020 (m-10) cc_final: 0.8701 (m-80)
REVERT: D 1097 MET cc_start: 0.9079 (ppp) cc_final: 0.8872 (ppp)
REVERT: D 1126 PHE cc_start: 0.8789 (t80) cc_final: 0.8435 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 250
  average time/residue: 0.0758
  time to fit residues: 27.3055
Evaluate side-chains
  203 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0770
   chunk 70 optimal weight:    3.9990
   chunk 40 optimal weight:    8.9990
   chunk 29 optimal weight:   20.0000
   chunk 52 optimal weight:    6.9990
   chunk 65 optimal weight:    0.3980
   chunk 49 optimal weight:    4.9990
   chunk 9 optimal weight:   30.0000
   chunk 97 optimal weight:    9.9990
   chunk 63 optimal weight:   10.0000
   overall best weight:    2.6944

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

Flipped N/Q/H residues before XYZ refinement:
D 362 ASN
D 363 ASN
D 572 ASN
** D 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 778 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.114218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.088935 restraints weight = 23025.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.090434 restraints weight = 12076.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.091403 restraints weight = 8524.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.091882 restraints weight = 7031.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.092113 restraints weight = 6452.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.3062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8806  Z= 0.168
  Angle     :  0.708  10.752  12014  Z= 0.359
  Chirality :  0.043   0.238   1383
  Planarity :  0.004   0.044   1465
  Dihedral  :  7.203  55.169   1710
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  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: -1.49 (0.26), residues: 1046
  helix:  0.43 (0.23), residues: 530
  sheet: -3.09 (0.64), residues: 51
  loop : -2.49 (0.29), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 331 
 TYR   0.024   0.001   TYR D 499 
 PHE   0.029   0.002   PHE D 996 
 TRP   0.018   0.001   TRP D1120 
 HIS   0.003   0.001   HIS D 778 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 8801)
  covalent geometry    : angle       0.70087 (12005)
  hydrogen bonds       : bond        0.04513 (  425)
  hydrogen bonds       : angle       4.94457 ( 1254)
  metal coordination   : bond        0.00273 (    2)
  link_NAG-ASN         : bond        0.00766 (    3)
  link_NAG-ASN         : angle       3.76500 (    9)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   80 TYR cc_start: 0.9229 (m-10) cc_final: 0.8894 (m-10)
REVERT: G   98 MET cc_start: 0.9006 (ptt) cc_final: 0.8648 (ptt)
REVERT: G  102 CYS cc_start: 0.8989 (t) cc_final: 0.7873 (t)
REVERT: G  141 TYR cc_start: 0.8248 (m-10) cc_final: 0.7940 (m-10)
REVERT: G  150 THR cc_start: 0.8041 (t) cc_final: 0.7751 (t)
REVERT: G  175 TYR cc_start: 0.7672 (t80) cc_final: 0.7231 (t80)
REVERT: D  218 ASP cc_start: 0.8582 (m-30) cc_final: 0.8328 (m-30)
REVERT: D  460 LYS cc_start: 0.9139 (pttp) cc_final: 0.8916 (pttm)
REVERT: D  502 MET cc_start: 0.8114 (tmm) cc_final: 0.7646 (tpp)
REVERT: D  530 MET cc_start: 0.9081 (tpp) cc_final: 0.8457 (tpp)
REVERT: D  554 PHE cc_start: 0.8351 (t80) cc_final: 0.7992 (t80)
REVERT: D  575 PHE cc_start: 0.8878 (m-10) cc_final: 0.8584 (m-10)
REVERT: D  722 LEU cc_start: 0.9192 (tt) cc_final: 0.8924 (tt)
REVERT: D  796 GLU cc_start: 0.8820 (mt-10) cc_final: 0.7927 (tm-30)
REVERT: D  926 GLU cc_start: 0.8002 (pm20) cc_final: 0.7672 (pm20)
REVERT: D 1011 TYR cc_start: 0.8863 (m-10) cc_final: 0.8569 (m-80)
REVERT: D 1126 PHE cc_start: 0.8824 (t80) cc_final: 0.8320 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 245
  average time/residue: 0.0769
  time to fit residues: 27.1999
Evaluate side-chains
  204 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 5 optimal weight:   20.0000
   chunk 21 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 6 optimal weight:    8.9990
   chunk 76 optimal weight:    6.9990
   chunk 55 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 64 optimal weight:    5.9990
   chunk 29 optimal weight:   20.0000
   chunk 81 optimal weight:    8.9990
   overall best weight:    3.9786

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

Flipped N/Q/H residues before XYZ refinement:
D 362 ASN
D 363 ASN
D 572 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.112339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.084190 restraints weight = 23382.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.086880 restraints weight = 13105.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.088630 restraints weight = 8960.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.089703 restraints weight = 6987.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.090440 restraints weight = 5987.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.3060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   8806  Z= 0.213
  Angle     :  0.752  10.217  12014  Z= 0.382
  Chirality :  0.043   0.243   1383
  Planarity :  0.004   0.045   1465
  Dihedral  :  7.349  56.507   1710
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 15.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.04 %
    Favored  : 89.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  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: -1.55 (0.26), residues: 1046
  helix:  0.32 (0.22), residues: 531
  sheet: -3.16 (0.64), residues: 51
  loop : -2.43 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 331 
 TYR   0.012   0.001   TYR D 499 
 PHE   0.018   0.002   PHE D1122 
 TRP   0.016   0.001   TRP D 651 
 HIS   0.005   0.001   HIS D 692 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 8801)
  covalent geometry    : angle       0.74533 (12005)
  hydrogen bonds       : bond        0.04670 (  425)
  hydrogen bonds       : angle       5.06383 ( 1254)
  metal coordination   : bond        0.00309 (    2)
  link_NAG-ASN         : bond        0.00735 (    3)
  link_NAG-ASN         : angle       3.76699 (    9)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   80 TYR cc_start: 0.9251 (m-10) cc_final: 0.8987 (m-10)
REVERT: G   98 MET cc_start: 0.9024 (ptt) cc_final: 0.8597 (ptt)
REVERT: G  102 CYS cc_start: 0.8945 (t) cc_final: 0.7973 (t)
REVERT: G  141 TYR cc_start: 0.8203 (m-10) cc_final: 0.7859 (m-10)
REVERT: G  150 THR cc_start: 0.7871 (t) cc_final: 0.7520 (t)
REVERT: G  175 TYR cc_start: 0.7458 (t80) cc_final: 0.7195 (t80)
REVERT: D  218 ASP cc_start: 0.8577 (m-30) cc_final: 0.8331 (m-30)
REVERT: D  453 MET cc_start: 0.9103 (tmm) cc_final: 0.8763 (tmm)
REVERT: D  460 LYS cc_start: 0.9157 (pttp) cc_final: 0.8902 (pttm)
REVERT: D  502 MET cc_start: 0.8334 (tmm) cc_final: 0.7887 (tpp)
REVERT: D  530 MET cc_start: 0.9068 (tpp) cc_final: 0.8355 (tpp)
REVERT: D  575 PHE cc_start: 0.8897 (m-10) cc_final: 0.8606 (m-10)
REVERT: D  595 GLU cc_start: 0.9054 (pt0) cc_final: 0.8823 (mp0)
REVERT: D  648 MET cc_start: 0.9266 (tpt) cc_final: 0.8958 (tpp)
REVERT: D  722 LEU cc_start: 0.9157 (tt) cc_final: 0.8955 (tt)
REVERT: D  796 GLU cc_start: 0.8859 (mt-10) cc_final: 0.7949 (tm-30)
REVERT: D  926 GLU cc_start: 0.8073 (pm20) cc_final: 0.7696 (pm20)
REVERT: D 1011 TYR cc_start: 0.8976 (m-10) cc_final: 0.8623 (m-80)
REVERT: D 1126 PHE cc_start: 0.8933 (t80) cc_final: 0.8483 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 233
  average time/residue: 0.0721
  time to fit residues: 24.3027
Evaluate side-chains
  195 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 0 optimal weight:   40.0000
   chunk 63 optimal weight:    3.9990
   chunk 82 optimal weight:    9.9990
   chunk 29 optimal weight:   30.0000
   chunk 20 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 9 optimal weight:   20.0000
   chunk 90 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 37 optimal weight:   10.0000
   chunk 24 optimal weight:    0.0770
   overall best weight:    1.7542

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

Flipped N/Q/H residues before XYZ refinement:
D 362 ASN
D 363 ASN
D 493 HIS
D 572 ASN
D1128 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.115961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.090103 restraints weight = 22719.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.092353 restraints weight = 11217.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.093982 restraints weight = 7861.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.094229 restraints weight = 6666.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.094496 restraints weight = 5843.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.3383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8806  Z= 0.148
  Angle     :  0.719  12.081  12014  Z= 0.361
  Chirality :  0.042   0.239   1383
  Planarity :  0.004   0.063   1465
  Dihedral  :  7.172  56.252   1710
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.35 %
    Favored  : 98.54 %
  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: -1.36 (0.27), residues: 1046
  helix:  0.53 (0.23), residues: 520
  sheet: -3.14 (0.64), residues: 51
  loop : -2.35 (0.29), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 331 
 TYR   0.027   0.001   TYR D 499 
 PHE   0.012   0.002   PHE D1122 
 TRP   0.017   0.001   TRP D 651 
 HIS   0.004   0.001   HIS D 692 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8801)
  covalent geometry    : angle       0.71264 (12005)
  hydrogen bonds       : bond        0.04422 (  425)
  hydrogen bonds       : angle       4.92161 ( 1254)
  metal coordination   : bond        0.00196 (    2)
  link_NAG-ASN         : bond        0.00781 (    3)
  link_NAG-ASN         : angle       3.67378 (    9)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 238
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   80 TYR cc_start: 0.9205 (m-10) cc_final: 0.8859 (m-10)
REVERT: G   98 MET cc_start: 0.9011 (ptt) cc_final: 0.8663 (ptt)
REVERT: G  102 CYS cc_start: 0.8910 (t) cc_final: 0.7872 (t)
REVERT: G  141 TYR cc_start: 0.8163 (m-10) cc_final: 0.7869 (m-10)
REVERT: G  150 THR cc_start: 0.7904 (t) cc_final: 0.7563 (t)
REVERT: G  157 LYS cc_start: 0.8056 (mmmt) cc_final: 0.7804 (mmmm)
REVERT: G  175 TYR cc_start: 0.7340 (t80) cc_final: 0.6923 (t80)
REVERT: D  218 ASP cc_start: 0.8605 (m-30) cc_final: 0.8400 (m-30)
REVERT: D  453 MET cc_start: 0.9111 (tmm) cc_final: 0.8838 (tmm)
REVERT: D  460 LYS cc_start: 0.9147 (pttp) cc_final: 0.8855 (pttm)
REVERT: D  502 MET cc_start: 0.8233 (tmm) cc_final: 0.7798 (tpp)
REVERT: D  530 MET cc_start: 0.9060 (tpp) cc_final: 0.8151 (mmm)
REVERT: D  575 PHE cc_start: 0.8894 (m-10) cc_final: 0.8646 (m-10)
REVERT: D  579 ASP cc_start: 0.8751 (m-30) cc_final: 0.8547 (m-30)
REVERT: D  595 GLU cc_start: 0.9067 (pt0) cc_final: 0.8812 (mp0)
REVERT: D  648 MET cc_start: 0.9273 (tpt) cc_final: 0.9053 (tpp)
REVERT: D  722 LEU cc_start: 0.9104 (tt) cc_final: 0.8872 (tp)
REVERT: D  747 LEU cc_start: 0.9146 (mm) cc_final: 0.8936 (mm)
REVERT: D  796 GLU cc_start: 0.8940 (mt-10) cc_final: 0.7929 (tm-30)
REVERT: D  926 GLU cc_start: 0.7971 (pm20) cc_final: 0.7568 (pm20)
REVERT: D  966 TRP cc_start: 0.7844 (m100) cc_final: 0.7217 (m100)
REVERT: D 1011 TYR cc_start: 0.8987 (m-10) cc_final: 0.8638 (m-80)
REVERT: D 1083 MET cc_start: 0.8260 (mmp) cc_final: 0.8007 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 239
  average time/residue: 0.0811
  time to fit residues: 27.7368
Evaluate side-chains
  205 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 8 optimal weight:   30.0000
   chunk 5 optimal weight:   20.0000
   chunk 60 optimal weight:   20.0000
   chunk 104 optimal weight:   30.0000
   chunk 30 optimal weight:    7.9990
   chunk 89 optimal weight:    0.9980
   chunk 61 optimal weight:    5.9990
   chunk 97 optimal weight:    8.9990
   chunk 3 optimal weight:    6.9990
   chunk 65 optimal weight:    0.0870
   overall best weight:    3.8164

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

Flipped N/Q/H residues before XYZ refinement:
D 362 ASN
D 363 ASN
D 572 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.113212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.087808 restraints weight = 23480.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.089362 restraints weight = 12770.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.090307 restraints weight = 9136.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.090533 restraints weight = 7987.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.090737 restraints weight = 7223.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.3346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   8806  Z= 0.207
  Angle     :  0.770  11.739  12014  Z= 0.391
  Chirality :  0.044   0.249   1383
  Planarity :  0.004   0.048   1465
  Dihedral  :  7.430  58.520   1710
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 15.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.75 %
    Favored  : 90.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  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: -1.44 (0.26), residues: 1046
  helix:  0.36 (0.22), residues: 532
  sheet: -3.17 (0.63), residues: 51
  loop : -2.32 (0.30), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 661 
 TYR   0.019   0.001   TYR D 499 
 PHE   0.031   0.002   PHE G  73 
 TRP   0.016   0.001   TRP D 651 
 HIS   0.003   0.001   HIS D 778 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 8801)
  covalent geometry    : angle       0.76326 (12005)
  hydrogen bonds       : bond        0.04643 (  425)
  hydrogen bonds       : angle       5.04060 ( 1254)
  metal coordination   : bond        0.00278 (    2)
  link_NAG-ASN         : bond        0.00728 (    3)
  link_NAG-ASN         : angle       3.76503 (    9)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   73 PHE cc_start: 0.9310 (t80) cc_final: 0.9107 (t80)
REVERT: G   80 TYR cc_start: 0.9238 (m-10) cc_final: 0.8989 (m-10)
REVERT: G   98 MET cc_start: 0.9035 (ptt) cc_final: 0.8601 (ptt)
REVERT: G  102 CYS cc_start: 0.8912 (t) cc_final: 0.7912 (t)
REVERT: G  141 TYR cc_start: 0.8106 (m-10) cc_final: 0.7796 (m-10)
REVERT: G  150 THR cc_start: 0.7836 (t) cc_final: 0.7437 (t)
REVERT: G  175 TYR cc_start: 0.7382 (t80) cc_final: 0.6909 (t80)
REVERT: D  218 ASP cc_start: 0.8572 (m-30) cc_final: 0.8361 (m-30)
REVERT: D  453 MET cc_start: 0.9133 (tmm) cc_final: 0.8117 (tmm)
REVERT: D  460 LYS cc_start: 0.9182 (pttp) cc_final: 0.8921 (pttm)
REVERT: D  502 MET cc_start: 0.8342 (tmm) cc_final: 0.7875 (tpp)
REVERT: D  530 MET cc_start: 0.9082 (tpp) cc_final: 0.8404 (tpp)
REVERT: D  575 PHE cc_start: 0.8870 (m-10) cc_final: 0.8593 (m-10)
REVERT: D  579 ASP cc_start: 0.8793 (m-30) cc_final: 0.8554 (m-30)
REVERT: D  595 GLU cc_start: 0.9075 (pt0) cc_final: 0.8838 (mp0)
REVERT: D  648 MET cc_start: 0.9250 (tpt) cc_final: 0.9000 (tpp)
REVERT: D  722 LEU cc_start: 0.9158 (tt) cc_final: 0.8943 (tt)
REVERT: D  796 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8047 (tm-30)
REVERT: D  926 GLU cc_start: 0.8045 (pm20) cc_final: 0.7647 (pm20)
REVERT: D 1011 TYR cc_start: 0.9055 (m-10) cc_final: 0.8669 (m-80)
REVERT: D 1083 MET cc_start: 0.8395 (mmp) cc_final: 0.8108 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 236
  average time/residue: 0.0803
  time to fit residues: 27.2750
Evaluate side-chains
  205 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 97 optimal weight:    5.9990
   chunk 76 optimal weight:    0.8980
   chunk 99 optimal weight:    9.9990
   chunk 65 optimal weight:    0.2980
   chunk 90 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 37 optimal weight:   10.0000
   chunk 8 optimal weight:   20.0000
   chunk 85 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
D 362 ASN
D 363 ASN
D 572 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.119372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.093777 restraints weight = 22491.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.095656 restraints weight = 11247.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.096729 restraints weight = 7765.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.097188 restraints weight = 6641.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.097508 restraints weight = 6006.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.3869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8806  Z= 0.141
  Angle     :  0.743  11.823  12014  Z= 0.370
  Chirality :  0.042   0.242   1383
  Planarity :  0.004   0.044   1465
  Dihedral  :  7.086  57.806   1710
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  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: -1.29 (0.26), residues: 1046
  helix:  0.55 (0.23), residues: 527
  sheet: -3.06 (0.63), residues: 49
  loop : -2.33 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D 331 
 TYR   0.017   0.001   TYR D 499 
 PHE   0.027   0.002   PHE G  73 
 TRP   0.015   0.001   TRP D 651 
 HIS   0.004   0.001   HIS D 692 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8801)
  covalent geometry    : angle       0.73638 (12005)
  hydrogen bonds       : bond        0.04194 (  425)
  hydrogen bonds       : angle       4.83521 ( 1254)
  metal coordination   : bond        0.00221 (    2)
  link_NAG-ASN         : bond        0.00788 (    3)
  link_NAG-ASN         : angle       3.60541 (    9)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 255
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   80 TYR cc_start: 0.9156 (m-10) cc_final: 0.8864 (m-10)
REVERT: G   98 MET cc_start: 0.9026 (ptt) cc_final: 0.8649 (ptt)
REVERT: G  102 CYS cc_start: 0.8932 (t) cc_final: 0.7869 (t)
REVERT: G  150 THR cc_start: 0.7834 (t) cc_final: 0.7480 (t)
REVERT: G  157 LYS cc_start: 0.7993 (mmmt) cc_final: 0.7701 (mmmm)
REVERT: G  160 MET cc_start: 0.8463 (tpt) cc_final: 0.8259 (tpp)
REVERT: G  175 TYR cc_start: 0.7327 (t80) cc_final: 0.7114 (t80)
REVERT: D  218 ASP cc_start: 0.8624 (m-30) cc_final: 0.8336 (m-30)
REVERT: D  460 LYS cc_start: 0.9151 (pttp) cc_final: 0.8866 (pttm)
REVERT: D  502 MET cc_start: 0.8235 (tmm) cc_final: 0.7835 (tpp)
REVERT: D  530 MET cc_start: 0.9067 (tpp) cc_final: 0.8406 (tpp)
REVERT: D  575 PHE cc_start: 0.8845 (m-10) cc_final: 0.8502 (m-10)
REVERT: D  579 ASP cc_start: 0.8787 (m-30) cc_final: 0.8529 (m-30)
REVERT: D  595 GLU cc_start: 0.9079 (pt0) cc_final: 0.8823 (mp0)
REVERT: D  648 MET cc_start: 0.9236 (tpt) cc_final: 0.8983 (tpp)
REVERT: D  744 LEU cc_start: 0.8863 (mp) cc_final: 0.8647 (mt)
REVERT: D  747 LEU cc_start: 0.9032 (mm) cc_final: 0.8799 (mm)
REVERT: D  796 GLU cc_start: 0.8873 (mt-10) cc_final: 0.7962 (tm-30)
REVERT: D  926 GLU cc_start: 0.7838 (pm20) cc_final: 0.7459 (pm20)
REVERT: D  966 TRP cc_start: 0.7444 (m100) cc_final: 0.6842 (m100)
REVERT: D  986 ILE cc_start: 0.9093 (tp) cc_final: 0.8861 (tp)
REVERT: D 1011 TYR cc_start: 0.8969 (m-10) cc_final: 0.8733 (m-80)
REVERT: D 1083 MET cc_start: 0.8084 (mmp) cc_final: 0.7708 (mmt)
REVERT: D 1085 MET cc_start: 0.8696 (tpp) cc_final: 0.7905 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 255
  average time/residue: 0.0754
  time to fit residues: 27.7587
Evaluate side-chains
  210 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    6.9990
   chunk 92 optimal weight:    4.9990
   chunk 38 optimal weight:   10.0000
   chunk 79 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 100 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0670
   chunk 10 optimal weight:   20.0000
   chunk 56 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    2.0126

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

Flipped N/Q/H residues before XYZ refinement:
D 362 ASN
D 363 ASN
D 493 HIS
** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.117296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.090760 restraints weight = 22585.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.092982 restraints weight = 13079.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.094484 restraints weight = 8178.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.094897 restraints weight = 7152.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.095057 restraints weight = 6206.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.3900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8806  Z= 0.154
  Angle     :  0.743  11.377  12014  Z= 0.371
  Chirality :  0.043   0.247   1383
  Planarity :  0.004   0.044   1465
  Dihedral  :  7.082  57.459   1710
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  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: -1.35 (0.26), residues: 1046
  helix:  0.50 (0.23), residues: 530
  sheet: -3.02 (0.63), residues: 49
  loop : -2.37 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 331 
 TYR   0.017   0.001   TYR D 499 
 PHE   0.037   0.002   PHE D 996 
 TRP   0.015   0.001   TRP D 651 
 HIS   0.009   0.001   HIS D1055 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 8801)
  covalent geometry    : angle       0.73741 (12005)
  hydrogen bonds       : bond        0.04301 (  425)
  hydrogen bonds       : angle       4.91149 ( 1254)
  metal coordination   : bond        0.00085 (    2)
  link_NAG-ASN         : bond        0.00749 (    3)
  link_NAG-ASN         : angle       3.50233 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1468.00 seconds
wall clock time: 26 minutes 12.44 seconds (1572.44 seconds total)