Starting phenix.real_space_refine
on Sun Jul 27 22:01:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7e2i_30958/07_2025/7e2i_30958.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7e2i_30958/07_2025/7e2i_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7e2i_30958/07_2025/7e2i_30958.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7e2i_30958/07_2025/7e2i_30958.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7e2i_30958/07_2025/7e2i_30958.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7e2i_30958/07_2025/7e2i_30958.cif"
  }
  resolution = 4.07
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5}
          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: 5.42, per 1000 atoms: 0.63
  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: 2.59
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  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: 0.89
  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: 2.60

  Time building geometry restraints manager: 3.00 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     25.070
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.740
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.022   0.002   TRP D1120 
 HIS   0.005   0.001   HIS D 778 
 PHE   0.024   0.002   PHE D 967 
 TYR   0.017   0.002   TYR D1060 
 ARG   0.012   0.001   ARG D 329 

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

*********************** 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  : 0.972 
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: 0.8999 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 261
  average time/residue: 0.1993
  time to fit residues: 72.2631
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  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    0.9990
   chunk 79 optimal weight:   10.0000
   chunk 44 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 42 optimal weight:    0.3980
   chunk 82 optimal weight:    8.9990
   chunk 31 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
D 252 ASN
** D 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3708 r_free = 0.3708 target = 0.113573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.087966 restraints weight = 22742.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.089133 restraints weight = 12564.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.090191 restraints weight = 8753.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.1803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8806  Z= 0.160
  Angle     :  0.708   9.351  12014  Z= 0.363
  Chirality :  0.043   0.254   1383
  Planarity :  0.005   0.042   1465
  Dihedral  :  7.354  54.891   1710
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.99 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  6.64 %
    Favored  : 93.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.52 (0.25), residues: 1046
  helix: -0.49 (0.21), residues: 538
  sheet: -3.26 (0.63), residues: 58
  loop : -2.96 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 651 
 HIS   0.003   0.001   HIS G 182 
 PHE   0.025   0.002   PHE D 291 
 TYR   0.013   0.001   TYR G  80 
 ARG   0.011   0.001   ARG G  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00643 (    3)
  link_NAG-ASN         : angle       3.51025 (    9)
  hydrogen bonds       : bond        0.04837 (  425)
  hydrogen bonds       : angle       5.27595 ( 1254)
  metal coordination   : bond        0.00294 (    2)
  covalent geometry    : bond        0.00350 ( 8801)
  covalent geometry    : angle       0.70177 (12005)

*********************** 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
  249 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 247
  time to evaluate  : 0.890 
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: 0.8464 (ptm) cc_final: 0.8218 (ptp)
REVERT: G  106 LEU cc_start: 0.9450 (tt) cc_final: 0.9178 (pp)
REVERT: G  141 TYR cc_start: 0.8262 (m-10) cc_final: 0.7870 (m-10)
REVERT: G  154 ASP cc_start: 0.8383 (m-30) cc_final: 0.8164 (m-30)
REVERT: G  175 TYR cc_start: 0.7353 (t80) cc_final: 0.7149 (t80)
REVERT: G  184 SER cc_start: 0.8620 (p) cc_final: 0.8371 (p)
REVERT: G  186 LYS cc_start: 0.8446 (ttmt) cc_final: 0.8208 (ttmt)
REVERT: D  373 ARG cc_start: 0.9358 (mmt-90) cc_final: 0.8804 (mmp80)
REVERT: D  454 LEU cc_start: 0.8480 (tp) cc_final: 0.8165 (tp)
REVERT: D  460 LYS cc_start: 0.9203 (pttp) cc_final: 0.8960 (pttm)
REVERT: D  502 MET cc_start: 0.8547 (tmm) cc_final: 0.8127 (tpp)
REVERT: D  518 MET cc_start: 0.8808 (mtm) cc_final: 0.8565 (mtm)
REVERT: D  530 MET cc_start: 0.9132 (tpp) cc_final: 0.8428 (tpp)
REVERT: D  575 PHE cc_start: 0.8871 (m-10) cc_final: 0.8090 (m-80)
REVERT: D  579 ASP cc_start: 0.8894 (m-30) cc_final: 0.8658 (m-30)
REVERT: D  753 GLN cc_start: 0.8734 (pt0) cc_final: 0.8467 (pt0)
REVERT: D  796 GLU cc_start: 0.8980 (mt-10) cc_final: 0.7974 (tm-30)
REVERT: D  926 GLU cc_start: 0.8042 (pm20) cc_final: 0.7696 (pm20)
REVERT: D  996 PHE cc_start: 0.8719 (t80) cc_final: 0.8510 (t80)
REVERT: D 1011 TYR cc_start: 0.8984 (m-80) cc_final: 0.8621 (m-80)
REVERT: D 1085 MET cc_start: 0.8862 (tpp) cc_final: 0.8445 (tpp)
REVERT: D 1126 PHE cc_start: 0.8719 (t80) cc_final: 0.8303 (t80)
  outliers start: 2
  outliers final: 1
  residues processed: 249
  average time/residue: 0.1822
  time to fit residues: 64.4475
Evaluate side-chains
  206 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 205
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 58 optimal weight:    0.8980
   chunk 42 optimal weight:    9.9990
   chunk 101 optimal weight:    0.9980
   chunk 13 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   chunk 84 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 86 optimal weight:    9.9990
   chunk 44 optimal weight:    0.2980
   chunk 79 optimal weight:    1.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 362 ASN
** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 842 GLN
D1107 GLN
D1128 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.115814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.089709 restraints weight = 22741.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.092136 restraints weight = 12738.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.092999 restraints weight = 8370.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8806  Z= 0.145
  Angle     :  0.683   9.314  12014  Z= 0.347
  Chirality :  0.042   0.234   1383
  Planarity :  0.004   0.046   1465
  Dihedral  :  7.031  52.833   1710
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.95 %
    Favored  : 94.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.26), residues: 1046
  helix:  0.19 (0.22), residues: 535
  sheet: -3.28 (0.62), residues: 57
  loop : -2.66 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 651 
 HIS   0.002   0.001   HIS D 333 
 PHE   0.028   0.002   PHE D 292 
 TYR   0.014   0.001   TYR D 468 
 ARG   0.010   0.001   ARG G  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00775 (    3)
  link_NAG-ASN         : angle       3.60779 (    9)
  hydrogen bonds       : bond        0.04444 (  425)
  hydrogen bonds       : angle       4.99870 ( 1254)
  metal coordination   : bond        0.00076 (    2)
  covalent geometry    : bond        0.00313 ( 8801)
  covalent geometry    : angle       0.67625 (12005)

*********************** 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
  252 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 251
  time to evaluate  : 0.983 
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  141 TYR cc_start: 0.8263 (m-10) cc_final: 0.7858 (m-80)
REVERT: G  150 THR cc_start: 0.7743 (t) cc_final: 0.7490 (t)
REVERT: G  157 LYS cc_start: 0.8175 (mmmt) cc_final: 0.7906 (tptt)
REVERT: G  184 SER cc_start: 0.9007 (p) cc_final: 0.8418 (p)
REVERT: G  186 LYS cc_start: 0.8433 (ttmt) cc_final: 0.8157 (tmtt)
REVERT: D  460 LYS cc_start: 0.9137 (pttp) cc_final: 0.8827 (pttm)
REVERT: D  465 MET cc_start: 0.8575 (ttt) cc_final: 0.8367 (tpp)
REVERT: D  467 ILE cc_start: 0.9259 (mp) cc_final: 0.8931 (mp)
REVERT: D  502 MET cc_start: 0.8318 (tmm) cc_final: 0.7993 (tpp)
REVERT: D  518 MET cc_start: 0.8834 (mtm) cc_final: 0.8531 (mtm)
REVERT: D  530 MET cc_start: 0.9120 (tpp) cc_final: 0.8342 (tpp)
REVERT: D  575 PHE cc_start: 0.8872 (m-10) cc_final: 0.8124 (m-80)
REVERT: D  579 ASP cc_start: 0.8723 (m-30) cc_final: 0.8480 (m-30)
REVERT: D  595 GLU cc_start: 0.9041 (pt0) cc_final: 0.8840 (mp0)
REVERT: D  722 LEU cc_start: 0.9166 (tt) cc_final: 0.8926 (tt)
REVERT: D  747 LEU cc_start: 0.9144 (mm) cc_final: 0.8936 (mm)
REVERT: D  753 GLN cc_start: 0.8626 (pt0) cc_final: 0.8314 (pt0)
REVERT: D  796 GLU cc_start: 0.8880 (mt-10) cc_final: 0.7882 (tm-30)
REVERT: D  805 LYS cc_start: 0.9094 (pttm) cc_final: 0.8767 (pttm)
REVERT: D  926 GLU cc_start: 0.7948 (pm20) cc_final: 0.7602 (pm20)
REVERT: D  966 TRP cc_start: 0.7839 (m100) cc_final: 0.7041 (m100)
REVERT: D 1006 ILE cc_start: 0.8991 (mp) cc_final: 0.8521 (mt)
REVERT: D 1011 TYR cc_start: 0.8791 (m-10) cc_final: 0.8553 (m-80)
REVERT: D 1051 ASN cc_start: 0.9339 (t0) cc_final: 0.9076 (t0)
REVERT: D 1126 PHE cc_start: 0.8840 (t80) cc_final: 0.8412 (t80)
REVERT: D 1129 CYS cc_start: 0.9141 (t) cc_final: 0.8915 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 252
  average time/residue: 0.1902
  time to fit residues: 67.2321
Evaluate side-chains
  214 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 57 optimal weight:    4.9990
   chunk 101 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 37 optimal weight:   10.0000
   chunk 52 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 67 optimal weight:    5.9990
   chunk 31 optimal weight:   10.0000
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
D 842 GLN
D1128 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.116983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.090841 restraints weight = 22450.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.093277 restraints weight = 10953.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.094831 restraints weight = 7414.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.2834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8806  Z= 0.146
  Angle     :  0.678   9.346  12014  Z= 0.342
  Chirality :  0.041   0.222   1383
  Planarity :  0.004   0.043   1465
  Dihedral  :  6.935  52.948   1710
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.16 %
    Favored  : 95.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.26), residues: 1046
  helix:  0.49 (0.23), residues: 523
  sheet: -3.04 (0.65), residues: 51
  loop : -2.50 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 651 
 HIS   0.002   0.000   HIS G 182 
 PHE   0.017   0.002   PHE D 455 
 TYR   0.018   0.001   TYR D 499 
 ARG   0.011   0.000   ARG G  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00831 (    3)
  link_NAG-ASN         : angle       3.55947 (    9)
  hydrogen bonds       : bond        0.04328 (  425)
  hydrogen bonds       : angle       4.86565 ( 1254)
  metal coordination   : bond        0.00187 (    2)
  covalent geometry    : bond        0.00319 ( 8801)
  covalent geometry    : angle       0.67081 (12005)

*********************** 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
  253 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 252
  time to evaluate  : 0.956 
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: 0.9266 (m-10) cc_final: 0.8848 (m-80)
REVERT: G  141 TYR cc_start: 0.8169 (m-10) cc_final: 0.7733 (m-10)
REVERT: G  150 THR cc_start: 0.7847 (t) cc_final: 0.7547 (t)
REVERT: G  175 TYR cc_start: 0.7566 (t80) cc_final: 0.7270 (t80)
REVERT: G  184 SER cc_start: 0.9156 (p) cc_final: 0.8710 (p)
REVERT: G  186 LYS cc_start: 0.8345 (ttmt) cc_final: 0.8001 (tmtt)
REVERT: D  460 LYS cc_start: 0.9112 (pttp) cc_final: 0.8746 (pttm)
REVERT: D  502 MET cc_start: 0.8400 (tmm) cc_final: 0.7984 (tmm)
REVERT: D  518 MET cc_start: 0.8845 (mtm) cc_final: 0.8612 (mtm)
REVERT: D  530 MET cc_start: 0.9106 (tpp) cc_final: 0.8247 (tpp)
REVERT: D  575 PHE cc_start: 0.8878 (m-10) cc_final: 0.8147 (m-80)
REVERT: D  579 ASP cc_start: 0.8699 (m-30) cc_final: 0.8447 (m-30)
REVERT: D  595 GLU cc_start: 0.9082 (pt0) cc_final: 0.8867 (mp0)
REVERT: D  722 LEU cc_start: 0.9150 (tt) cc_final: 0.8946 (tt)
REVERT: D  739 ASN cc_start: 0.7214 (t0) cc_final: 0.6979 (t0)
REVERT: D  747 LEU cc_start: 0.9119 (mm) cc_final: 0.8891 (mm)
REVERT: D  753 GLN cc_start: 0.8646 (pt0) cc_final: 0.8295 (pt0)
REVERT: D  796 GLU cc_start: 0.9029 (mt-10) cc_final: 0.7964 (tm-30)
REVERT: D  805 LYS cc_start: 0.9167 (pttm) cc_final: 0.8966 (pttm)
REVERT: D  926 GLU cc_start: 0.7911 (pm20) cc_final: 0.7518 (pm20)
REVERT: D  986 ILE cc_start: 0.9192 (tp) cc_final: 0.8991 (tp)
REVERT: D 1006 ILE cc_start: 0.8961 (mp) cc_final: 0.8515 (mt)
REVERT: D 1011 TYR cc_start: 0.8919 (m-10) cc_final: 0.8523 (m-80)
REVERT: D 1113 MET cc_start: 0.9146 (ttp) cc_final: 0.8937 (tmm)
REVERT: D 1126 PHE cc_start: 0.8816 (t80) cc_final: 0.8406 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 252
  average time/residue: 0.1944
  time to fit residues: 67.8787
Evaluate side-chains
  208 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 99 optimal weight:    5.9990
   chunk 101 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 63 optimal weight:   10.0000
   chunk 22 optimal weight:    0.0980
   chunk 102 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 103 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 87 optimal weight:    0.9980
   chunk 28 optimal weight:    6.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.118169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.092881 restraints weight = 21938.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.095243 restraints weight = 10471.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.096673 restraints weight = 7243.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.3220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8806  Z= 0.134
  Angle     :  0.677  11.104  12014  Z= 0.339
  Chirality :  0.041   0.235   1383
  Planarity :  0.004   0.044   1465
  Dihedral  :  6.738  53.999   1710
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.26), residues: 1046
  helix:  0.69 (0.23), residues: 522
  sheet: -3.09 (0.63), residues: 52
  loop : -2.46 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 651 
 HIS   0.007   0.001   HIS D 829 
 PHE   0.014   0.001   PHE D 455 
 TYR   0.015   0.001   TYR G  62 
 ARG   0.007   0.000   ARG G  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00805 (    3)
  link_NAG-ASN         : angle       3.83039 (    9)
  hydrogen bonds       : bond        0.04230 (  425)
  hydrogen bonds       : angle       4.80091 ( 1254)
  metal coordination   : bond        0.00137 (    2)
  covalent geometry    : bond        0.00285 ( 8801)
  covalent geometry    : angle       0.66890 (12005)

*********************** 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
  247 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   80 TYR cc_start: 0.9244 (m-10) cc_final: 0.9026 (m-10)
REVERT: G  141 TYR cc_start: 0.8100 (m-10) cc_final: 0.7762 (m-10)
REVERT: G  150 THR cc_start: 0.7898 (t) cc_final: 0.7582 (t)
REVERT: G  175 TYR cc_start: 0.7707 (t80) cc_final: 0.7401 (t80)
REVERT: D  460 LYS cc_start: 0.9097 (pttp) cc_final: 0.8747 (pttm)
REVERT: D  467 ILE cc_start: 0.9190 (mp) cc_final: 0.8887 (mp)
REVERT: D  502 MET cc_start: 0.8276 (tmm) cc_final: 0.7917 (tmm)
REVERT: D  518 MET cc_start: 0.8779 (mtm) cc_final: 0.8449 (mtt)
REVERT: D  530 MET cc_start: 0.9096 (tpp) cc_final: 0.8305 (tpp)
REVERT: D  575 PHE cc_start: 0.8930 (m-10) cc_final: 0.8204 (m-80)
REVERT: D  579 ASP cc_start: 0.8668 (m-30) cc_final: 0.8412 (m-30)
REVERT: D  595 GLU cc_start: 0.9053 (pt0) cc_final: 0.8834 (mp0)
REVERT: D  747 LEU cc_start: 0.9093 (mm) cc_final: 0.8834 (mm)
REVERT: D  796 GLU cc_start: 0.8865 (mt-10) cc_final: 0.7914 (tm-30)
REVERT: D  805 LYS cc_start: 0.9146 (pttm) cc_final: 0.8833 (pttm)
REVERT: D  896 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8253 (mt-10)
REVERT: D  926 GLU cc_start: 0.7860 (pm20) cc_final: 0.7498 (pm20)
REVERT: D  966 TRP cc_start: 0.7529 (m100) cc_final: 0.6763 (m100)
REVERT: D  986 ILE cc_start: 0.9194 (tp) cc_final: 0.8966 (tp)
REVERT: D 1011 TYR cc_start: 0.8902 (m-10) cc_final: 0.8550 (m-80)
REVERT: D 1126 PHE cc_start: 0.8836 (t80) cc_final: 0.8383 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 247
  average time/residue: 0.1923
  time to fit residues: 66.4650
Evaluate side-chains
  215 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 11 optimal weight:   20.0000
   chunk 3 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 16 optimal weight:    7.9990
   chunk 60 optimal weight:    9.9990
   chunk 101 optimal weight:    0.9990
   chunk 53 optimal weight:   10.0000
   chunk 82 optimal weight:   10.0000
   chunk 79 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    1.9186

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.117297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.091786 restraints weight = 21717.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.094175 restraints weight = 10380.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.095537 restraints weight = 7183.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.3380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8806  Z= 0.147
  Angle     :  0.693  10.734  12014  Z= 0.349
  Chirality :  0.041   0.242   1383
  Planarity :  0.004   0.064   1465
  Dihedral  :  6.765  55.339   1710
  Min Nonbonded Distance : 1.577

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.60 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.26), residues: 1046
  helix:  0.59 (0.23), residues: 524
  sheet: -2.87 (0.65), residues: 50
  loop : -2.39 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 651 
 HIS   0.015   0.001   HIS G 182 
 PHE   0.016   0.001   PHE D 830 
 TYR   0.012   0.001   TYR G  62 
 ARG   0.013   0.001   ARG G  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00758 (    3)
  link_NAG-ASN         : angle       3.60365 (    9)
  hydrogen bonds       : bond        0.04340 (  425)
  hydrogen bonds       : angle       4.78650 ( 1254)
  metal coordination   : bond        0.01654 (    2)
  covalent geometry    : bond        0.00319 ( 8801)
  covalent geometry    : angle       0.68640 (12005)

*********************** 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
  249 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 0.878 
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: 0.9229 (m-10) cc_final: 0.8999 (m-10)
REVERT: G   98 MET cc_start: 0.8423 (ppp) cc_final: 0.8051 (ppp)
REVERT: G  141 TYR cc_start: 0.8126 (m-10) cc_final: 0.7799 (m-10)
REVERT: G  150 THR cc_start: 0.7868 (t) cc_final: 0.7492 (t)
REVERT: G  175 TYR cc_start: 0.7680 (t80) cc_final: 0.7401 (t80)
REVERT: D  454 LEU cc_start: 0.8417 (tp) cc_final: 0.8210 (tp)
REVERT: D  460 LYS cc_start: 0.9152 (pttp) cc_final: 0.8797 (pttm)
REVERT: D  502 MET cc_start: 0.8334 (tmm) cc_final: 0.7915 (tpp)
REVERT: D  518 MET cc_start: 0.8828 (mtm) cc_final: 0.8524 (mtt)
REVERT: D  530 MET cc_start: 0.9093 (tpp) cc_final: 0.8427 (tpp)
REVERT: D  575 PHE cc_start: 0.8816 (m-10) cc_final: 0.8086 (m-80)
REVERT: D  579 ASP cc_start: 0.8695 (m-30) cc_final: 0.8415 (m-30)
REVERT: D  595 GLU cc_start: 0.9055 (pt0) cc_final: 0.8840 (mp0)
REVERT: D  747 LEU cc_start: 0.9109 (mm) cc_final: 0.8880 (mm)
REVERT: D  753 GLN cc_start: 0.8661 (pm20) cc_final: 0.8437 (pt0)
REVERT: D  796 GLU cc_start: 0.8943 (mt-10) cc_final: 0.7957 (tm-30)
REVERT: D  805 LYS cc_start: 0.9115 (pttm) cc_final: 0.8766 (pttm)
REVERT: D  926 GLU cc_start: 0.7980 (pm20) cc_final: 0.7565 (pm20)
REVERT: D  966 TRP cc_start: 0.7759 (m100) cc_final: 0.6968 (m100)
REVERT: D  986 ILE cc_start: 0.9150 (tp) cc_final: 0.8937 (tp)
REVERT: D 1011 TYR cc_start: 0.8966 (m-10) cc_final: 0.8579 (m-80)
REVERT: D 1126 PHE cc_start: 0.8794 (t80) cc_final: 0.8431 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 249
  average time/residue: 0.1746
  time to fit residues: 62.0988
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  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 82 optimal weight:    8.9990
   chunk 79 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9980
   chunk 80 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 99 optimal weight:    9.9990
   chunk 23 optimal weight:    0.0030
   chunk 72 optimal weight:    5.9990
   chunk 78 optimal weight:    0.0060
   chunk 59 optimal weight:    0.7980
   chunk 11 optimal weight:    7.9990
   overall best weight:    0.5606

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

Flipped N/Q/H residues before XYZ refinement:
** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 362 ASN
** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 572 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.120283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.092489 restraints weight = 22030.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.095340 restraints weight = 12256.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.097221 restraints weight = 8359.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.3850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8806  Z= 0.136
  Angle     :  0.695  10.545  12014  Z= 0.346
  Chirality :  0.041   0.242   1383
  Planarity :  0.005   0.076   1465
  Dihedral  :  6.731  59.133   1710
  Min Nonbonded Distance : 1.549

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.26), residues: 1046
  helix:  0.60 (0.23), residues: 529
  sheet: -2.85 (0.64), residues: 50
  loop : -2.33 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP D 352 
 HIS   0.011   0.001   HIS G 182 
 PHE   0.016   0.002   PHE D1091 
 TYR   0.020   0.001   TYR D 499 
 ARG   0.012   0.000   ARG G  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00792 (    3)
  link_NAG-ASN         : angle       3.44222 (    9)
  hydrogen bonds       : bond        0.04287 (  425)
  hydrogen bonds       : angle       4.73585 ( 1254)
  metal coordination   : bond        0.04356 (    2)
  covalent geometry    : bond        0.00282 ( 8801)
  covalent geometry    : angle       0.68891 (12005)

*********************** 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
  256 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 256
  time to evaluate  : 1.613 
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   80 TYR cc_start: 0.9182 (m-10) cc_final: 0.8938 (m-10)
REVERT: G   98 MET cc_start: 0.8610 (ppp) cc_final: 0.7981 (ppp)
REVERT: G  139 LEU cc_start: 0.8423 (mm) cc_final: 0.7970 (mm)
REVERT: G  141 TYR cc_start: 0.8002 (m-10) cc_final: 0.7728 (m-10)
REVERT: G  150 THR cc_start: 0.7893 (t) cc_final: 0.7544 (t)
REVERT: G  160 MET cc_start: 0.8501 (tpt) cc_final: 0.8293 (tpp)
REVERT: G  175 TYR cc_start: 0.7629 (t80) cc_final: 0.7171 (t80)
REVERT: D  460 LYS cc_start: 0.9178 (pttp) cc_final: 0.8805 (pttm)
REVERT: D  502 MET cc_start: 0.8237 (tmm) cc_final: 0.7943 (tmm)
REVERT: D  530 MET cc_start: 0.9056 (tpp) cc_final: 0.8699 (tpp)
REVERT: D  575 PHE cc_start: 0.8768 (m-10) cc_final: 0.8471 (m-10)
REVERT: D  579 ASP cc_start: 0.8640 (m-30) cc_final: 0.8392 (m-30)
REVERT: D  595 GLU cc_start: 0.9009 (pt0) cc_final: 0.8790 (mp0)
REVERT: D  747 LEU cc_start: 0.9001 (mm) cc_final: 0.8762 (mm)
REVERT: D  762 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8820 (mm-30)
REVERT: D  796 GLU cc_start: 0.8750 (mt-10) cc_final: 0.7914 (tm-30)
REVERT: D  805 LYS cc_start: 0.9076 (pttm) cc_final: 0.8783 (pttm)
REVERT: D  926 GLU cc_start: 0.7788 (pm20) cc_final: 0.7442 (pm20)
REVERT: D  966 TRP cc_start: 0.7836 (m100) cc_final: 0.7086 (m100)
REVERT: D 1055 HIS cc_start: 0.9048 (m170) cc_final: 0.8837 (m170)
REVERT: D 1085 MET cc_start: 0.8766 (tpp) cc_final: 0.8055 (tpp)
REVERT: D 1126 PHE cc_start: 0.8713 (t80) cc_final: 0.8386 (t80)
REVERT: D 1129 CYS cc_start: 0.8849 (t) cc_final: 0.8602 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 256
  average time/residue: 0.2252
  time to fit residues: 82.2576
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  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 102 optimal weight:    0.9980
   chunk 7 optimal weight:   10.0000
   chunk 74 optimal weight:    8.9990
   chunk 91 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 46 optimal weight:    9.9990
   chunk 18 optimal weight:    0.0870
   chunk 47 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 43 optimal weight:    0.8980
   chunk 23 optimal weight:   30.0000
   overall best weight:    1.7962

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

Flipped N/Q/H residues before XYZ refinement:
** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 362 ASN
D 572 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.118717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.092774 restraints weight = 22438.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.095166 restraints weight = 11141.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.096326 restraints weight = 7641.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.3888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8806  Z= 0.145
  Angle     :  0.713  10.301  12014  Z= 0.356
  Chirality :  0.042   0.247   1383
  Planarity :  0.004   0.044   1465
  Dihedral  :  6.737  58.649   1710
  Min Nonbonded Distance : 1.615

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.80 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.26), residues: 1046
  helix:  0.57 (0.23), residues: 529
  sheet: -2.80 (0.65), residues: 50
  loop : -2.23 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 352 
 HIS   0.012   0.001   HIS G 182 
 PHE   0.036   0.002   PHE D 996 
 TYR   0.035   0.001   TYR D1011 
 ARG   0.006   0.000   ARG G  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00740 (    3)
  link_NAG-ASN         : angle       3.42587 (    9)
  hydrogen bonds       : bond        0.04267 (  425)
  hydrogen bonds       : angle       4.77312 ( 1254)
  metal coordination   : bond        0.02554 (    2)
  covalent geometry    : bond        0.00316 ( 8801)
  covalent geometry    : angle       0.70659 (12005)

*********************** 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
  246 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 246
  time to evaluate  : 1.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   61 ARG cc_start: 0.8810 (pmt-80) cc_final: 0.8400 (pmt-80)
REVERT: G   73 PHE cc_start: 0.9348 (t80) cc_final: 0.9119 (t80)
REVERT: G   80 TYR cc_start: 0.9169 (m-10) cc_final: 0.8941 (m-10)
REVERT: G   98 MET cc_start: 0.8664 (ppp) cc_final: 0.7883 (ppp)
REVERT: G  139 LEU cc_start: 0.8432 (mm) cc_final: 0.8136 (mm)
REVERT: G  141 TYR cc_start: 0.8009 (m-10) cc_final: 0.7728 (m-10)
REVERT: G  150 THR cc_start: 0.7904 (t) cc_final: 0.7487 (t)
REVERT: G  175 TYR cc_start: 0.7560 (t80) cc_final: 0.6957 (t80)
REVERT: D  218 ASP cc_start: 0.8500 (m-30) cc_final: 0.8290 (m-30)
REVERT: D  460 LYS cc_start: 0.9171 (pttp) cc_final: 0.8807 (pttm)
REVERT: D  502 MET cc_start: 0.8239 (tmm) cc_final: 0.7861 (tpp)
REVERT: D  530 MET cc_start: 0.9075 (tpp) cc_final: 0.8700 (tpp)
REVERT: D  575 PHE cc_start: 0.8749 (m-10) cc_final: 0.7948 (m-80)
REVERT: D  579 ASP cc_start: 0.8660 (m-30) cc_final: 0.8363 (m-30)
REVERT: D  595 GLU cc_start: 0.9044 (pt0) cc_final: 0.8820 (mp0)
REVERT: D  648 MET cc_start: 0.9205 (tpt) cc_final: 0.8978 (tpp)
REVERT: D  747 LEU cc_start: 0.9119 (mm) cc_final: 0.8901 (mm)
REVERT: D  796 GLU cc_start: 0.8869 (mt-10) cc_final: 0.7957 (tm-30)
REVERT: D  805 LYS cc_start: 0.9084 (pttm) cc_final: 0.8884 (pttm)
REVERT: D  926 GLU cc_start: 0.7842 (pm20) cc_final: 0.7458 (pm20)
REVERT: D  986 ILE cc_start: 0.9185 (tp) cc_final: 0.8959 (tp)
REVERT: D 1085 MET cc_start: 0.8831 (tpp) cc_final: 0.7763 (tpp)
REVERT: D 1126 PHE cc_start: 0.8752 (t80) cc_final: 0.8443 (t80)
REVERT: D 1129 CYS cc_start: 0.8866 (t) cc_final: 0.8587 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 246
  average time/residue: 0.2089
  time to fit residues: 73.6545
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  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 3 optimal weight:    9.9990
   chunk 24 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 100 optimal weight:    9.9990
   chunk 80 optimal weight:    6.9990
   chunk 0 optimal weight:   30.0000
   chunk 18 optimal weight:    0.7980
   chunk 76 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9980
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 362 ASN
** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.117357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.091307 restraints weight = 22329.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.093973 restraints weight = 11104.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.095710 restraints weight = 7361.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.3823

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= 0.173
  Angle     :  0.746  12.108  12014  Z= 0.374
  Chirality :  0.043   0.218   1383
  Planarity :  0.005   0.070   1465
  Dihedral  :  6.950  58.306   1710
  Min Nonbonded Distance : 1.625

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.18 %
    Favored  : 90.82 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.26), residues: 1046
  helix:  0.51 (0.23), residues: 528
  sheet: -3.01 (0.64), residues: 52
  loop : -2.20 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP D 859 
 HIS   0.011   0.001   HIS G 182 
 PHE   0.035   0.002   PHE D 996 
 TYR   0.037   0.002   TYR D1011 
 ARG   0.014   0.001   ARG G  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00752 (    3)
  link_NAG-ASN         : angle       3.33821 (    9)
  hydrogen bonds       : bond        0.04424 (  425)
  hydrogen bonds       : angle       4.84686 ( 1254)
  metal coordination   : bond        0.02369 (    2)
  covalent geometry    : bond        0.00383 ( 8801)
  covalent geometry    : angle       0.74023 (12005)

*********************** 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  : 1.060 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   61 ARG cc_start: 0.8614 (pmt-80) cc_final: 0.8246 (pmt-80)
REVERT: G   80 TYR cc_start: 0.9225 (m-10) cc_final: 0.8984 (m-10)
REVERT: G   98 MET cc_start: 0.8616 (ppp) cc_final: 0.7808 (ppp)
REVERT: G  141 TYR cc_start: 0.7996 (m-10) cc_final: 0.7729 (m-10)
REVERT: G  150 THR cc_start: 0.7796 (t) cc_final: 0.7346 (t)
REVERT: G  175 TYR cc_start: 0.7581 (t80) cc_final: 0.7214 (t80)
REVERT: D  460 LYS cc_start: 0.9147 (pttp) cc_final: 0.8808 (pttm)
REVERT: D  502 MET cc_start: 0.8246 (tmm) cc_final: 0.7911 (tpp)
REVERT: D  518 MET cc_start: 0.8928 (mtm) cc_final: 0.8609 (mtm)
REVERT: D  530 MET cc_start: 0.9082 (tpp) cc_final: 0.8718 (tpp)
REVERT: D  546 TYR cc_start: 0.8114 (t80) cc_final: 0.7853 (t80)
REVERT: D  575 PHE cc_start: 0.8764 (m-10) cc_final: 0.8447 (m-10)
REVERT: D  579 ASP cc_start: 0.8675 (m-30) cc_final: 0.8422 (m-30)
REVERT: D  595 GLU cc_start: 0.9048 (pt0) cc_final: 0.8825 (mp0)
REVERT: D  648 MET cc_start: 0.9237 (tpt) cc_final: 0.8982 (tpp)
REVERT: D  747 LEU cc_start: 0.9164 (mm) cc_final: 0.8953 (mm)
REVERT: D  796 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8036 (tm-30)
REVERT: D  926 GLU cc_start: 0.7871 (pm20) cc_final: 0.7470 (pm20)
REVERT: D  966 TRP cc_start: 0.7784 (m100) cc_final: 0.7067 (m100)
REVERT: D 1085 MET cc_start: 0.8877 (tpp) cc_final: 0.8032 (tpp)
REVERT: D 1126 PHE cc_start: 0.8912 (t80) cc_final: 0.8453 (t80)
REVERT: D 1129 CYS cc_start: 0.8887 (t) cc_final: 0.8607 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 236
  average time/residue: 0.1881
  time to fit residues: 64.0393
Evaluate side-chains
  198 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 82 optimal weight:    9.9990
   chunk 45 optimal weight:    2.9990
   chunk 42 optimal weight:   10.0000
   chunk 84 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 46 optimal weight:    8.9990
   chunk 23 optimal weight:   20.0000
   chunk 69 optimal weight:    7.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
G  50 ASN
** G 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 362 ASN
D 363 ASN
** 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 = 0.3713 r_free = 0.3713 target = 0.114295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.088092 restraints weight = 22247.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.090070 restraints weight = 12920.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.092175 restraints weight = 8278.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.3734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081   8806  Z= 0.218
  Angle     :  0.772  11.665  12014  Z= 0.389
  Chirality :  0.044   0.248   1383
  Planarity :  0.005   0.062   1465
  Dihedral  :  7.268  59.618   1710
  Min Nonbonded Distance : 1.400

Molprobity Statistics.
  All-atom Clashscore : 14.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.80 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.26), residues: 1046
  helix:  0.42 (0.23), residues: 533
  sheet: -2.79 (0.67), residues: 49
  loop : -2.21 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP D 859 
 HIS   0.037   0.003   HIS G 182 
 PHE   0.037   0.002   PHE D 996 
 TYR   0.034   0.002   TYR D1011 
 ARG   0.013   0.001   ARG G  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00772 (    3)
  link_NAG-ASN         : angle       3.58431 (    9)
  hydrogen bonds       : bond        0.04676 (  425)
  hydrogen bonds       : angle       4.92505 ( 1254)
  metal coordination   : bond        0.06747 (    2)
  covalent geometry    : bond        0.00476 ( 8801)
  covalent geometry    : angle       0.76617 (12005)

********************** 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
  235 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.885 
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   61 ARG cc_start: 0.8656 (pmt-80) cc_final: 0.8291 (pmt-80)
REVERT: G   80 TYR cc_start: 0.9226 (m-10) cc_final: 0.8978 (m-10)
REVERT: G   98 MET cc_start: 0.8649 (ppp) cc_final: 0.7880 (ppp)
REVERT: G  141 TYR cc_start: 0.7899 (m-10) cc_final: 0.7584 (m-10)
REVERT: G  150 THR cc_start: 0.7716 (t) cc_final: 0.7217 (t)
REVERT: G  175 TYR cc_start: 0.7636 (t80) cc_final: 0.7283 (t80)
REVERT: D  218 ASP cc_start: 0.8598 (m-30) cc_final: 0.8392 (m-30)
REVERT: D  291 PHE cc_start: 0.7960 (p90) cc_final: 0.7754 (p90)
REVERT: D  460 LYS cc_start: 0.9165 (pttp) cc_final: 0.8916 (pttm)
REVERT: D  502 MET cc_start: 0.8290 (tmm) cc_final: 0.7884 (tpp)
REVERT: D  530 MET cc_start: 0.9087 (tpp) cc_final: 0.8747 (tpp)
REVERT: D  546 TYR cc_start: 0.8271 (t80) cc_final: 0.7964 (t80)
REVERT: D  554 PHE cc_start: 0.8524 (t80) cc_final: 0.8127 (t80)
REVERT: D  575 PHE cc_start: 0.8826 (m-10) cc_final: 0.8522 (m-10)
REVERT: D  579 ASP cc_start: 0.8687 (m-30) cc_final: 0.8455 (m-30)
REVERT: D  648 MET cc_start: 0.9203 (tpt) cc_final: 0.8952 (tpp)
REVERT: D  796 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8103 (tm-30)
REVERT: D  926 GLU cc_start: 0.7891 (pm20) cc_final: 0.7505 (pm20)
REVERT: D  966 TRP cc_start: 0.7875 (m100) cc_final: 0.7244 (m100)
REVERT: D 1085 MET cc_start: 0.8911 (tpp) cc_final: 0.8102 (tpp)
REVERT: D 1098 MET cc_start: 0.8817 (tpp) cc_final: 0.8473 (tpp)
REVERT: D 1126 PHE cc_start: 0.8856 (t80) cc_final: 0.8494 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 235
  average time/residue: 0.1872
  time to fit residues: 64.0837
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  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 14 optimal weight:   20.0000
   chunk 50 optimal weight:    0.9990
   chunk 91 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0970
   chunk 99 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 22 optimal weight:    0.2980
   chunk 48 optimal weight:    2.9990
   chunk 72 optimal weight:   10.0000
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
G  50 ASN
** G 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 362 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 = 0.3776 r_free = 0.3776 target = 0.118566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.092921 restraints weight = 22049.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.094862 restraints weight = 11463.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.096594 restraints weight = 7691.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.4033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   8806  Z= 0.143
  Angle     :  0.751  11.870  12014  Z= 0.367
  Chirality :  0.042   0.243   1383
  Planarity :  0.004   0.047   1465
  Dihedral  :  6.985  59.261   1710
  Min Nonbonded Distance : 1.451

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.26), residues: 1046
  helix:  0.59 (0.23), residues: 524
  sheet: -2.96 (0.65), residues: 51
  loop : -2.23 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP D 859 
 HIS   0.030   0.002   HIS G 182 
 PHE   0.034   0.002   PHE D 996 
 TYR   0.034   0.001   TYR D1011 
 ARG   0.009   0.001   ARG G  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00820 (    3)
  link_NAG-ASN         : angle       3.50401 (    9)
  hydrogen bonds       : bond        0.04305 (  425)
  hydrogen bonds       : angle       4.77282 ( 1254)
  metal coordination   : bond        0.06020 (    2)
  covalent geometry    : bond        0.00305 ( 8801)
  covalent geometry    : angle       0.74526 (12005)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3073.80 seconds
wall clock time: 54 minutes 58.11 seconds (3298.11 seconds total)