Starting phenix.real_space_refine
on Wed Mar  4 04:13:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rpk_24617/03_2026/7rpk_24617.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rpk_24617/03_2026/7rpk_24617.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rpk_24617/03_2026/7rpk_24617.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rpk_24617/03_2026/7rpk_24617.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rpk_24617/03_2026/7rpk_24617.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rpk_24617/03_2026/7rpk_24617.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.011 sd=   0.574
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 8
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Zn      1      6.06       5
     P       1      5.49       5
     S      71      5.16       5
     Na      2      4.78       5
     C    6659      2.51       5
     N    1455      2.21       5
     O    1827      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10018
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7606
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 953, 7598
          Classifications: {'peptide': 953}
          Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 912}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 953, 7598
          Classifications: {'peptide': 953}
          Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 912}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 7793
    Chain: "H"
      Number of atoms: 1215
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 1215
          Classifications: {'peptide': 151}
          Link IDs: {'PTRANS': 5, 'TRANS': 145}
    Chain: "A"
      Number of atoms: 1147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 1147
          Unusual residues: {' NA': 2, '6OE': 1, 'AV0': 2, 'NAG': 5, 'Y01': 26}
          Classifications: {'undetermined': 36}
          Link IDs: {None: 35}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "H"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 8
          Unusual residues: {' CA': 2, ' ZN': 1, 'SO4': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 42
          Classifications: {'water': 42}
          Link IDs: {None: 41}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AMET A 557 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CE BMET A 557 " occ=0.50
  Time building chain proxies: 3.55, per 1000 atoms: 0.35
  Number of scatterers: 10018
  At special positions: 0
  Unit cell: (91.015, 85.17, 132.765, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     Zn      1     29.99
     Ca      2     19.99
     S      71     16.00
     P       1     15.00
     Na      2     11.00
     O    1827      8.00
     N    1455      7.00
     C    6659      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 292 " - pdb=" SG  CYS A 348 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 322 " - pdb=" SG  CYS A 366 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 339 " - pdb=" SG  CYS A 347 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 384 " - pdb=" SG  CYS A 417 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 397 " - pdb=" SG  CYS A 410 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 829 " - pdb=" SG  CYS A 849 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 863 " - pdb=" SG  CYS A 872 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 871 " - pdb=" SG  CYS A 887 " distance=2.04

  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 A2132 " - " ASN A 915 "
      " NAG A2133 " - " ASN A 475 "
      " NAG A2134 " - " ASN A 834 "
      " NAG A2135 " - " ASN A 362 "
      " NAG A2136 " - " ASN A 390 "
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 771.7 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN H 203 "
        pdb="ZN    ZN H 203 " - pdb=" NE2 HIS H 141 "
        pdb="ZN    ZN H 203 " - pdb=" ND1 HIS H 183 "


  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2102

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 4 sheets defined
      62.9% alpha, 6.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 179 through 187
    Processing helix  chain 'A' and resid 187 through 209
    Processing helix  chain 'A' and resid 227 through 242
    Processing helix  chain 'A' and resid 253 through 268
    Processing helix  chain 'A' and resid 268 through 273
    Processing helix  chain 'A' and resid 314 through 329
    Processing helix  chain 'A' and resid 334 through 339
    Processing helix  chain 'A' and resid 352 through 361
    Processing helix  chain 'A' and resid 365 through 369
    Processing helix  chain 'A' and resid 370 through 390
      removed outlier: 4.980A  pdb=" N   LYS A 386 " --> pdb=" O   ARG A 382 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   HIS A 387 " --> pdb=" O   THR A 383 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   TYR A 388 " --> pdb=" O   CYS A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 404
    Processing helix  chain 'A' and resid 414 through 419
      removed outlier: 3.762A  pdb=" N   LYS A 419 " --> pdb=" O   LYS A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 430
    Processing helix  chain 'A' and resid 460 through 462
      No H-bonds generated for 'chain 'A' and resid 460 through 462'
    Processing helix  chain 'A' and resid 463 through 471
    Processing helix  chain 'A' and resid 490 through 502
      removed outlier: 4.147A  pdb=" N   GLN A 496 " --> pdb=" O   HIS A 492 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   ASP A 497 " --> pdb=" O   SER A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 522
    Processing helix  chain 'A' and resid 523 through 548
      removed outlier: 3.813A  pdb=" N   LEU A 538 " --> pdb=" O   ILE A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 559
    Processing helix  chain 'A' and resid 560 through 570
      removed outlier: 4.514A  pdb=" N   ALA A 570 " --> pdb=" O   VAL A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 587
    Processing helix  chain 'A' and resid 591 through 620
      removed outlier: 5.241A  pdb=" N   LEU A 605 " --> pdb=" O   GLN A 601 " (cutoff:3.500A)
      removed outlier: 5.336A  pdb=" N   SER A 606 " --> pdb=" O   HIS A 602 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   THR A 614 " --> pdb=" O   THR A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 624
    Processing helix  chain 'A' and resid 626 through 649
    Processing helix  chain 'A' and resid 649 through 661
    Processing helix  chain 'A' and resid 681 through 685
      removed outlier: 3.625A  pdb=" N   VAL A 684 " --> pdb=" O   CYS A 681 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LEU A 685 " --> pdb=" O   TRP A 682 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 681 through 685'
    Processing helix  chain 'A' and resid 688 through 706
    Processing helix  chain 'A' and resid 706 through 715
      removed outlier: 3.563A  pdb=" N   PHE A 715 " --> pdb=" O   ILE A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 736
    Processing helix  chain 'A' and resid 746 through 750
    Processing helix  chain 'A' and resid 757 through 766
    Processing helix  chain 'A' and resid 770 through 778
      removed outlier: 3.645A  pdb=" N   HIS A 776 " --> pdb=" O   PHE A 772 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLY A 778 " --> pdb=" O   ARG A 774 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 818 through 833
    Processing helix  chain 'A' and resid 849 through 860
      removed outlier: 3.540A  pdb=" N   THR A 853 " --> pdb=" O   CYS A 849 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 872
      Proline residue:  A 870  - end of helix
    Processing helix  chain 'A' and resid 880 through 899
      removed outlier: 4.225A  pdb=" N   LYS A 889 " --> pdb=" O   GLU A 885 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 934 through 954
    Processing helix  chain 'A' and resid 955 through 956
      No H-bonds generated for 'chain 'A' and resid 955 through 956'
    Processing helix  chain 'A' and resid 957 through 961
      removed outlier: 3.800A  pdb=" N   SER A 961 " --> pdb=" O   GLU A 958 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 969 through 1001
    Processing helix  chain 'A' and resid 1003 through 1028
    Processing helix  chain 'A' and resid 1033 through 1061
      removed outlier: 3.650A  pdb=" N   VAL A1038 " --> pdb=" O   VAL A1034 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ILE A1040 " --> pdb=" O   GLU A1036 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   SER A1041 " --> pdb=" O   SER A1037 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   VAL A1044 " --> pdb=" O   ILE A1040 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLY A1045 " --> pdb=" O   SER A1041 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   ASP A1049 " --> pdb=" O   GLY A1045 " (cutoff:3.500A)
      removed outlier: 4.904A  pdb=" N   PHE A1050 " --> pdb=" O   LEU A1046 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   ALA A1051 " --> pdb=" O   SER A1047 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1065 through 1094
      removed outlier: 4.952A  pdb=" N   SER A1079 " --> pdb=" O   SER A1075 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   ALA A1080 " --> pdb=" O   ARG A1076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1100 through 1123
    Processing helix  chain 'A' and resid 1123 through 1133
    Processing helix  chain 'H' and resid 71 through 77
    Processing helix  chain 'H' and resid 94 through 96
      No H-bonds generated for 'chain 'H' and resid 94 through 96'
    Processing helix  chain 'H' and resid 100 through 118
    Processing helix  chain 'H' and resid 139 through 144
    Processing helix  chain 'H' and resid 155 through 157
      No H-bonds generated for 'chain 'H' and resid 155 through 157'
    Processing helix  chain 'H' and resid 158 through 170
    Processing sheet with id=AA1, first strand: chain 'A' and resid 450 through 458
      removed outlier: 3.938A  pdb=" N   SER A 300 " --> pdb=" O   SER A 455 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY A 485 " --> pdb=" O   VAL A 303 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   ALA A 305 " --> pdb=" O   VAL A 483 " (cutoff:3.500A)
      removed outlier: 5.413A  pdb=" N   VAL A 483 " --> pdb=" O   ALA A 305 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 909 through 912
      removed outlier: 4.490A  pdb=" N   MET A 783 " --> pdb=" O   SER A 927 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 78 through 79
    Processing sheet with id=AA4, first strand: chain 'H' and resid 85 through 87
      removed outlier: 6.518A  pdb=" N   ILE H  86 " --> pdb=" O   VAL H 125 " (cutoff:3.500A)
      removed outlier: 7.813A  pdb=" N   GLU H 127 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   ASP H 148 " --> pdb=" O   THR H 126 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   HIS H 181 " --> pdb=" O   GLU H 177 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   GLU H 177 " --> pdb=" O   HIS H 181 " (cutoff:3.500A)

    509 hydrogen bonds defined for protein.
    1458 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.45

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1493
        1.29 -     1.43: 2608
        1.43 -     1.56: 5756
        1.56 -     1.69: 321
        1.69 -     1.82: 106
  Bond restraints: 10284
  Sorted by residual:
  bond pdb=" C   PHE A 556 "
       pdb=" N  BMET A 557 "
    ideal  model  delta    sigma   weight residual
    1.331  1.473 -0.142 1.48e-02 4.57e+03 9.19e+01
  bond pdb=" C   SER A1037 "
       pdb=" O   SER A1037 "
    ideal  model  delta    sigma   weight residual
    1.237  1.161  0.076 1.16e-02 7.43e+03 4.25e+01
  bond pdb=" CA  ALA H 166 "
       pdb=" CB  ALA H 166 "
    ideal  model  delta    sigma   weight residual
    1.529  1.430  0.099 1.55e-02 4.16e+03 4.07e+01
  bond pdb=" C   ARG A 268 "
       pdb=" O   ARG A 268 "
    ideal  model  delta    sigma   weight residual
    1.235  1.169  0.066 1.26e-02 6.30e+03 2.76e+01
  bond pdb=" C02 6OE A2131 "
       pdb=" N01 6OE A2131 "
    ideal  model  delta    sigma   weight residual
    1.452  1.537 -0.085 2.00e-02 2.50e+03 1.83e+01
  ... (remaining 10279 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 11070
        2.12 -     4.24: 2750
        4.24 -     6.37: 262
        6.37 -     8.49: 19
        8.49 -    10.61: 6
  Bond angle restraints: 14107
  Sorted by residual:
  angle pdb=" N   VAL A1034 "
        pdb=" CA  VAL A1034 "
        pdb=" C   VAL A1034 "
      ideal   model   delta    sigma   weight residual
     110.53  119.77   -9.24 9.40e-01 1.13e+00 9.67e+01
  angle pdb=" O   PHE A 556 "
        pdb=" C   PHE A 556 "
        pdb=" N  BMET A 557 "
      ideal   model   delta    sigma   weight residual
     122.39  111.78   10.61 1.30e+00 5.92e-01 6.66e+01
  angle pdb=" CA  PHE A 556 "
        pdb=" C   PHE A 556 "
        pdb=" N  BMET A 557 "
      ideal   model   delta    sigma   weight residual
     118.08  126.82   -8.74 1.30e+00 5.92e-01 4.52e+01
  angle pdb=" N   ARG H  62 "
        pdb=" CA  ARG H  62 "
        pdb=" C   ARG H  62 "
      ideal   model   delta    sigma   weight residual
     110.10  119.89   -9.79 1.49e+00 4.50e-01 4.31e+01
  angle pdb=" CA  ASP H 155 "
        pdb=" CB  ASP H 155 "
        pdb=" CG  ASP H 155 "
      ideal   model   delta    sigma   weight residual
     112.60  118.36   -5.76 1.00e+00 1.00e+00 3.32e+01
  ... (remaining 14102 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.31: 7326
       30.31 -    60.63: 208
       60.63 -    90.94: 30
       90.94 -   121.26: 15
      121.26 -   151.57: 5
  Dihedral angle restraints: 7584
    sinusoidal: 4335
      harmonic: 3249
  Sorted by residual:
  dihedral pdb=" CA  PRO A 438 "
           pdb=" C   PRO A 438 "
           pdb=" N   LYS A 439 "
           pdb=" CA  LYS A 439 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.31   28.69     0      5.00e+00 4.00e-02 3.29e+01
  dihedral pdb=" CA  TYR A 420 "
           pdb=" C   TYR A 420 "
           pdb=" N   ASN A 421 "
           pdb=" CA  ASN A 421 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.51  -26.49     0      5.00e+00 4.00e-02 2.81e+01
  dihedral pdb=" CA  ASP A 396 "
           pdb=" C   ASP A 396 "
           pdb=" N   CYS A 397 "
           pdb=" CA  CYS A 397 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.45  -25.55     0      5.00e+00 4.00e-02 2.61e+01
  ... (remaining 7581 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.113: 1242
       0.113 -    0.226: 364
       0.226 -    0.340: 35
       0.340 -    0.453: 3
       0.453 -    0.566: 3
  Chirality restraints: 1647
  Sorted by residual:
  chirality pdb=" CB  THR A1099 "
            pdb=" CA  THR A1099 "
            pdb=" OG1 THR A1099 "
            pdb=" CG2 THR A1099 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    1.99    0.57 2.00e-01 2.50e+01 8.00e+00
  chirality pdb=" CA  ALA H 166 "
            pdb=" N   ALA H 166 "
            pdb=" C   ALA H 166 "
            pdb=" CB  ALA H 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.94    0.54 2.00e-01 2.50e+01 7.43e+00
  chirality pdb=" CA  THR A1099 "
            pdb=" N   THR A1099 "
            pdb=" C   THR A1099 "
            pdb=" CB  THR A1099 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.05    0.47 2.00e-01 2.50e+01 5.56e+00
  ... (remaining 1644 not shown)

  Planarity restraints: 1612
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 398 "    0.155 2.00e-02 2.50e+03   7.81e-02 1.52e+02
        pdb=" CG  TRP A 398 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 398 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 398 "   -0.083 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 398 "   -0.040 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 398 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 398 "   -0.107 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 398 "    0.082 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 398 "   -0.018 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 398 "    0.088 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 719 "    0.126 2.00e-02 2.50e+03   7.71e-02 1.48e+02
        pdb=" CG  TRP A 719 "    0.006 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 719 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 719 "   -0.084 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 719 "   -0.055 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 719 "   -0.032 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 719 "   -0.125 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 719 "    0.061 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 719 "   -0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 719 "    0.114 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 362 "   -0.099 2.00e-02 2.50e+03   1.03e-01 1.34e+02
        pdb=" CG  ASN A 362 "    0.055 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 362 "    0.011 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 362 "    0.158 2.00e-02 2.50e+03
        pdb=" C1  NAG A2135 "   -0.125 2.00e-02 2.50e+03
  ... (remaining 1609 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.34: 14
        2.34 -     2.98: 4271
        2.98 -     3.62: 14413
        3.62 -     4.26: 23786
        4.26 -     4.90: 39452
  Nonbonded interactions: 81936
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP H 148 "
            pdb="ZN    ZN H 203 "
     model   vdw
     1.695 2.230
  nonbonded pdb=" OD1 ASP A1049 "
            pdb="NA    NA A2129 "
     model   vdw
     2.125 2.470
  nonbonded pdb=" OD1 ASP A 571 "
            pdb="NA    NA A2130 "
     model   vdw
     2.149 2.470
  nonbonded pdb=" O   GLY A1045 "
            pdb="NA    NA A2129 "
     model   vdw
     2.208 2.470
  nonbonded pdb=" O   GLY A 567 "
            pdb="NA    NA A2130 "
     model   vdw
     2.252 2.470
  ... (remaining 81931 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     12.550
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:6.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
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      :  0.016   0.396  10299  Z= 0.877
  Angle     :  1.759  10.611  14138  Z= 1.135
  Chirality :  0.101   0.566   1647
  Planarity :  0.014   0.100   1607
  Dihedral  : 14.856 151.569   5458
  Min Nonbonded Distance : 1.695

Molprobity Statistics.
  All-atom Clashscore : 0.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  3.20 %
    Favored  : 96.59 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.24), residues: 1099
  helix: -0.14 (0.19), residues: 595
  sheet:  0.81 (0.96), residues: 26
  loop :  0.43 (0.30), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 341 
 TYR   0.115   0.021   TYR A 388 
 PHE   0.064   0.012   PHE A 877 
 TRP   0.155   0.025   TRP A 398 
 HIS   0.011   0.003   HIS A 777 

Details of bonding type rmsd
  covalent geometry    : bond        0.01526 (10284)
  covalent geometry    : angle       1.75426 (14107)
  SS BOND              : bond        0.00710 (    8)
  SS BOND              : angle       1.68378 (   16)
  hydrogen bonds       : bond        0.19055 (  509)
  hydrogen bonds       : angle       6.97410 ( 1458)
  metal coordination   : bond        0.36440 (    2)
  link_NAG-ASN         : bond        0.01453 (    5)
  link_NAG-ASN         : angle       4.46144 (   15)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 158
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 THR cc_start: 0.9077 (m) cc_final: 0.8845 (p)
REVERT: A  436 MET cc_start: 0.6797 (mmt) cc_final: 0.6540 (mpt)
REVERT: A  449 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7353 (tptt)
REVERT: A  701 ARG cc_start: 0.7857 (tmm160) cc_final: 0.7572 (tpm170)
REVERT: A  940 GLN cc_start: 0.7646 (tt0) cc_final: 0.7247 (tm-30)
REVERT: A  997 MET cc_start: 0.8130 (tpp) cc_final: 0.7880 (tpt)
REVERT: A 1066 ARG cc_start: 0.7604 (ptp-170) cc_final: 0.7147 (ptp-170)
REVERT: A 1140 GLN cc_start: 0.7519 (tt0) cc_final: 0.7175 (tm-30)
REVERT: H   55 LYS cc_start: 0.7669 (ptmt) cc_final: 0.7364 (mmtm)
REVERT: H  104 LYS cc_start: 0.7944 (ttpp) cc_final: 0.7726 (ttpp)
REVERT: H  122 LYS cc_start: 0.7345 (mttt) cc_final: 0.7144 (mmtp)
REVERT: H  165 LEU cc_start: 0.8113 (mt) cc_final: 0.7861 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 159
  average time/residue: 0.5898
  time to fit residues: 100.3074
Evaluate side-chains
  94 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.2980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    5.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 968 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.162995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.111528 restraints weight = 22215.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 2.61
r_work: 0.3136 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3124
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3124 r_free = 0.3124    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3124 r_free = 0.3124    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3124
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10299  Z= 0.145
  Angle     :  0.720  24.082  14138  Z= 0.338
  Chirality :  0.061   1.761   1647
  Planarity :  0.004   0.044   1607
  Dihedral  : 12.157 169.794   3421
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.28 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  7.75 %
    Favored  : 90.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.01 (0.26), residues: 1099
  helix:  1.90 (0.21), residues: 593
  sheet:  0.09 (0.75), residues: 46
  loop :  0.89 (0.32), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 363 
 TYR   0.018   0.002   TYR A 619 
 PHE   0.014   0.002   PHE A 877 
 TRP   0.027   0.002   TRP A 398 
 HIS   0.012   0.001   HIS A 777 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (10284)
  covalent geometry    : angle       0.67142 (14107)
  SS BOND              : bond        0.00280 (    8)
  SS BOND              : angle       1.21984 (   16)
  hydrogen bonds       : bond        0.05838 (  509)
  hydrogen bonds       : angle       4.61497 ( 1458)
  metal coordination   : bond        0.00551 (    2)
  link_NAG-ASN         : bond        0.01064 (    5)
  link_NAG-ASN         : angle       7.90850 (   15)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A  436 MET cc_start: 0.6487 (mmt) cc_final: 0.6162 (mpt)
REVERT: A  449 LYS cc_start: 0.8070 (ttmt) cc_final: 0.7675 (tptm)
REVERT: A  647 MET cc_start: 0.9071 (mmt) cc_final: 0.8871 (mmp)
REVERT: A  690 ARG cc_start: 0.6247 (mtt180) cc_final: 0.5961 (ptp-170)
REVERT: A  698 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7088 (mm-30)
REVERT: A  701 ARG cc_start: 0.8242 (tmm160) cc_final: 0.7584 (tpm170)
REVERT: A  813 THR cc_start: 0.8740 (t) cc_final: 0.8473 (t)
REVERT: A  940 GLN cc_start: 0.8360 (tt0) cc_final: 0.7957 (tm-30)
REVERT: A  986 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8443 (ttt)
REVERT: A  997 MET cc_start: 0.8286 (tpp) cc_final: 0.7951 (tpt)
REVERT: A 1140 GLN cc_start: 0.7856 (tt0) cc_final: 0.7399 (mt0)
REVERT: H   55 LYS cc_start: 0.8255 (ptmt) cc_final: 0.7654 (mmtm)
REVERT: H   76 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7522 (tt0)
REVERT: H  122 LYS cc_start: 0.7267 (mttt) cc_final: 0.6959 (mptm)
REVERT: H  165 LEU cc_start: 0.8273 (mt) cc_final: 0.8047 (mt)
  outliers start: 17
  outliers final: 2
  residues processed: 129
  average time/residue: 0.5542
  time to fit residues: 76.9101
Evaluate side-chains
  96 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain A residue  416 LYS
Chi-restraints excluded: chain A residue  986 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9980
   chunk 21 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 79 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 95 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 874 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.160081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.110367 restraints weight = 16250.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 2.22
r_work: 0.3124 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2967
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2967 r_free = 0.2967    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2967 r_free = 0.2967    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2967
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.2430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10299  Z= 0.162
  Angle     :  0.675  22.687  14138  Z= 0.319
  Chirality :  0.046   0.643   1647
  Planarity :  0.004   0.043   1607
  Dihedral  : 11.279 179.255   3421
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  :  8.37 %
    Favored  : 89.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.12 (0.26), residues: 1099
  helix:  2.13 (0.21), residues: 594
  sheet:  0.03 (0.72), residues: 49
  loop :  0.73 (0.32), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 774 
 TYR   0.018   0.002   TYR A 619 
 PHE   0.022   0.002   PHE A 608 
 TRP   0.022   0.002   TRP A 398 
 HIS   0.010   0.002   HIS A 777 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (10284)
  covalent geometry    : angle       0.63506 (14107)
  SS BOND              : bond        0.00262 (    8)
  SS BOND              : angle       1.08363 (   16)
  hydrogen bonds       : bond        0.05992 (  509)
  hydrogen bonds       : angle       4.44712 ( 1458)
  metal coordination   : bond        0.00130 (    2)
  link_NAG-ASN         : bond        0.01229 (    5)
  link_NAG-ASN         : angle       6.98336 (   15)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A  223 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7767 (mp0)
REVERT: A  449 LYS cc_start: 0.8166 (ttmt) cc_final: 0.7665 (tptm)
REVERT: A  698 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7242 (mm-30)
REVERT: A  701 ARG cc_start: 0.8286 (tmm160) cc_final: 0.7608 (mmp-170)
REVERT: A  746 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6488 (pm20)
REVERT: A  940 GLN cc_start: 0.8519 (tt0) cc_final: 0.8081 (tm-30)
REVERT: A  997 MET cc_start: 0.8425 (tpp) cc_final: 0.8068 (tpt)
REVERT: A 1140 GLN cc_start: 0.7962 (tt0) cc_final: 0.7481 (mt0)
REVERT: H   55 LYS cc_start: 0.8240 (ptmt) cc_final: 0.7692 (mmtm)
REVERT: H   76 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7840 (mt-10)
REVERT: H  122 LYS cc_start: 0.7287 (mttt) cc_final: 0.6920 (mptm)
REVERT: H  165 LEU cc_start: 0.8290 (mt) cc_final: 0.8042 (mt)
  outliers start: 24
  outliers final: 8
  residues processed: 119
  average time/residue: 0.5714
  time to fit residues: 73.2123
Evaluate side-chains
  105 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  223 GLU
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  696 VAL
Chi-restraints excluded: chain A residue  746 GLU
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain H residue   68 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 107 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 97 optimal weight:    0.3980
   chunk 104 optimal weight:    8.9990
   chunk 67 optimal weight:    0.1980
   chunk 47 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 92 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
A 496 GLN
** A 860 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 = 0.3967 r_free = 0.3967 target = 0.162630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.113391 restraints weight = 15809.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 2.40
r_work: 0.3164 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3148
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3148
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.2798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10299  Z= 0.111
  Angle     :  0.587  20.786  14138  Z= 0.275
  Chirality :  0.041   0.474   1647
  Planarity :  0.004   0.039   1607
  Dihedral  : 10.699 178.827   3421
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 10.85 %
    Favored  : 87.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.38 (0.26), residues: 1099
  helix:  2.39 (0.21), residues: 593
  sheet:  0.61 (0.76), residues: 44
  loop :  0.72 (0.31), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 774 
 TYR   0.013   0.001   TYR A 545 
 PHE   0.011   0.001   PHE A 495 
 TRP   0.020   0.001   TRP A 313 
 HIS   0.009   0.001   HIS A 777 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 (10284)
  covalent geometry    : angle       0.54718 (14107)
  SS BOND              : bond        0.00227 (    8)
  SS BOND              : angle       0.90706 (   16)
  hydrogen bonds       : bond        0.04647 (  509)
  hydrogen bonds       : angle       4.17969 ( 1458)
  metal coordination   : bond        0.00080 (    2)
  link_NAG-ASN         : bond        0.01177 (    5)
  link_NAG-ASN         : angle       6.50179 (   15)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: A  223 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7619 (mp0)
REVERT: A  449 LYS cc_start: 0.8023 (ttmt) cc_final: 0.7554 (tptm)
REVERT: A  690 ARG cc_start: 0.7546 (ttp-170) cc_final: 0.7073 (tpp-160)
REVERT: A  698 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7155 (mm-30)
REVERT: A  701 ARG cc_start: 0.8241 (tmm160) cc_final: 0.7571 (mmm160)
REVERT: A  997 MET cc_start: 0.8110 (tpp) cc_final: 0.7853 (tpt)
REVERT: A 1140 GLN cc_start: 0.7848 (tt0) cc_final: 0.7386 (mt0)
REVERT: H   55 LYS cc_start: 0.8104 (ptmt) cc_final: 0.7558 (mptt)
REVERT: H   76 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7521 (mt-10)
REVERT: H  122 LYS cc_start: 0.7262 (mttt) cc_final: 0.6951 (mptm)
REVERT: H  165 LEU cc_start: 0.8206 (mt) cc_final: 0.7926 (mt)
  outliers start: 12
  outliers final: 3
  residues processed: 106
  average time/residue: 0.5965
  time to fit residues: 67.9332
Evaluate side-chains
  97 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 93
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 GLU
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue 1008 LEU
Chi-restraints excluded: chain H residue   68 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0770
   chunk 76 optimal weight:    6.9990
   overall best weight:    0.7542

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

Flipped N/Q/H residues before XYZ refinement:
A 496 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.162868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.112776 restraints weight = 16782.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 2.35
r_work: 0.3164 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3152
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3152
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.2926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10299  Z= 0.114
  Angle     :  0.581  20.526  14138  Z= 0.271
  Chirality :  0.041   0.428   1647
  Planarity :  0.004   0.039   1607
  Dihedral  : 10.556 178.287   3421
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 10.33 %
    Favored  : 87.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.43 (0.26), residues: 1099
  helix:  2.47 (0.21), residues: 594
  sheet:  0.29 (0.75), residues: 49
  loop :  0.70 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 774 
 TYR   0.013   0.001   TYR A 545 
 PHE   0.013   0.001   PHE A 608 
 TRP   0.019   0.001   TRP A 313 
 HIS   0.008   0.001   HIS A 777 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (10284)
  covalent geometry    : angle       0.54010 (14107)
  SS BOND              : bond        0.00225 (    8)
  SS BOND              : angle       0.88196 (   16)
  hydrogen bonds       : bond        0.04703 (  509)
  hydrogen bonds       : angle       4.13033 ( 1458)
  metal coordination   : bond        0.00063 (    2)
  link_NAG-ASN         : bond        0.01435 (    5)
  link_NAG-ASN         : angle       6.53075 (   15)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  223 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7637 (mp0)
REVERT: A  449 LYS cc_start: 0.7994 (ttmt) cc_final: 0.7548 (tptt)
REVERT: A  698 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7185 (mm-30)
REVERT: A  701 ARG cc_start: 0.8238 (tmm160) cc_final: 0.7682 (mmp-170)
REVERT: A  997 MET cc_start: 0.8101 (tpp) cc_final: 0.7859 (tpt)
REVERT: A 1008 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.7899 (mm)
REVERT: A 1140 GLN cc_start: 0.7851 (tt0) cc_final: 0.7402 (mt0)
REVERT: H   55 LYS cc_start: 0.8058 (ptmt) cc_final: 0.7510 (mptt)
REVERT: H   76 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7434 (mt-10)
REVERT: H  122 LYS cc_start: 0.7347 (mttt) cc_final: 0.7005 (mptm)
REVERT: H  165 LEU cc_start: 0.8238 (mt) cc_final: 0.7949 (mt)
  outliers start: 19
  outliers final: 4
  residues processed: 108
  average time/residue: 0.5317
  time to fit residues: 62.1536
Evaluate side-chains
  101 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 GLU
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain A residue 1008 LEU
Chi-restraints excluded: chain H residue   68 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9980
   chunk 108 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 496 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.162339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.110855 restraints weight = 21032.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 2.63
r_work: 0.3117 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3111
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3111 r_free = 0.3111    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3111 r_free = 0.3111    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3111
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.3010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10299  Z= 0.120
  Angle     :  0.573  20.024  14138  Z= 0.270
  Chirality :  0.041   0.416   1647
  Planarity :  0.004   0.040   1607
  Dihedral  : 10.470 178.690   3421
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 11.05 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.39 (0.26), residues: 1099
  helix:  2.51 (0.21), residues: 596
  sheet:  0.33 (0.75), residues: 49
  loop :  0.56 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 774 
 TYR   0.014   0.001   TYR A 644 
 PHE   0.013   0.001   PHE A 608 
 TRP   0.017   0.001   TRP A 313 
 HIS   0.008   0.001   HIS A 777 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (10284)
  covalent geometry    : angle       0.53488 (14107)
  SS BOND              : bond        0.00221 (    8)
  SS BOND              : angle       0.87526 (   16)
  hydrogen bonds       : bond        0.04907 (  509)
  hydrogen bonds       : angle       4.13598 ( 1458)
  metal coordination   : bond        0.00089 (    2)
  link_NAG-ASN         : bond        0.01226 (    5)
  link_NAG-ASN         : angle       6.32753 (   15)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
REVERT: A  223 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7716 (mp0)
REVERT: A  449 LYS cc_start: 0.7990 (ttmt) cc_final: 0.7570 (tptt)
REVERT: A  698 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7222 (mm-30)
REVERT: A  701 ARG cc_start: 0.8271 (tmm160) cc_final: 0.7622 (mmm160)
REVERT: A 1008 LEU cc_start: 0.8718 (tp) cc_final: 0.7952 (mm)
REVERT: A 1140 GLN cc_start: 0.7870 (tt0) cc_final: 0.7416 (mt0)
REVERT: H   55 LYS cc_start: 0.8056 (ptmt) cc_final: 0.7574 (mptt)
REVERT: H   76 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7440 (mt-10)
REVERT: H  122 LYS cc_start: 0.7394 (mttt) cc_final: 0.7000 (mptm)
REVERT: H  165 LEU cc_start: 0.8291 (mt) cc_final: 0.7987 (mt)
  outliers start: 18
  outliers final: 8
  residues processed: 110
  average time/residue: 0.5677
  time to fit residues: 67.5424
Evaluate side-chains
  107 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  223 GLU
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  696 VAL
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain H residue   48 PHE
Chi-restraints excluded: chain H residue   68 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 100 optimal weight:    0.4980
   chunk 51 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 107 optimal weight:    5.9990
   chunk 101 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 106 optimal weight:    9.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 496 GLN
A 874 HIS
A 940 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.161283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.110254 restraints weight = 20320.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 2.54
r_work: 0.3090 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3086
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3086 r_free = 0.3086    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3086 r_free = 0.3086    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3086
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.3034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10299  Z= 0.139
  Angle     :  0.596  19.904  14138  Z= 0.283
  Chirality :  0.042   0.427   1647
  Planarity :  0.004   0.039   1607
  Dihedral  : 10.545 177.831   3421
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.36 %
    Favored  : 86.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.30 (0.26), residues: 1099
  helix:  2.45 (0.21), residues: 597
  sheet:  0.28 (0.75), residues: 49
  loop :  0.49 (0.31), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 145 
 TYR   0.016   0.001   TYR A 644 
 PHE   0.016   0.001   PHE A 608 
 TRP   0.017   0.001   TRP A 313 
 HIS   0.010   0.001   HIS A 874 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (10284)
  covalent geometry    : angle       0.56036 (14107)
  SS BOND              : bond        0.00227 (    8)
  SS BOND              : angle       0.93587 (   16)
  hydrogen bonds       : bond        0.05239 (  509)
  hydrogen bonds       : angle       4.19182 ( 1458)
  metal coordination   : bond        0.00129 (    2)
  link_NAG-ASN         : bond        0.01185 (    5)
  link_NAG-ASN         : angle       6.23878 (   15)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A  223 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7748 (mp0)
REVERT: A  449 LYS cc_start: 0.8049 (ttmt) cc_final: 0.7577 (tptt)
REVERT: A  698 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7248 (mm-30)
REVERT: A  701 ARG cc_start: 0.8278 (tmm160) cc_final: 0.7707 (mmp-170)
REVERT: A 1008 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.7970 (mm)
REVERT: A 1140 GLN cc_start: 0.7872 (tt0) cc_final: 0.7401 (mt0)
REVERT: H   55 LYS cc_start: 0.8038 (ptmt) cc_final: 0.7551 (mptt)
REVERT: H   76 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7452 (mt-10)
REVERT: H  122 LYS cc_start: 0.7387 (mttt) cc_final: 0.7036 (mptm)
REVERT: H  165 LEU cc_start: 0.8311 (mt) cc_final: 0.8024 (mt)
  outliers start: 16
  outliers final: 9
  residues processed: 105
  average time/residue: 0.5994
  time to fit residues: 67.8012
Evaluate side-chains
  102 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  223 GLU
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  696 VAL
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain A residue 1008 LEU
Chi-restraints excluded: chain H residue   48 PHE
Chi-restraints excluded: chain H residue   68 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 94 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0040
   chunk 10 optimal weight:    9.9990
   chunk 63 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 1 optimal weight:    0.2980
   chunk 37 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.8594

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

Flipped N/Q/H residues before XYZ refinement:
A 496 GLN
A 874 HIS
A 940 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.162514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.111099 restraints weight = 20437.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 2.75
r_work: 0.3124 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3120
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3120
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10299  Z= 0.117
  Angle     :  0.576  19.665  14138  Z= 0.270
  Chirality :  0.041   0.422   1647
  Planarity :  0.003   0.039   1607
  Dihedral  : 10.424 178.236   3421
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.36 %
    Favored  : 86.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.40 (0.26), residues: 1099
  helix:  2.53 (0.21), residues: 596
  sheet:  0.68 (0.78), residues: 44
  loop :  0.50 (0.31), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 774 
 TYR   0.013   0.001   TYR A 545 
 PHE   0.012   0.001   PHE A 608 
 TRP   0.019   0.001   TRP A 313 
 HIS   0.010   0.001   HIS A 874 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (10284)
  covalent geometry    : angle       0.53890 (14107)
  SS BOND              : bond        0.00213 (    8)
  SS BOND              : angle       0.87508 (   16)
  hydrogen bonds       : bond        0.04779 (  509)
  hydrogen bonds       : angle       4.12390 ( 1458)
  metal coordination   : bond        0.00079 (    2)
  link_NAG-ASN         : bond        0.01236 (    5)
  link_NAG-ASN         : angle       6.23599 (   15)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
REVERT: A  223 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7708 (mp0)
REVERT: A  449 LYS cc_start: 0.7978 (ttmt) cc_final: 0.7509 (tptt)
REVERT: A  698 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7194 (mm-30)
REVERT: A  701 ARG cc_start: 0.8246 (tmm160) cc_final: 0.7582 (mmm160)
REVERT: A  843 GLN cc_start: 0.6888 (tp40) cc_final: 0.6637 (tm-30)
REVERT: A 1008 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.7894 (mm)
REVERT: A 1140 GLN cc_start: 0.7839 (tt0) cc_final: 0.7357 (mt0)
REVERT: H   55 LYS cc_start: 0.8008 (ptmt) cc_final: 0.7519 (mptt)
REVERT: H   76 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7394 (mt-10)
REVERT: H  122 LYS cc_start: 0.7329 (mttt) cc_final: 0.6977 (mptm)
REVERT: H  165 LEU cc_start: 0.8273 (mt) cc_final: 0.7955 (mt)
  outliers start: 16
  outliers final: 7
  residues processed: 108
  average time/residue: 0.5681
  time to fit residues: 66.3680
Evaluate side-chains
  104 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 GLU
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  696 VAL
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain A residue 1008 LEU
Chi-restraints excluded: chain H residue   48 PHE
Chi-restraints excluded: chain H residue   68 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 76 optimal weight:    0.6980
   chunk 54 optimal weight:    0.2980
   chunk 8 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 94 optimal weight:    0.0170
   chunk 27 optimal weight:    0.8980
   chunk 102 optimal weight:    8.9990
   chunk 5 optimal weight:    0.8980
   chunk 50 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
A 496 GLN
A 874 HIS
A 940 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.164447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.113600 restraints weight = 17893.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 2.48
r_work: 0.3178 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3178
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3178
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10299  Z= 0.103
  Angle     :  0.549  19.315  14138  Z= 0.257
  Chirality :  0.040   0.421   1647
  Planarity :  0.003   0.039   1607
  Dihedral  : 10.187 178.738   3421
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 11.57 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.46 (0.26), residues: 1099
  helix:  2.59 (0.21), residues: 597
  sheet:  0.46 (0.77), residues: 46
  loop :  0.53 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 774 
 TYR   0.013   0.001   TYR A 545 
 PHE   0.009   0.001   PHE A 495 
 TRP   0.017   0.001   TRP A 313 
 HIS   0.010   0.001   HIS A 874 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 (10284)
  covalent geometry    : angle       0.51144 (14107)
  SS BOND              : bond        0.00199 (    8)
  SS BOND              : angle       0.82280 (   16)
  hydrogen bonds       : bond        0.04223 (  509)
  hydrogen bonds       : angle       4.04197 ( 1458)
  metal coordination   : bond        0.00068 (    2)
  link_NAG-ASN         : bond        0.01334 (    5)
  link_NAG-ASN         : angle       6.10985 (   15)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.521 
Fit side-chains
REVERT: A  223 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7593 (pm20)
REVERT: A  449 LYS cc_start: 0.7958 (ttmt) cc_final: 0.7509 (tptt)
REVERT: A  531 MET cc_start: 0.8848 (tpt) cc_final: 0.8623 (tpp)
REVERT: A  698 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7029 (pp20)
REVERT: A  701 ARG cc_start: 0.8227 (tmm160) cc_final: 0.7560 (mmm160)
REVERT: A  940 GLN cc_start: 0.8066 (tt0) cc_final: 0.7730 (pt0)
REVERT: A 1008 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.7833 (mm)
REVERT: A 1140 GLN cc_start: 0.7795 (tt0) cc_final: 0.7352 (mt0)
REVERT: H   55 LYS cc_start: 0.7890 (ptmt) cc_final: 0.7422 (mptt)
REVERT: H   76 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7313 (mt-10)
REVERT: H  122 LYS cc_start: 0.7352 (mttt) cc_final: 0.6993 (mptm)
REVERT: H  165 LEU cc_start: 0.8214 (mt) cc_final: 0.7895 (mt)
  outliers start: 13
  outliers final: 7
  residues processed: 106
  average time/residue: 0.5964
  time to fit residues: 68.5667
Evaluate side-chains
  102 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  223 GLU
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain A residue 1008 LEU
Chi-restraints excluded: chain H residue   48 PHE
Chi-restraints excluded: chain H residue   68 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 98 optimal weight:    0.5980
   chunk 87 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0670
   chunk 59 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
A 389 GLN
A 496 GLN
A 874 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.164375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.112195 restraints weight = 24804.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.80
r_work: 0.3122 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3118
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3118
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.3352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049  10299  Z= 0.107
  Angle     :  0.564  19.227  14138  Z= 0.265
  Chirality :  0.040   0.421   1647
  Planarity :  0.003   0.039   1607
  Dihedral  : 10.172 178.648   3421
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 11.88 %
    Favored  : 86.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.46 (0.26), residues: 1099
  helix:  2.60 (0.21), residues: 597
  sheet:  0.41 (0.77), residues: 46
  loop :  0.52 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 774 
 TYR   0.013   0.001   TYR A 545 
 PHE   0.009   0.001   PHE A 495 
 TRP   0.017   0.001   TRP A 789 
 HIS   0.010   0.001   HIS A 874 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (10284)
  covalent geometry    : angle       0.52830 (14107)
  SS BOND              : bond        0.00209 (    8)
  SS BOND              : angle       0.82246 (   16)
  hydrogen bonds       : bond        0.04322 (  509)
  hydrogen bonds       : angle       4.07990 ( 1458)
  metal coordination   : bond        0.00055 (    2)
  link_NAG-ASN         : bond        0.01264 (    5)
  link_NAG-ASN         : angle       6.03045 (   15)

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.390 
Fit side-chains
REVERT: A  223 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7759 (pm20)
REVERT: A  318 ILE cc_start: 0.7837 (mm) cc_final: 0.7614 (mm)
REVERT: A  449 LYS cc_start: 0.8012 (ttmt) cc_final: 0.7629 (tptt)
REVERT: A  698 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7158 (pp20)
REVERT: A  701 ARG cc_start: 0.8334 (tmm160) cc_final: 0.7671 (mmm160)
REVERT: A  940 GLN cc_start: 0.8185 (tt0) cc_final: 0.7882 (pt0)
REVERT: A 1008 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8014 (mm)
REVERT: A 1140 GLN cc_start: 0.7862 (tt0) cc_final: 0.7450 (mt0)
REVERT: H   55 LYS cc_start: 0.7919 (ptmt) cc_final: 0.7502 (mptt)
REVERT: H   76 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7468 (mt-10)
REVERT: H  122 LYS cc_start: 0.7410 (mttt) cc_final: 0.7043 (mptm)
REVERT: H  165 LEU cc_start: 0.8306 (mt) cc_final: 0.7980 (mt)
  outliers start: 11
  outliers final: 7
  residues processed: 101
  average time/residue: 0.5804
  time to fit residues: 63.4451
Evaluate side-chains
  103 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  223 GLU
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue 1008 LEU
Chi-restraints excluded: chain H residue   48 PHE
Chi-restraints excluded: chain H residue   68 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 106 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0980
   chunk 107 optimal weight:    7.9990
   chunk 55 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 496 GLN
A 643 ASN
A 874 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.164358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.112721 restraints weight = 17694.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 2.57
r_work: 0.3181 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3174
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3174
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.3403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10299  Z= 0.108
  Angle     :  0.565  19.031  14138  Z= 0.265
  Chirality :  0.040   0.426   1647
  Planarity :  0.003   0.039   1607
  Dihedral  : 10.227 178.540   3421
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 11.47 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.45 (0.26), residues: 1099
  helix:  2.60 (0.21), residues: 598
  sheet:  0.39 (0.77), residues: 46
  loop :  0.51 (0.31), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 774 
 TYR   0.013   0.001   TYR A 545 
 PHE   0.010   0.001   PHE A 608 
 TRP   0.018   0.001   TRP A 313 
 HIS   0.010   0.001   HIS A 874 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (10284)
  covalent geometry    : angle       0.52913 (14107)
  SS BOND              : bond        0.00209 (    8)
  SS BOND              : angle       0.81696 (   16)
  hydrogen bonds       : bond        0.04399 (  509)
  hydrogen bonds       : angle       4.10894 ( 1458)
  metal coordination   : bond        0.00063 (    2)
  link_NAG-ASN         : bond        0.01321 (    5)
  link_NAG-ASN         : angle       6.07381 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3719.64 seconds
wall clock time: 64 minutes 0.61 seconds (3840.61 seconds total)