Starting phenix.real_space_refine
on Mon Jul 28 22:31:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rpk_24617/07_2025/7rpk_24617.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rpk_24617/07_2025/7rpk_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_24617/07_2025/7rpk_24617.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rpk_24617/07_2025/7rpk_24617.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rpk_24617/07_2025/7rpk_24617.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rpk_24617/07_2025/7rpk_24617.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.011 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 11.62, per 1000 atoms: 1.16
  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: 2.71
  Conformation dependent library (CDL) restraints added in 2.8 seconds
  
  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: 1.70
  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: 4.21

  Time building geometry restraints manager: 3.20 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:             1.470
  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:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     39.030
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.050
  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:18.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   59.500
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.155   0.025   TRP A 398 
 HIS   0.011   0.003   HIS A 777 
 PHE   0.064   0.012   PHE A 877 
 TYR   0.115   0.021   TYR A 388 
 ARG   0.007   0.001   ARG A 341 

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

*********************** 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  : 0.949 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 THR cc_start: 0.9077 (m) cc_final: 0.8846 (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: 0.7148 (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: 0.7896 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 159
  average time/residue: 1.3179
  time to fit residues: 224.3508
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  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 83 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 86 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 52 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 99 optimal weight:    0.0010
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 376 HIS
A 968 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.163690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.111658 restraints weight = 28696.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 2.95
r_work: 0.3097 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3083
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3083
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10299  Z= 0.139
  Angle     :  0.715  25.481  14138  Z= 0.334
  Chirality :  0.058   1.543   1647
  Planarity :  0.004   0.046   1607
  Dihedral  : 12.126 171.141   3421
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.19 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  :  7.95 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.26), residues: 1099
  helix:  1.93 (0.21), residues: 593
  sheet:  0.12 (0.76), residues: 46
  loop :  0.88 (0.32), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 398 
 HIS   0.012   0.001   HIS A 777 
 PHE   0.014   0.001   PHE A 585 
 TYR   0.015   0.002   TYR A 619 
 ARG   0.003   0.000   ARG A 774 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01919 (    5)
  link_NAG-ASN         : angle       8.15777 (   15)
  hydrogen bonds       : bond        0.05539 (  509)
  hydrogen bonds       : angle       4.57245 ( 1458)
  metal coordination   : bond        0.01146 (    2)
  SS BOND              : bond        0.00284 (    8)
  SS BOND              : angle       1.20674 (   16)
  covalent geometry    : bond        0.00282 (10284)
  covalent geometry    : angle       0.66309 (14107)

*********************** 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
  141 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 1.064 
Fit side-chains
REVERT: A  436 MET cc_start: 0.6481 (mmt) cc_final: 0.6126 (mpt)
REVERT: A  449 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7744 (tptm)
REVERT: A  531 MET cc_start: 0.8989 (tpt) cc_final: 0.8760 (tpp)
REVERT: A  690 ARG cc_start: 0.6260 (mtt180) cc_final: 0.5960 (ptp-170)
REVERT: A  698 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7124 (mm-30)
REVERT: A  701 ARG cc_start: 0.8288 (tmm160) cc_final: 0.7645 (tpm170)
REVERT: A  940 GLN cc_start: 0.8453 (tt0) cc_final: 0.8065 (tm-30)
REVERT: A  986 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8570 (ttt)
REVERT: A  997 MET cc_start: 0.8332 (tpp) cc_final: 0.8028 (tpt)
REVERT: A 1140 GLN cc_start: 0.7913 (tt0) cc_final: 0.7477 (mt0)
REVERT: H   55 LYS cc_start: 0.8291 (ptmt) cc_final: 0.7693 (mmtm)
REVERT: H   76 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7600 (tt0)
REVERT: H  112 ILE cc_start: 0.7896 (mt) cc_final: 0.7624 (mp)
REVERT: H  115 MET cc_start: 0.7396 (mtp) cc_final: 0.7041 (mtt)
REVERT: H  122 LYS cc_start: 0.7275 (mttt) cc_final: 0.6844 (mptm)
REVERT: H  165 LEU cc_start: 0.8280 (mt) cc_final: 0.8062 (mt)
  outliers start: 15
  outliers final: 2
  residues processed: 135
  average time/residue: 1.1964
  time to fit residues: 174.6980
Evaluate side-chains
  99 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 96
  time to evaluate  : 1.360 
-------------------------------------------------------------------------------
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 2 optimal weight:    0.9980
   chunk 97 optimal weight:    7.9990
   chunk 79 optimal weight:    0.8980
   chunk 60 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 84 optimal weight:    0.3980
   chunk 10 optimal weight:    7.9990
   chunk 74 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 874 HIS
A1135 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.163057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.112388 restraints weight = 15557.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 2.35
r_work: 0.3162 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3161
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3161
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10299  Z= 0.123
  Angle     :  0.631  22.518  14138  Z= 0.295
  Chirality :  0.044   0.614   1647
  Planarity :  0.004   0.041   1607
  Dihedral  : 10.998 178.523   3421
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  :  9.19 %
    Favored  : 88.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.33 (0.26), residues: 1099
  helix:  2.31 (0.21), residues: 594
  sheet:  0.12 (0.74), residues: 49
  loop :  0.82 (0.32), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 313 
 HIS   0.010   0.001   HIS A 874 
 PHE   0.014   0.001   PHE A 608 
 TYR   0.014   0.001   TYR A 545 
 ARG   0.004   0.000   ARG A 372 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01245 (    5)
  link_NAG-ASN         : angle       6.96690 (   15)
  hydrogen bonds       : bond        0.05109 (  509)
  hydrogen bonds       : angle       4.31700 ( 1458)
  metal coordination   : bond        0.00085 (    2)
  SS BOND              : bond        0.00222 (    8)
  SS BOND              : angle       0.95860 (   16)
  covalent geometry    : bond        0.00263 (10284)
  covalent geometry    : angle       0.58900 (14107)

*********************** 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
  130 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 1.054 
Fit side-chains
REVERT: A  223 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7481 (mp0)
REVERT: A  449 LYS cc_start: 0.8016 (ttmt) cc_final: 0.7562 (tptm)
REVERT: A  698 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7111 (mm-30)
REVERT: A  701 ARG cc_start: 0.8195 (tmm160) cc_final: 0.7544 (mmp-170)
REVERT: A  940 GLN cc_start: 0.8247 (tt0) cc_final: 0.7831 (tm-30)
REVERT: A  997 MET cc_start: 0.8050 (tpp) cc_final: 0.7788 (tpt)
REVERT: A 1140 GLN cc_start: 0.7822 (tt0) cc_final: 0.7371 (mt0)
REVERT: H   55 LYS cc_start: 0.8216 (ptmt) cc_final: 0.7618 (mmtm)
REVERT: H   76 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7570 (mt-10)
REVERT: H  112 ILE cc_start: 0.7782 (mt) cc_final: 0.7526 (mp)
REVERT: H  165 LEU cc_start: 0.8111 (mt) cc_final: 0.7859 (mt)
  outliers start: 21
  outliers final: 6
  residues processed: 119
  average time/residue: 1.6144
  time to fit residues: 207.2607
Evaluate side-chains
  102 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 1.484 
-------------------------------------------------------------------------------
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  410 CYS
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  813 THR
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 14 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   chunk 83 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 105 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.162510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.111960 restraints weight = 16263.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 2.46
r_work: 0.3166 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work: 0.3019 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3005
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3005 r_free = 0.3005    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3005 r_free = 0.3005    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3005
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.2811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10299  Z= 0.122
  Angle     :  0.590  20.777  14138  Z= 0.278
  Chirality :  0.042   0.468   1647
  Planarity :  0.004   0.040   1607
  Dihedral  : 10.582 177.848   3421
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 10.33 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.45 (0.26), residues: 1099
  helix:  2.47 (0.21), residues: 593
  sheet:  0.13 (0.74), residues: 49
  loop :  0.78 (0.31), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 313 
 HIS   0.008   0.001   HIS A 777 
 PHE   0.015   0.001   PHE A 608 
 TYR   0.014   0.001   TYR A 644 
 ARG   0.003   0.000   ARG A 774 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01112 (    5)
  link_NAG-ASN         : angle       6.49206 (   15)
  hydrogen bonds       : bond        0.04938 (  509)
  hydrogen bonds       : angle       4.19811 ( 1458)
  metal coordination   : bond        0.00069 (    2)
  SS BOND              : bond        0.00239 (    8)
  SS BOND              : angle       0.94154 (   16)
  covalent geometry    : bond        0.00268 (10284)
  covalent geometry    : angle       0.55003 (14107)

*********************** 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
  120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
REVERT: A  223 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7653 (mp0)
REVERT: A  449 LYS cc_start: 0.8060 (ttmt) cc_final: 0.7552 (tptm)
REVERT: A  690 ARG cc_start: 0.7537 (ttp-170) cc_final: 0.7106 (tpp-160)
REVERT: A  698 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7213 (mm-30)
REVERT: A  701 ARG cc_start: 0.8353 (tmm160) cc_final: 0.7715 (mmp-170)
REVERT: A  940 GLN cc_start: 0.8415 (tt0) cc_final: 0.8035 (tm-30)
REVERT: A  997 MET cc_start: 0.8181 (tpp) cc_final: 0.7848 (tpt)
REVERT: A 1140 GLN cc_start: 0.7941 (tt0) cc_final: 0.7487 (mt0)
REVERT: H   55 LYS cc_start: 0.8200 (ptmt) cc_final: 0.7616 (mptt)
REVERT: H   76 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7654 (mt-10)
REVERT: H  165 LEU cc_start: 0.8205 (mt) cc_final: 0.7915 (mt)
  outliers start: 20
  outliers final: 5
  residues processed: 112
  average time/residue: 1.1624
  time to fit residues: 141.4621
Evaluate side-chains
  100 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
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  464 MET
Chi-restraints excluded: chain A residue  947 SER
Chi-restraints excluded: chain A residue  996 VAL
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 57 optimal weight:    0.8980
   chunk 104 optimal weight:    8.9990
   chunk 49 optimal weight:    0.6980
   chunk 83 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 58 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 37 optimal weight:    0.4980
   chunk 26 optimal weight:    6.9990
   chunk 80 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3973 r_free = 0.3973 target = 0.163287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.111081 restraints weight = 25681.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.87
r_work: 0.3101 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3085
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3085 r_free = 0.3085    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3085 r_free = 0.3085    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3085
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.2976

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= 0.113
  Angle     :  0.576  20.389  14138  Z= 0.269
  Chirality :  0.040   0.428   1647
  Planarity :  0.003   0.040   1607
  Dihedral  : 10.453 178.347   3421
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 10.95 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.49 (0.26), residues: 1099
  helix:  2.54 (0.21), residues: 594
  sheet:  0.29 (0.76), residues: 49
  loop :  0.71 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 313 
 HIS   0.008   0.001   HIS A 777 
 PHE   0.011   0.001   PHE A 608 
 TYR   0.013   0.001   TYR A 545 
 ARG   0.002   0.000   ARG A 774 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01165 (    5)
  link_NAG-ASN         : angle       6.33538 (   15)
  hydrogen bonds       : bond        0.04636 (  509)
  hydrogen bonds       : angle       4.12050 ( 1458)
  metal coordination   : bond        0.00083 (    2)
  SS BOND              : bond        0.00229 (    8)
  SS BOND              : angle       0.88837 (   16)
  covalent geometry    : bond        0.00243 (10284)
  covalent geometry    : angle       0.53712 (14107)

*********************** 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
  118 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 1.049 
Fit side-chains
REVERT: A  223 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7739 (mp0)
REVERT: A  449 LYS cc_start: 0.8009 (ttmt) cc_final: 0.7626 (tptt)
REVERT: A  698 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7270 (mm-30)
REVERT: A  701 ARG cc_start: 0.8339 (tmm160) cc_final: 0.7787 (mmp-170)
REVERT: A  815 ASN cc_start: 0.8815 (t0) cc_final: 0.8605 (t0)
REVERT: A 1140 GLN cc_start: 0.7906 (tt0) cc_final: 0.7484 (mt0)
REVERT: H   55 LYS cc_start: 0.8128 (ptmt) cc_final: 0.7595 (mptt)
REVERT: H   76 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7556 (mt-10)
REVERT: H  112 ILE cc_start: 0.7897 (mt) cc_final: 0.7646 (mp)
REVERT: H  165 LEU cc_start: 0.8301 (mt) cc_final: 0.8008 (mt)
  outliers start: 20
  outliers final: 7
  residues processed: 112
  average time/residue: 1.5855
  time to fit residues: 192.3713
Evaluate side-chains
  105 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 2.248 
-------------------------------------------------------------------------------
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  410 CYS
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  947 SER
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 85 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 84 optimal weight:    4.9990
   chunk 100 optimal weight:    0.0770
   chunk 38 optimal weight:    0.1980
   chunk 9 optimal weight:    6.9990
   chunk 83 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.5538

-------------------------------------------------------------------------------
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 = 0.3981 r_free = 0.3981 target = 0.164263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.113497 restraints weight = 22379.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 2.57
r_work: 0.3142 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3139
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3139 r_free = 0.3139    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3139 r_free = 0.3139    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3139
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.3116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  10299  Z= 0.106
  Angle     :  0.564  20.114  14138  Z= 0.265
  Chirality :  0.040   0.411   1647
  Planarity :  0.003   0.041   1607
  Dihedral  : 10.346 179.246   3421
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 12.29 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.26), residues: 1099
  helix:  2.58 (0.21), residues: 596
  sheet:  0.79 (0.79), residues: 44
  loop :  0.56 (0.31), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 650 
 HIS   0.008   0.001   HIS A 777 
 PHE   0.009   0.001   PHE A 608 
 TYR   0.013   0.001   TYR A 545 
 ARG   0.002   0.000   ARG A 774 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01431 (    5)
  link_NAG-ASN         : angle       6.36320 (   15)
  hydrogen bonds       : bond        0.04345 (  509)
  hydrogen bonds       : angle       4.07947 ( 1458)
  metal coordination   : bond        0.00052 (    2)
  SS BOND              : bond        0.00197 (    8)
  SS BOND              : angle       0.82824 (   16)
  covalent geometry    : bond        0.00221 (10284)
  covalent geometry    : angle       0.52422 (14107)

*********************** 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
  121 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 1.218 
Fit side-chains
   revert: symmetry clash
REVERT: A  223 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7678 (mp0)
REVERT: A  449 LYS cc_start: 0.7974 (ttmt) cc_final: 0.7544 (tptt)
REVERT: A  698 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7190 (mm-30)
REVERT: A  701 ARG cc_start: 0.8284 (tmm160) cc_final: 0.7725 (mmp-170)
REVERT: A  815 ASN cc_start: 0.8780 (t0) cc_final: 0.8554 (t0)
REVERT: A 1008 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.7941 (mm)
REVERT: A 1140 GLN cc_start: 0.7868 (tt0) cc_final: 0.7453 (mt0)
REVERT: H   55 LYS cc_start: 0.8034 (ptmt) cc_final: 0.7535 (mptt)
REVERT: H   76 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7438 (mt-10)
REVERT: H  112 ILE cc_start: 0.7799 (mt) cc_final: 0.7541 (mp)
REVERT: H  165 LEU cc_start: 0.8248 (mt) cc_final: 0.7950 (mt)
  outliers start: 16
  outliers final: 7
  residues processed: 114
  average time/residue: 1.0589
  time to fit residues: 131.5842
Evaluate side-chains
  106 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
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  947 SER
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain A residue  996 VAL
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 77 optimal weight:    0.2980
   chunk 31 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 10 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9980
   chunk 20 optimal weight:    8.9990
   chunk 100 optimal weight:    0.0020
   chunk 42 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.8590

-------------------------------------------------------------------------------
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 = 0.3968 r_free = 0.3968 target = 0.163037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.111807 restraints weight = 20487.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 2.71
r_work: 0.3121 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3097
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3097
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.3143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10299  Z= 0.117
  Angle     :  0.572  19.894  14138  Z= 0.269
  Chirality :  0.041   0.413   1647
  Planarity :  0.003   0.040   1607
  Dihedral  : 10.315 178.693   3421
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 12.29 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.47 (0.26), residues: 1099
  helix:  2.59 (0.21), residues: 596
  sheet:  0.25 (0.76), residues: 49
  loop :  0.59 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 313 
 HIS   0.011   0.001   HIS A 874 
 PHE   0.013   0.001   PHE A 608 
 TYR   0.013   0.001   TYR A 644 
 ARG   0.002   0.000   ARG A 774 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01245 (    5)
  link_NAG-ASN         : angle       6.28535 (   15)
  hydrogen bonds       : bond        0.04704 (  509)
  hydrogen bonds       : angle       4.10275 ( 1458)
  metal coordination   : bond        0.00103 (    2)
  SS BOND              : bond        0.00207 (    8)
  SS BOND              : angle       0.89695 (   16)
  covalent geometry    : bond        0.00256 (10284)
  covalent geometry    : angle       0.53341 (14107)

*********************** 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
  115 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
REVERT: A  223 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7780 (mp0)
REVERT: A  449 LYS cc_start: 0.7986 (ttmt) cc_final: 0.7603 (tptt)
REVERT: A  698 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7268 (mm-30)
REVERT: A  701 ARG cc_start: 0.8317 (tmm160) cc_final: 0.7762 (mmp-170)
REVERT: A  815 ASN cc_start: 0.8793 (t0) cc_final: 0.8582 (t0)
REVERT: A  843 GLN cc_start: 0.6794 (tp40) cc_final: 0.6555 (tm-30)
REVERT: A 1008 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8012 (mm)
REVERT: A 1140 GLN cc_start: 0.7869 (tt0) cc_final: 0.7463 (mt0)
REVERT: H   55 LYS cc_start: 0.8032 (ptmt) cc_final: 0.7574 (mptt)
REVERT: H   76 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7432 (mt-10)
REVERT: H  165 LEU cc_start: 0.8316 (mt) cc_final: 0.8024 (mt)
  outliers start: 16
  outliers final: 11
  residues processed: 107
  average time/residue: 1.5985
  time to fit residues: 189.0357
Evaluate side-chains
  110 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
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  372 ARG
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  947 SER
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain A residue  996 VAL
Chi-restraints excluded: chain A residue 1008 LEU
Chi-restraints excluded: chain H residue   48 PHE
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   89 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 94 optimal weight:    0.2980
   chunk 81 optimal weight:    2.9990
   chunk 10 optimal weight:   10.0000
   chunk 38 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.7384

-------------------------------------------------------------------------------
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 = 0.3972 r_free = 0.3972 target = 0.163405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.112490 restraints weight = 19787.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.58
r_work: 0.3141 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3136
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3136 r_free = 0.3136    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3136 r_free = 0.3136    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3136
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10299  Z= 0.110
  Angle     :  0.563  19.693  14138  Z= 0.265
  Chirality :  0.040   0.416   1647
  Planarity :  0.003   0.040   1607
  Dihedral  : 10.254 178.848   3421
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 12.29 %
    Favored  : 86.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.51 (0.26), residues: 1099
  helix:  2.63 (0.21), residues: 596
  sheet:  0.56 (0.80), residues: 44
  loop :  0.56 (0.31), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 313 
 HIS   0.010   0.001   HIS A 874 
 PHE   0.011   0.001   PHE A 608 
 TYR   0.013   0.001   TYR A 545 
 ARG   0.003   0.000   ARG A 265 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01295 (    5)
  link_NAG-ASN         : angle       6.21332 (   15)
  hydrogen bonds       : bond        0.04548 (  509)
  hydrogen bonds       : angle       4.07551 ( 1458)
  metal coordination   : bond        0.00064 (    2)
  SS BOND              : bond        0.00205 (    8)
  SS BOND              : angle       0.86157 (   16)
  covalent geometry    : bond        0.00238 (10284)
  covalent geometry    : angle       0.52519 (14107)

*********************** 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
  115 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 1.151 
Fit side-chains
   revert: symmetry clash
REVERT: A  223 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7715 (mp0)
REVERT: A  449 LYS cc_start: 0.7964 (ttmt) cc_final: 0.7536 (tptt)
REVERT: A  698 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7184 (mm-30)
REVERT: A  701 ARG cc_start: 0.8258 (tmm160) cc_final: 0.7683 (mmp-170)
REVERT: A  815 ASN cc_start: 0.8785 (t0) cc_final: 0.8565 (t0)
REVERT: A 1008 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.7915 (mm)
REVERT: A 1140 GLN cc_start: 0.7841 (tt0) cc_final: 0.7410 (mt0)
REVERT: H   55 LYS cc_start: 0.7965 (ptmt) cc_final: 0.7497 (mptt)
REVERT: H   76 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7344 (mt-10)
REVERT: H  165 LEU cc_start: 0.8298 (mt) cc_final: 0.7991 (mt)
  outliers start: 15
  outliers final: 8
  residues processed: 108
  average time/residue: 1.1211
  time to fit residues: 132.0819
Evaluate side-chains
  107 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
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  360 LEU
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  947 SER
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 12 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 83 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 104 optimal weight:   10.0000
   chunk 71 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 69 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0020
   overall best weight:    0.9392

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.162685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.111363 restraints weight = 16835.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 2.37
r_work: 0.3142 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3132
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3132
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.3231

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= 0.122
  Angle     :  0.584  19.443  14138  Z= 0.278
  Chirality :  0.041   0.426   1647
  Planarity :  0.004   0.040   1607
  Dihedral  : 10.268 178.171   3421
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.98 %
    Favored  : 86.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.26), residues: 1099
  helix:  2.62 (0.21), residues: 596
  sheet:  0.09 (0.76), residues: 49
  loop :  0.58 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 313 
 HIS   0.010   0.001   HIS A 874 
 PHE   0.014   0.001   PHE A 608 
 TYR   0.014   0.001   TYR A 644 
 ARG   0.002   0.000   ARG A 774 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01262 (    5)
  link_NAG-ASN         : angle       6.12470 (   15)
  hydrogen bonds       : bond        0.04853 (  509)
  hydrogen bonds       : angle       4.11492 ( 1458)
  metal coordination   : bond        0.00097 (    2)
  SS BOND              : bond        0.00218 (    8)
  SS BOND              : angle       0.89594 (   16)
  covalent geometry    : bond        0.00270 (10284)
  covalent geometry    : angle       0.54912 (14107)

*********************** 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
  113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 1.053 
Fit side-chains
REVERT: A  223 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7742 (mp0)
REVERT: A  449 LYS cc_start: 0.8008 (ttmt) cc_final: 0.7618 (tptt)
REVERT: A  587 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.7069 (mtpt)
REVERT: A  698 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7250 (mm-30)
REVERT: A  701 ARG cc_start: 0.8293 (tmm160) cc_final: 0.7768 (mmp-170)
REVERT: A 1008 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.7995 (mm)
REVERT: A 1140 GLN cc_start: 0.7850 (tt0) cc_final: 0.7445 (mt0)
REVERT: H   55 LYS cc_start: 0.7949 (ptmt) cc_final: 0.7526 (mptt)
REVERT: H   76 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7400 (mt-10)
REVERT: H  165 LEU cc_start: 0.8359 (mt) cc_final: 0.8056 (mt)
  outliers start: 16
  outliers final: 11
  residues processed: 106
  average time/residue: 1.0787
  time to fit residues: 124.7788
Evaluate side-chains
  106 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
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  372 ARG
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain A residue  947 SER
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain A residue  996 VAL
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 36 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 96 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0570
   chunk 63 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0970
   chunk 89 optimal weight:    4.9990
   chunk 102 optimal weight:    6.9990
   chunk 56 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.8100

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

Flipped N/Q/H residues before XYZ refinement:
A 643 ASN
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 = 0.3971 r_free = 0.3971 target = 0.163266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.112165 restraints weight = 16396.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.55
r_work: 0.3165 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3165
-------------------------------------------------------------------------------
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 = 0.43   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 = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3152
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.3292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10299  Z= 0.115
  Angle     :  0.573  19.337  14138  Z= 0.271
  Chirality :  0.040   0.425   1647
  Planarity :  0.003   0.040   1607
  Dihedral  : 10.207 178.200   3421
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 12.60 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.49 (0.26), residues: 1099
  helix:  2.63 (0.21), residues: 596
  sheet:  0.51 (0.82), residues: 41
  loop :  0.54 (0.31), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 313 
 HIS   0.010   0.001   HIS A 874 
 PHE   0.011   0.001   PHE A 608 
 TYR   0.013   0.001   TYR A 644 
 ARG   0.002   0.000   ARG A 774 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01280 (    5)
  link_NAG-ASN         : angle       6.04620 (   15)
  hydrogen bonds       : bond        0.04622 (  509)
  hydrogen bonds       : angle       4.10739 ( 1458)
  metal coordination   : bond        0.00071 (    2)
  SS BOND              : bond        0.00211 (    8)
  SS BOND              : angle       0.85714 (   16)
  covalent geometry    : bond        0.00253 (10284)
  covalent geometry    : angle       0.53759 (14107)

********************** 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
  112 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 1.164 
Fit side-chains
   revert: symmetry clash
REVERT: A  223 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7715 (mp0)
REVERT: A  449 LYS cc_start: 0.7995 (ttmt) cc_final: 0.7609 (tptt)
REVERT: A  587 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.7047 (mtpt)
REVERT: A  698 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7140 (pp20)
REVERT: A  701 ARG cc_start: 0.8308 (tmm160) cc_final: 0.7657 (mmm160)
REVERT: A 1008 LEU cc_start: 0.8739 (tp) cc_final: 0.7974 (mm)
REVERT: A 1140 GLN cc_start: 0.7852 (tt0) cc_final: 0.7452 (mt0)
REVERT: H   55 LYS cc_start: 0.7919 (ptmt) cc_final: 0.7512 (mptt)
REVERT: H   76 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7413 (mt-10)
REVERT: H  165 LEU cc_start: 0.8355 (mt) cc_final: 0.8037 (mt)
  outliers start: 13
  outliers final: 9
  residues processed: 106
  average time/residue: 1.1367
  time to fit residues: 132.0579
Evaluate side-chains
  106 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 1.269 
-------------------------------------------------------------------------------
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  360 LEU
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain A residue  947 SER
Chi-restraints excluded: chain A residue  961 SER
Chi-restraints excluded: chain A residue  996 VAL
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 71 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   chunk 95 optimal weight:    6.9990
   chunk 96 optimal weight:    0.9990
   chunk 49 optimal weight:    7.9990
   chunk 93 optimal weight:    3.9990
   chunk 108 optimal weight:    2.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 389 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 = 0.3943 r_free = 0.3943 target = 0.160982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.108052 restraints weight = 21754.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.87
r_work: 0.3072 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3067
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3067 r_free = 0.3067    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3067 r_free = 0.3067    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3067
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10299  Z= 0.159
  Angle     :  0.620  19.176  14138  Z= 0.297
  Chirality :  0.043   0.450   1647
  Planarity :  0.004   0.039   1607
  Dihedral  : 10.484 176.557   3421
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 12.29 %
    Favored  : 86.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.33 (0.26), residues: 1099
  helix:  2.50 (0.21), residues: 596
  sheet:  0.09 (0.78), residues: 46
  loop :  0.50 (0.31), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 313 
 HIS   0.010   0.001   HIS A 874 
 PHE   0.019   0.001   PHE A 608 
 TYR   0.017   0.002   TYR A 644 
 ARG   0.003   0.000   ARG H 145 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01184 (    5)
  link_NAG-ASN         : angle       5.98232 (   15)
  hydrogen bonds       : bond        0.05573 (  509)
  hydrogen bonds       : angle       4.25024 ( 1458)
  metal coordination   : bond        0.00206 (    2)
  SS BOND              : bond        0.00246 (    8)
  SS BOND              : angle       0.96024 (   16)
  covalent geometry    : bond        0.00374 (10284)
  covalent geometry    : angle       0.58853 (14107)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9021.10 seconds
wall clock time: 164 minutes 7.21 seconds (9847.21 seconds total)