Starting phenix.real_space_refine
on Thu Jul 31 17:49:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hlw_52273/07_2025/9hlw_52273.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hlw_52273/07_2025/9hlw_52273.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hlw_52273/07_2025/9hlw_52273.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hlw_52273/07_2025/9hlw_52273.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hlw_52273/07_2025/9hlw_52273.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hlw_52273/07_2025/9hlw_52273.cif"
  }
  resolution = 2.66
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.022
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: 7
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Zn      4      6.06       5
     S      48      5.16       5
     Cl      1      4.86       5
     C    8519      2.51       5
     N    2208      2.21       5
     O    2593      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13375
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 5525
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 690, 5504
          Classifications: {'peptide': 690}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 645}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 690, 5504
          Classifications: {'peptide': 690}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 645}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 5634
    Chain: "E"
      Number of atoms: 5545
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 690, 5504
          Classifications: {'peptide': 690}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 645}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 690, 5504
          Classifications: {'peptide': 690}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 645}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 5612
    Chain: "H"
      Number of atoms: 965
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 965
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 4, 'TRANS': 121}
    Chain: "Q"
      Number of atoms: 965
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 965
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 4, 'TRANS': 121}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "F"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "G"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "I"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "A"
      Number of atoms: 59
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 59
          Unusual residues: {' CA': 1, ' ZN': 2, 'NAG': 4}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "E"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 60
          Unusual residues: {' CA': 1, ' CL': 1, ' ZN': 2, 'NAG': 4}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Residues with excluded nonbonded symmetry interactions: 7
    residue:
      pdb=" N  AGLU A 183 " occ=0.50
      ... (16 atoms not shown)
      pdb=" OE2BGLU A 183 " occ=0.50
    residue:
      pdb=" N  ASER A 613 " occ=0.70
      ... (10 atoms not shown)
      pdb=" OG BSER A 613 " occ=0.30
    residue:
      pdb=" N  AGLN E  79 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NE2BGLN E  79 " occ=0.50
    residue:
      pdb=" N  ASER E 155 " occ=0.50
      ... (10 atoms not shown)
      pdb=" OG BSER E 155 " occ=0.50
    residue:
      pdb=" N  AGLU E 183 " occ=0.50
      ... (16 atoms not shown)
      pdb=" OE2BGLU E 183 " occ=0.50
    residue:
      pdb=" N  ASER E 613 " occ=0.70
      ... (10 atoms not shown)
      pdb=" OG BSER E 613 " occ=0.30
    residue:
      pdb=" N  AVAL E 660 " occ=0.50
      ... (12 atoms not shown)
      pdb=" CG2BVAL E 660 " occ=0.50
  Time building chain proxies: 13.79, per 1000 atoms: 1.03
  Number of scatterers: 13375
  At special positions: 0
  Unit cell: (107.69, 126.38, 91.67, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      4     29.99
     Ca      2     19.99
     Cl      1     17.00
     S      48     16.00
     O    2593      8.00
     N    2208      7.00
     C    8519      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 101 " - pdb=" SG  CYS H 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS Q  22 " - pdb=" SG  CYS Q  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS Q 101 " - pdb=" SG  CYS Q 104 " distance=2.03

  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
    ALPHA1-3
      " BMA F   3 " - " MAN F   4 "
      " BMA I   3 " - " MAN I   4 "
    ALPHA1-6
      " BMA F   3 " - " MAN F   5 "
      " BMA I   3 " - " MAN I   5 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
      " NAG I   1 " - " NAG I   2 "
      " NAG I   2 " - " BMA I   3 "
    NAG-ASN
      " NAG A 801 " - " ASN A 121 "
      " NAG A 802 " - " ASN A 140 "
      " NAG A 804 " - " ASN A 459 "
      " NAG E 801 " - " ASN E 121 "
      " NAG E 802 " - " ASN E 140 "
      " NAG E 804 " - " ASN E 459 "
  Time building additional restraints: 4.04
  Conformation dependent library (CDL) restraints added in 2.8 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 805 "
        pdb="ZN    ZN A 805 " - pdb=" NE2 HIS A 553 "
      pdb="  ZN A 806 "
        pdb="ZN    ZN A 806 " - pdb=" NE2 HIS A 377 "
      pdb="  ZN E 805 "
        pdb="ZN    ZN E 805 " - pdb=" NE2 HIS E 553 "
      pdb="  ZN E 806 "
        pdb="ZN    ZN E 806 " - pdb=" NE2 HIS E 377 "


  3276 Ramachandran restraints generated.
    1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3012

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 15 sheets defined
      35.1% alpha, 15.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 57 through 63
      removed outlier: 3.653A  pdb=" N   PHE A  61 " --> pdb=" O   ASN A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 78
      removed outlier: 3.523A  pdb=" N   ILE A  70 " --> pdb=" O   LYS A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 104
    Processing helix  chain 'A' and resid 181 through 191
    Processing helix  chain 'A' and resid 209 through 220
    Processing helix  chain 'A' and resid 230 through 235
    Processing helix  chain 'A' and resid 298 through 304
    Processing helix  chain 'A' and resid 388 through 409
      removed outlier: 4.045A  pdb=" N   VAL A 394 " --> pdb=" O   SER A 390 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLY A 409 " --> pdb=" O   LEU A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 438
    Processing helix  chain 'A' and resid 438 through 445
    Processing helix  chain 'A' and resid 470 through 479
      removed outlier: 3.714A  pdb=" N   LYS A 479 " --> pdb=" O   HIS A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 501
      removed outlier: 3.508A  pdb=" N   SER A 496 " --> pdb=" O   SER A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 526
    Processing helix  chain 'A' and resid 558 through 566
      removed outlier: 3.546A  pdb=" N   VAL A 562 " --> pdb=" O   THR A 558 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 590
    Processing helix  chain 'A' and resid 596 through 616
      removed outlier: 3.775A  pdb=" N   TYR A 600 " --> pdb=" O   ASP A 596 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   VAL A 602 " --> pdb=" O   ARG A 598 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   VAL A 603 " --> pdb=" O   ASP A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 618 through 626
    Processing helix  chain 'A' and resid 629 through 653
    Processing helix  chain 'A' and resid 657 through 670
      removed outlier: 3.810A  pdb=" N   MET A 663 " --> pdb=" O   ILE A 659 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU A 668 " --> pdb=" O   MET A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 671 through 676
    Processing helix  chain 'A' and resid 705 through 712
    Processing helix  chain 'A' and resid 720 through 746
      removed outlier: 3.839A  pdb=" N   LEU A 746 " --> pdb=" O   ALA A 742 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 57 through 63
      removed outlier: 3.625A  pdb=" N   PHE E  61 " --> pdb=" O   ASN E  57 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 66 through 78
      removed outlier: 3.569A  pdb=" N   ILE E  70 " --> pdb=" O   LYS E  66 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 104
    Processing helix  chain 'E' and resid 181 through 193
      removed outlier: 3.639A  pdb=" N   ASP E 191 " --> pdb=" O   LYS E 187 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 209 through 220
    Processing helix  chain 'E' and resid 230 through 235
    Processing helix  chain 'E' and resid 298 through 304
    Processing helix  chain 'E' and resid 388 through 409
      removed outlier: 4.072A  pdb=" N   VAL E 394 " --> pdb=" O   SER E 390 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY E 409 " --> pdb=" O   LEU E 405 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 430 through 438
    Processing helix  chain 'E' and resid 438 through 445
    Processing helix  chain 'E' and resid 470 through 479
      removed outlier: 3.664A  pdb=" N   LYS E 479 " --> pdb=" O   HIS E 475 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 492 through 501
    Processing helix  chain 'E' and resid 521 through 526
    Processing helix  chain 'E' and resid 558 through 566
      removed outlier: 3.531A  pdb=" N   VAL E 562 " --> pdb=" O   THR E 558 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 570 through 590
    Processing helix  chain 'E' and resid 596 through 617
      removed outlier: 3.812A  pdb=" N   TYR E 600 " --> pdb=" O   ASP E 596 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   VAL E 602 " --> pdb=" O   ARG E 598 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   VAL E 603 " --> pdb=" O   ASP E 599 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 618 through 626
    Processing helix  chain 'E' and resid 629 through 653
    Processing helix  chain 'E' and resid 657 through 670
    Processing helix  chain 'E' and resid 671 through 676
    Processing helix  chain 'E' and resid 705 through 712
    Processing helix  chain 'E' and resid 720 through 746
      removed outlier: 3.834A  pdb=" N   LEU E 746 " --> pdb=" O   ALA E 742 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 110 through 114
    Processing helix  chain 'Q' and resid 110 through 114
    Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 119
      removed outlier: 3.781A  pdb=" N   SER A 107 " --> pdb=" O   THR A 361 " (cutoff:3.500A)
      removed outlier: 5.160A  pdb=" N   THR A 415 " --> pdb=" O   PRO A 368 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   ARG A 370 " --> pdb=" O   THR A 415 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   LEU A 417 " --> pdb=" O   ARG A 370 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   VAL A 372 " --> pdb=" O   LEU A 417 " (cutoff:3.500A)
      removed outlier: 7.816A  pdb=" N   ALA A 419 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   LEU A 374 " --> pdb=" O   ALA A 419 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   TRP A 421 " --> pdb=" O   LEU A 374 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   GLY A 376 " --> pdb=" O   TRP A 421 " (cutoff:3.500A)
      removed outlier: 10.090A  pdb=" N   GLY A 446 " --> pdb=" O   GLU A 367 " (cutoff:3.500A)
      removed outlier: 10.860A  pdb=" N   ASP A 369 " --> pdb=" O   GLY A 446 " (cutoff:3.500A)
      removed outlier: 9.349A  pdb=" N   ALA A 448 " --> pdb=" O   ASP A 369 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   TYR A 371 " --> pdb=" O   ALA A 448 " (cutoff:3.500A)
      removed outlier: 8.097A  pdb=" N   ILE A 450 " --> pdb=" O   TYR A 371 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   ILE A 373 " --> pdb=" O   ILE A 450 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ALA A 531 " --> pdb=" O   VAL A 447 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   ALA A 535 " --> pdb=" O   ASN A 451 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 140
    Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 163
    Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 204
      removed outlier: 7.229A  pdb=" N   VAL A 225 " --> pdb=" O   HIS A 295 " (cutoff:3.500A)
      removed outlier: 8.225A  pdb=" N   ILE A 297 " --> pdb=" O   VAL A 225 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   LEU A 227 " --> pdb=" O   ILE A 297 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 107 through 119
      removed outlier: 3.798A  pdb=" N   SER E 107 " --> pdb=" O   THR E 361 " (cutoff:3.500A)
      removed outlier: 4.756A  pdb=" N   THR E 415 " --> pdb=" O   PRO E 368 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   ARG E 370 " --> pdb=" O   THR E 415 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   LEU E 417 " --> pdb=" O   ARG E 370 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   VAL E 372 " --> pdb=" O   LEU E 417 " (cutoff:3.500A)
      removed outlier: 7.828A  pdb=" N   ALA E 419 " --> pdb=" O   VAL E 372 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   LEU E 374 " --> pdb=" O   ALA E 419 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   TRP E 421 " --> pdb=" O   LEU E 374 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   GLY E 376 " --> pdb=" O   TRP E 421 " (cutoff:3.500A)
      removed outlier: 10.067A  pdb=" N   GLY E 446 " --> pdb=" O   GLU E 367 " (cutoff:3.500A)
      removed outlier: 10.772A  pdb=" N   ASP E 369 " --> pdb=" O   GLY E 446 " (cutoff:3.500A)
      removed outlier: 9.297A  pdb=" N   ALA E 448 " --> pdb=" O   ASP E 369 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   TYR E 371 " --> pdb=" O   ALA E 448 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   ILE E 450 " --> pdb=" O   TYR E 371 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ILE E 373 " --> pdb=" O   ILE E 450 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   ALA E 531 " --> pdb=" O   VAL E 447 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   ALA E 535 " --> pdb=" O   ASN E 451 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 137 through 140
      removed outlier: 3.630A  pdb=" N   PHE E 139 " --> pdb=" O   ILE E 130 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 162 through 163
    Processing sheet with id=AA8, first strand: chain 'E' and resid 174 through 176
      removed outlier: 6.561A  pdb=" N   VAL E 175 " --> pdb=" O   ILE E 202 " (cutoff:3.500A)
      removed outlier: 8.617A  pdb=" N   ARG E 204 " --> pdb=" O   VAL E 175 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   VAL E 225 " --> pdb=" O   HIS E 295 " (cutoff:3.500A)
      removed outlier: 8.098A  pdb=" N   ILE E 297 " --> pdb=" O   VAL E 225 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   LEU E 227 " --> pdb=" O   ILE E 297 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 6 through 7
    Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12
      removed outlier: 4.028A  pdb=" N   VAL H  12 " --> pdb=" O   VAL H 123 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'H' and resid 31 through 32
      removed outlier: 3.785A  pdb=" N   ASN H  31 " --> pdb=" O   CYS H 101 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 57 through 60
      removed outlier: 6.123A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 5.670A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ALA H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL H  98 " --> pdb=" O   LEU H 116 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LEU H 116 " --> pdb=" O   VAL H  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'Q' and resid 6 through 7
    Processing sheet with id=AB5, first strand: chain 'Q' and resid 31 through 32
      removed outlier: 3.791A  pdb=" N   ASN Q  31 " --> pdb=" O   CYS Q 101 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'Q' and resid 57 through 60
      removed outlier: 6.838A  pdb=" N   TRP Q  36 " --> pdb=" O   VAL Q  48 " (cutoff:3.500A)

    508 hydrogen bonds defined for protein.
    1455 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: 4.31

  Time building geometry restraints manager: 4.58 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4258
        1.34 -     1.46: 3081
        1.46 -     1.58: 6305
        1.58 -     1.69: 0
        1.69 -     1.81: 82
  Bond restraints: 13726
  Sorted by residual:
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.453 -0.047 2.00e-02 2.50e+03 5.46e+00
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.452 -0.046 2.00e-02 2.50e+03 5.32e+00
  bond pdb=" C1  NAG E 803 "
       pdb=" O5  NAG E 803 "
    ideal  model  delta    sigma   weight residual
    1.406  1.451 -0.045 2.00e-02 2.50e+03 5.01e+00
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.66e+00
  bond pdb=" C1  MAN I   5 "
       pdb=" C2  MAN I   5 "
    ideal  model  delta    sigma   weight residual
    1.526  1.559 -0.033 2.00e-02 2.50e+03 2.78e+00
  ... (remaining 13721 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.73: 18380
        2.73 -     5.47: 206
        5.47 -     8.20: 24
        8.20 -    10.94: 5
       10.94 -    13.67: 4
  Bond angle restraints: 18619
  Sorted by residual:
  angle pdb=" CA  LEU Q 116 "
        pdb=" CB  LEU Q 116 "
        pdb=" CG  LEU Q 116 "
      ideal   model   delta    sigma   weight residual
     116.30  129.97  -13.67 3.50e+00 8.16e-02 1.53e+01
  angle pdb=" CA  LEU H  81 "
        pdb=" CB  LEU H  81 "
        pdb=" CG  LEU H  81 "
      ideal   model   delta    sigma   weight residual
     116.30  129.49  -13.19 3.50e+00 8.16e-02 1.42e+01
  angle pdb=" CA  GLU A 102 "
        pdb=" CB  GLU A 102 "
        pdb=" CG  GLU A 102 "
      ideal   model   delta    sigma   weight residual
     114.10  121.41   -7.31 2.00e+00 2.50e-01 1.34e+01
  angle pdb=" CA  LEU H 116 "
        pdb=" CB  LEU H 116 "
        pdb=" CG  LEU H 116 "
      ideal   model   delta    sigma   weight residual
     116.30  128.93  -12.63 3.50e+00 8.16e-02 1.30e+01
  angle pdb=" CA  ARG A 190 "
        pdb=" CB  ARG A 190 "
        pdb=" CG  ARG A 190 "
      ideal   model   delta    sigma   weight residual
     114.10  120.86   -6.76 2.00e+00 2.50e-01 1.14e+01
  ... (remaining 18614 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.69: 7953
       25.69 -    51.39: 426
       51.39 -    77.08: 66
       77.08 -   102.78: 32
      102.78 -   128.47: 20
  Dihedral angle restraints: 8497
    sinusoidal: 3755
      harmonic: 4742
  Sorted by residual:
  dihedral pdb=" C2  NAG B   1 "
           pdb=" C1  NAG B   1 "
           pdb=" O5  NAG B   1 "
           pdb=" C5  NAG B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   65.51 -128.47     1      3.00e+01 1.11e-03 1.73e+01
  dihedral pdb=" C2  NAG E 803 "
           pdb=" C1  NAG E 803 "
           pdb=" O5  NAG E 803 "
           pdb=" C5  NAG E 803 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   64.90 -127.86     1      3.00e+01 1.11e-03 1.72e+01
  dihedral pdb=" C2  NAG C   1 "
           pdb=" C1  NAG C   1 "
           pdb=" O5  NAG C   1 "
           pdb=" C5  NAG C   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   62.72 -125.68     1      3.00e+01 1.11e-03 1.69e+01
  ... (remaining 8494 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1681
       0.058 -    0.117: 310
       0.117 -    0.175: 23
       0.175 -    0.234: 1
       0.234 -    0.292: 4
  Chirality restraints: 2019
  Sorted by residual:
  chirality pdb=" C5  BMA F   3 "
            pdb=" C4  BMA F   3 "
            pdb=" C6  BMA F   3 "
            pdb=" O5  BMA F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.57    0.29 2.00e-01 2.50e+01 2.14e+00
  chirality pdb=" C5  BMA I   3 "
            pdb=" C4  BMA I   3 "
            pdb=" C6  BMA I   3 "
            pdb=" O5  BMA I   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.56    0.29 2.00e-01 2.50e+01 2.06e+00
  chirality pdb=" C5  BMA G   3 "
            pdb=" C4  BMA G   3 "
            pdb=" C6  BMA G   3 "
            pdb=" O5  BMA G   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.77e+00
  ... (remaining 2016 not shown)

  Planarity restraints: 2400
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP E 714 "    0.012 2.00e-02 2.50e+03   2.45e-02 6.02e+00
        pdb=" C   ASP E 714 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   ASP E 714 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ILE E 715 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 387 "    0.034 5.00e-02 4.00e+02   5.05e-02 4.07e+00
        pdb=" N   PRO A 388 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A 388 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 388 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E 387 "   -0.033 5.00e-02 4.00e+02   5.00e-02 4.00e+00
        pdb=" N   PRO E 388 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO E 388 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO E 388 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 2397 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 188
        2.57 -     3.16: 11264
        3.16 -     3.74: 22023
        3.74 -     4.32: 31439
        4.32 -     4.90: 50756
  Nonbonded interactions: 115670
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 425 "
            pdb="ZN    ZN A 805 "
     model   vdw
     1.993 2.230
  nonbonded pdb=" OE2 GLU E 425 "
            pdb="ZN    ZN E 805 "
     model   vdw
     1.995 2.230
  nonbonded pdb=" OD1 ASP E 387 "
            pdb="ZN    ZN E 806 "
     model   vdw
     2.038 2.230
  nonbonded pdb=" OD1 ASP A 387 "
            pdb="ZN    ZN A 806 "
     model   vdw
     2.039 2.230
  nonbonded pdb=" OG ASER E 613 "
            pdb=" O   ALA H 100 "
     model   vdw
     2.110 3.040
  ... (remaining 115665 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 56 through 78 or resid 80 through 154 or resid 156 through \ 
 182 or resid 184 through 525 or resid 527 through 612 or resid 614 through 659  \ 
or resid 661 through 750 or resid 801 through 807))
  selection = (chain 'E' and (resid 56 through 78 or resid 80 through 154 or resid 156 through \ 
 182 or resid 184 through 525 or resid 527 through 612 or resid 614 through 659  \ 
or resid 661 through 750 or resid 801 through 807))
}
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'H'
  selection = chain 'Q'
}

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=0.30 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:             0.990
  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:          0.550
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     43.310
  Find NCS groups from input model:        0.600
  Set up NCS constraints:                  0.080
  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:12.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   58.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
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      :  0.004   0.047  13754  Z= 0.176
  Angle     :  0.719  13.673  18687  Z= 0.339
  Chirality :  0.046   0.292   2019
  Planarity :  0.004   0.050   2394
  Dihedral  : 17.568 128.474   5473
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 21.22 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.18 (0.21), residues: 1638
  helix:  1.41 (0.23), residues: 520
  sheet: -0.23 (0.31), residues: 284
  loop : -0.53 (0.21), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 410 
 HIS   0.007   0.001   HIS A 697 
 PHE   0.028   0.001   PHE Q  68 
 TYR   0.011   0.001   TYR E 299 
 ARG   0.011   0.000   ARG A 190 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00209 (    6)
  link_NAG-ASN         : angle       1.19674 (   18)
  link_ALPHA1-6        : bond        0.00431 (    2)
  link_ALPHA1-6        : angle       1.64539 (    6)
  link_BETA1-4         : bond        0.00252 (   10)
  link_BETA1-4         : angle       1.53850 (   30)
  link_ALPHA1-3        : bond        0.00270 (    2)
  link_ALPHA1-3        : angle       1.95750 (    6)
  hydrogen bonds       : bond        0.15703 (  508)
  hydrogen bonds       : angle       6.49536 ( 1455)
  metal coordination   : bond        0.00323 (    4)
  SS BOND              : bond        0.00389 (    4)
  SS BOND              : angle       0.41532 (    8)
  covalent geometry    : bond        0.00381 (13726)
  covalent geometry    : angle       0.71525 (18619)

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

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

  3276 Ramachandran restraints generated.
    1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3276 Ramachandran restraints generated.
    1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 146
  time to evaluate  : 1.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   55 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8187 (mtt-85)
REVERT: Q    5 GLN cc_start: 0.9158 (mp10) cc_final: 0.8942 (mp10)
  outliers start: 18
  outliers final: 15
  residues processed: 162
  average time/residue: 1.0771
  time to fit residues: 194.6508
Evaluate side-chains
  155 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 1.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  396 HIS
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  522 GLU
Chi-restraints excluded: chain A residue  627 VAL
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue  126 ASN
Chi-restraints excluded: chain E residue  259 LEU
Chi-restraints excluded: chain E residue  396 HIS
Chi-restraints excluded: chain E residue  517 SER
Chi-restraints excluded: chain E residue  575 THR
Chi-restraints excluded: chain E residue  627 VAL
Chi-restraints excluded: chain H residue   55 ARG
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain Q residue  110 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 136 optimal weight:    2.9990
   chunk 122 optimal weight:    0.7980
   chunk 68 optimal weight:    9.9990
   chunk 41 optimal weight:    5.9990
   chunk 82 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 126 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 77 optimal weight:    0.5980
   chunk 94 optimal weight:    4.9990
   chunk 147 optimal weight:    7.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 247 ASN
A 260 ASN
** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 544 ASN
** A 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 247 ASN
** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.131879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.105796 restraints weight = 70141.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 5.11
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3693
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3693 r_free = 0.3693    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3693 r_free = 0.3693    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3693
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.0822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13754  Z= 0.133
  Angle     :  0.673  11.500  18687  Z= 0.324
  Chirality :  0.043   0.206   2019
  Planarity :  0.005   0.051   2394
  Dihedral  : 12.336  97.645   2405
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.14 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.23 (0.21), residues: 1638
  helix:  1.53 (0.23), residues: 518
  sheet: -0.28 (0.32), residues: 268
  loop : -0.52 (0.21), residues: 852

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP E 410 
 HIS   0.008   0.001   HIS A 475 
 PHE   0.017   0.001   PHE A 186 
 TYR   0.025   0.001   TYR Q 114 
 ARG   0.006   0.000   ARG H  67 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00197 (    6)
  link_NAG-ASN         : angle       1.32444 (   18)
  link_ALPHA1-6        : bond        0.00898 (    2)
  link_ALPHA1-6        : angle       2.71759 (    6)
  link_BETA1-4         : bond        0.00361 (   10)
  link_BETA1-4         : angle       2.02560 (   30)
  link_ALPHA1-3        : bond        0.00960 (    2)
  link_ALPHA1-3        : angle       2.30122 (    6)
  hydrogen bonds       : bond        0.04495 (  508)
  hydrogen bonds       : angle       5.20250 ( 1455)
  metal coordination   : bond        0.00233 (    4)
  SS BOND              : bond        0.00385 (    4)
  SS BOND              : angle       0.60596 (    8)
  covalent geometry    : bond        0.00301 (13726)
  covalent geometry    : angle       0.66487 (18619)

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

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

  3276 Ramachandran restraints generated.
    1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3276 Ramachandran restraints generated.
    1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 148
  time to evaluate  : 1.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  537 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.7403 (m-80)
REVERT: A  714 ASP cc_start: 0.7451 (t70) cc_final: 0.7222 (t0)
REVERT: Q    5 GLN cc_start: 0.9225 (mp10) cc_final: 0.8941 (mp10)
REVERT: Q   87 LYS cc_start: 0.8161 (mppt) cc_final: 0.7950 (mppt)
  outliers start: 29
  outliers final: 11
  residues processed: 165
  average time/residue: 1.1336
  time to fit residues: 207.1254
Evaluate side-chains
  147 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 1.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  396 HIS
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue  259 LEU
Chi-restraints excluded: chain E residue  396 HIS
Chi-restraints excluded: chain E residue  575 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   87 LYS
Chi-restraints excluded: chain Q residue    7 SER
Chi-restraints excluded: chain Q residue   20 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 131 optimal weight:    0.0070
   chunk 83 optimal weight:    4.9990
   chunk 116 optimal weight:    6.9990
   chunk 5 optimal weight:   10.0000
   chunk 28 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   chunk 16 optimal weight:    9.9990
   chunk 91 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    2.4004

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

Flipped N/Q/H residues before XYZ refinement:
A 260 ASN
** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 396 HIS
A 544 ASN
** A 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 544 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.129743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.103547 restraints weight = 74266.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 5.28
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3650
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3650 r_free = 0.3650    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3650 r_free = 0.3650    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3650
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.0968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  13754  Z= 0.197
  Angle     :  0.686  11.060  18687  Z= 0.335
  Chirality :  0.045   0.164   2019
  Planarity :  0.005   0.046   2394
  Dihedral  :  8.456  81.196   2389
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 18.49 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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: -0.00 (0.20), residues: 1638
  helix:  1.32 (0.23), residues: 526
  sheet: -0.62 (0.29), residues: 312
  loop : -0.57 (0.21), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP E 410 
 HIS   0.007   0.001   HIS E 697 
 PHE   0.011   0.001   PHE A 653 
 TYR   0.018   0.002   TYR E 733 
 ARG   0.005   0.000   ARG A 190 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00209 (    6)
  link_NAG-ASN         : angle       1.36239 (   18)
  link_ALPHA1-6        : bond        0.00721 (    2)
  link_ALPHA1-6        : angle       1.81366 (    6)
  link_BETA1-4         : bond        0.00467 (   10)
  link_BETA1-4         : angle       1.89592 (   30)
  link_ALPHA1-3        : bond        0.00985 (    2)
  link_ALPHA1-3        : angle       1.56691 (    6)
  hydrogen bonds       : bond        0.05089 (  508)
  hydrogen bonds       : angle       5.21016 ( 1455)
  metal coordination   : bond        0.00647 (    4)
  SS BOND              : bond        0.00224 (    4)
  SS BOND              : angle       0.85214 (    8)
  covalent geometry    : bond        0.00464 (13726)
  covalent geometry    : angle       0.67975 (18619)

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

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

  3276 Ramachandran restraints generated.
    1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3276 Ramachandran restraints generated.
    1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 138
  time to evaluate  : 1.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 PHE cc_start: 0.8488 (t80) cc_final: 0.8163 (t80)
REVERT: A  190 ARG cc_start: 0.8924 (mmt180) cc_final: 0.8675 (ppt170)
REVERT: A  537 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7839 (m-80)
REVERT: A  714 ASP cc_start: 0.7503 (t70) cc_final: 0.7198 (t70)
REVERT: E  537 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.7720 (m-80)
REVERT: H   34 MET cc_start: 0.7449 (tpt) cc_final: 0.7217 (tpt)
REVERT: H   44 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8779 (mp0)
REVERT: H   79 MET cc_start: 0.6977 (mpt) cc_final: 0.6305 (mpt)
REVERT: Q    5 GLN cc_start: 0.9263 (mp10) cc_final: 0.8982 (mp10)
  outliers start: 33
  outliers final: 11
  residues processed: 158
  average time/residue: 1.1757
  time to fit residues: 205.3224
Evaluate side-chains
  144 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 1.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  396 HIS
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue  259 LEU
Chi-restraints excluded: chain E residue  396 HIS
Chi-restraints excluded: chain E residue  537 TYR
Chi-restraints excluded: chain E residue  575 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   87 LYS
Chi-restraints excluded: chain Q residue    7 SER
Chi-restraints excluded: chain Q residue   20 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 109 optimal weight:    3.9990
   chunk 113 optimal weight:    0.7980
   chunk 119 optimal weight:    0.9980
   chunk 115 optimal weight:    0.6980
   chunk 110 optimal weight:    0.9990
   chunk 138 optimal weight:    8.9990
   chunk 161 optimal weight:    2.9990
   chunk 158 optimal weight:   20.0000
   chunk 146 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   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 260 ASN
** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 544 ASN
A 618 HIS
** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 544 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.132419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.105652 restraints weight = 91823.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3691 rms_B_bonded: 5.71
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3695
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3695 r_free = 0.3695    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3695 r_free = 0.3695    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3695
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.1145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13754  Z= 0.115
  Angle     :  0.626  12.155  18687  Z= 0.303
  Chirality :  0.042   0.147   2019
  Planarity :  0.004   0.049   2394
  Dihedral  :  6.366  82.273   2389
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 18.57 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.24 (0.21), residues: 1638
  helix:  1.56 (0.23), residues: 522
  sheet: -0.22 (0.31), residues: 286
  loop : -0.57 (0.21), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP E 410 
 HIS   0.007   0.001   HIS A 475 
 PHE   0.016   0.001   PHE H  80 
 TYR   0.019   0.001   TYR Q 114 
 ARG   0.003   0.000   ARG A 463 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00266 (    6)
  link_NAG-ASN         : angle       1.37711 (   18)
  link_ALPHA1-6        : bond        0.00520 (    2)
  link_ALPHA1-6        : angle       1.84513 (    6)
  link_BETA1-4         : bond        0.00421 (   10)
  link_BETA1-4         : angle       1.90310 (   30)
  link_ALPHA1-3        : bond        0.00975 (    2)
  link_ALPHA1-3        : angle       1.54615 (    6)
  hydrogen bonds       : bond        0.03999 (  508)
  hydrogen bonds       : angle       4.99139 ( 1455)
  metal coordination   : bond        0.00103 (    4)
  SS BOND              : bond        0.00316 (    4)
  SS BOND              : angle       0.52987 (    8)
  covalent geometry    : bond        0.00263 (13726)
  covalent geometry    : angle       0.61905 (18619)

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

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

  3276 Ramachandran restraints generated.
    1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3276 Ramachandran restraints generated.
    1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 152
  time to evaluate  : 1.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 PHE cc_start: 0.8492 (t80) cc_final: 0.8155 (t80)
REVERT: A  537 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7487 (m-80)
REVERT: A  714 ASP cc_start: 0.7438 (t70) cc_final: 0.6834 (t70)
REVERT: E  307 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8249 (mp0)
REVERT: E  714 ASP cc_start: 0.7035 (t70) cc_final: 0.6684 (t70)
REVERT: H   44 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8754 (mp0)
REVERT: H   79 MET cc_start: 0.7080 (mpt) cc_final: 0.6373 (mpt)
REVERT: H   80 PHE cc_start: 0.7433 (m-80) cc_final: 0.7013 (m-80)
REVERT: Q    5 GLN cc_start: 0.9265 (mp10) cc_final: 0.9003 (mp10)
REVERT: Q   46 GLU cc_start: 0.8719 (tt0) cc_final: 0.8311 (pt0)
  outliers start: 31
  outliers final: 12
  residues processed: 172
  average time/residue: 1.2133
  time to fit residues: 229.3492
Evaluate side-chains
  144 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 1.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  396 HIS
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue  259 LEU
Chi-restraints excluded: chain E residue  307 GLU
Chi-restraints excluded: chain E residue  396 HIS
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   87 LYS
Chi-restraints excluded: chain H residue   98 VAL
Chi-restraints excluded: chain Q residue    7 SER
Chi-restraints excluded: chain Q residue   20 LEU
Chi-restraints excluded: chain Q residue   23 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 102 optimal weight:    0.0000
   chunk 15 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 112 optimal weight:    1.9990
   chunk 90 optimal weight:    4.9990
   chunk 26 optimal weight:    7.9990
   chunk 118 optimal weight:    0.4980
   chunk 151 optimal weight:    9.9990
   chunk 132 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 50 optimal weight:    8.9990
   overall best weight:    1.4788

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Q   1 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.131351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.104773 restraints weight = 82255.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 5.45
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3680
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3680 r_free = 0.3680    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3680 r_free = 0.3680    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3680
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.1213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13754  Z= 0.143
  Angle     :  0.636  12.149  18687  Z= 0.309
  Chirality :  0.042   0.145   2019
  Planarity :  0.004   0.047   2394
  Dihedral  :  6.035  82.067   2388
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 18.92 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.22 (0.21), residues: 1638
  helix:  1.60 (0.23), residues: 522
  sheet: -0.45 (0.29), residues: 306
  loop : -0.52 (0.21), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP E 410 
 HIS   0.006   0.001   HIS A 697 
 PHE   0.010   0.001   PHE H  80 
 TYR   0.016   0.001   TYR A 299 
 ARG   0.009   0.001   ARG E 190 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00236 (    6)
  link_NAG-ASN         : angle       1.35423 (   18)
  link_ALPHA1-6        : bond        0.00224 (    2)
  link_ALPHA1-6        : angle       1.53041 (    6)
  link_BETA1-4         : bond        0.00354 (   10)
  link_BETA1-4         : angle       1.72167 (   30)
  link_ALPHA1-3        : bond        0.00916 (    2)
  link_ALPHA1-3        : angle       1.51557 (    6)
  hydrogen bonds       : bond        0.04224 (  508)
  hydrogen bonds       : angle       4.94379 ( 1455)
  metal coordination   : bond        0.00417 (    4)
  SS BOND              : bond        0.00297 (    4)
  SS BOND              : angle       0.58056 (    8)
  covalent geometry    : bond        0.00337 (13726)
  covalent geometry    : angle       0.63098 (18619)

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

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

  3276 Ramachandran restraints generated.
    1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3276 Ramachandran restraints generated.
    1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 139
  time to evaluate  : 1.526 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 PHE cc_start: 0.8457 (t80) cc_final: 0.8179 (t80)
REVERT: A  537 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.7714 (m-80)
REVERT: A  714 ASP cc_start: 0.7149 (t70) cc_final: 0.6798 (t70)
REVERT: E  307 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8231 (mp0)
REVERT: E  537 TYR cc_start: 0.8127 (OUTLIER) cc_final: 0.7480 (m-80)
REVERT: E  714 ASP cc_start: 0.7134 (t70) cc_final: 0.6740 (t70)
REVERT: H   44 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8776 (mp0)
REVERT: H   79 MET cc_start: 0.7152 (mpt) cc_final: 0.6426 (mpt)
REVERT: Q    5 GLN cc_start: 0.9254 (mp10) cc_final: 0.8965 (mp10)
REVERT: Q   46 GLU cc_start: 0.8747 (tt0) cc_final: 0.8356 (pt0)
  outliers start: 32
  outliers final: 14
  residues processed: 162
  average time/residue: 1.0842
  time to fit residues: 195.0266
Evaluate side-chains
  148 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 1.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  396 HIS
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue  259 LEU
Chi-restraints excluded: chain E residue  307 GLU
Chi-restraints excluded: chain E residue  396 HIS
Chi-restraints excluded: chain E residue  537 TYR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   23 THR
Chi-restraints excluded: chain H residue   87 LYS
Chi-restraints excluded: chain H residue   98 VAL
Chi-restraints excluded: chain Q residue    7 SER
Chi-restraints excluded: chain Q residue   19 ARG
Chi-restraints excluded: chain Q residue   20 LEU
Chi-restraints excluded: chain Q residue   23 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 161 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 6 optimal weight:    6.9990
   chunk 25 optimal weight:    0.8980
   chunk 78 optimal weight:    3.9990
   chunk 118 optimal weight:    1.9990
   chunk 116 optimal weight:    6.9990
   chunk 101 optimal weight:    3.9990
   chunk 103 optimal weight:    7.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 519 ASN
A 544 ASN
** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 544 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.132169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.106702 restraints weight = 68479.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 4.97
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3711
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3711 r_free = 0.3711    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3711 r_free = 0.3711    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3711
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.1352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13754  Z= 0.125
  Angle     :  0.625  12.862  18687  Z= 0.303
  Chirality :  0.042   0.149   2019
  Planarity :  0.004   0.057   2394
  Dihedral  :  5.853  82.368   2388
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 18.92 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.27 (0.21), residues: 1638
  helix:  1.63 (0.23), residues: 524
  sheet: -0.39 (0.29), residues: 306
  loop : -0.51 (0.21), residues: 808

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP E 410 
 HIS   0.006   0.001   HIS A 697 
 PHE   0.011   0.001   PHE Q  68 
 TYR   0.018   0.001   TYR Q 114 
 ARG   0.006   0.000   ARG E 190 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00275 (    6)
  link_NAG-ASN         : angle       1.32256 (   18)
  link_ALPHA1-6        : bond        0.00315 (    2)
  link_ALPHA1-6        : angle       1.51570 (    6)
  link_BETA1-4         : bond        0.00329 (   10)
  link_BETA1-4         : angle       1.63337 (   30)
  link_ALPHA1-3        : bond        0.00723 (    2)
  link_ALPHA1-3        : angle       1.34032 (    6)
  hydrogen bonds       : bond        0.03951 (  508)
  hydrogen bonds       : angle       4.85865 ( 1455)
  metal coordination   : bond        0.00283 (    4)
  SS BOND              : bond        0.00405 (    4)
  SS BOND              : angle       0.53218 (    8)
  covalent geometry    : bond        0.00295 (13726)
  covalent geometry    : angle       0.62064 (18619)

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

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

  3276 Ramachandran restraints generated.
    1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3276 Ramachandran restraints generated.
    1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 141
  time to evaluate  : 1.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 PHE cc_start: 0.8448 (t80) cc_final: 0.8231 (t80)
REVERT: A  537 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.7603 (m-80)
REVERT: A  714 ASP cc_start: 0.7257 (t70) cc_final: 0.6649 (t70)
REVERT: E  307 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8152 (mp0)
REVERT: E  714 ASP cc_start: 0.7161 (t70) cc_final: 0.6702 (t70)
REVERT: H   44 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8759 (mp0)
REVERT: H   79 MET cc_start: 0.7219 (mpt) cc_final: 0.6418 (mpt)
REVERT: Q    5 GLN cc_start: 0.9230 (mp10) cc_final: 0.8957 (mp10)
REVERT: Q   46 GLU cc_start: 0.8791 (tt0) cc_final: 0.8386 (pt0)
REVERT: Q   81 LEU cc_start: 0.6854 (mp) cc_final: 0.6591 (mp)
  outliers start: 26
  outliers final: 13
  residues processed: 157
  average time/residue: 1.2416
  time to fit residues: 216.3351
Evaluate side-chains
  149 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 1.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  396 HIS
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue  259 LEU
Chi-restraints excluded: chain E residue  307 GLU
Chi-restraints excluded: chain E residue  396 HIS
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   44 GLU
Chi-restraints excluded: chain H residue   87 LYS
Chi-restraints excluded: chain H residue   98 VAL
Chi-restraints excluded: chain Q residue   19 ARG
Chi-restraints excluded: chain Q residue   20 LEU
Chi-restraints excluded: chain Q residue   23 THR
Chi-restraints excluded: chain Q residue   64 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 88 optimal weight:    0.8980
   chunk 142 optimal weight:    5.9990
   chunk 6 optimal weight:    0.0870
   chunk 2 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 140 optimal weight:    0.9980
   chunk 96 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9980
   chunk 130 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 128 optimal weight:    1.9990
   overall best weight:    0.7358

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 377 HIS ** 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 = 0.4106 r_free = 0.4106 target = 0.133546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.107680 restraints weight = 81107.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 5.42
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3726
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3726 r_free = 0.3726    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3726 r_free = 0.3726    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3726
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13754  Z= 0.113
  Angle     :  0.619  13.087  18687  Z= 0.300
  Chirality :  0.042   0.165   2019
  Planarity :  0.004   0.049   2394
  Dihedral  :  5.685  82.410   2388
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 19.71 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.36 (0.21), residues: 1638
  helix:  1.71 (0.23), residues: 524
  sheet: -0.11 (0.31), residues: 286
  loop : -0.56 (0.21), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP E 410 
 HIS   0.005   0.001   HIS A 697 
 PHE   0.008   0.001   PHE E 653 
 TYR   0.017   0.001   TYR E 299 
 ARG   0.010   0.000   ARG E 190 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00282 (    6)
  link_NAG-ASN         : angle       1.30017 (   18)
  link_ALPHA1-6        : bond        0.00423 (    2)
  link_ALPHA1-6        : angle       1.53837 (    6)
  link_BETA1-4         : bond        0.00356 (   10)
  link_BETA1-4         : angle       1.58389 (   30)
  link_ALPHA1-3        : bond        0.00787 (    2)
  link_ALPHA1-3        : angle       1.40858 (    6)
  hydrogen bonds       : bond        0.03664 (  508)
  hydrogen bonds       : angle       4.78355 ( 1455)
  metal coordination   : bond        0.00196 (    4)
  SS BOND              : bond        0.00445 (    4)
  SS BOND              : angle       0.53850 (    8)
  covalent geometry    : bond        0.00264 (13726)
  covalent geometry    : angle       0.61417 (18619)

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

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

  3276 Ramachandran restraints generated.
    1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3276 Ramachandran restraints generated.
    1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 140
  time to evaluate  : 1.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  537 TYR cc_start: 0.7953 (OUTLIER) cc_final: 0.7566 (m-80)
REVERT: A  714 ASP cc_start: 0.7341 (t70) cc_final: 0.6748 (t70)
REVERT: E  307 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7931 (mp0)
REVERT: E  616 MET cc_start: 0.7969 (mmm) cc_final: 0.7746 (tpp)
REVERT: E  714 ASP cc_start: 0.7260 (t70) cc_final: 0.6757 (t70)
REVERT: H   44 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8730 (mp0)
REVERT: H   79 MET cc_start: 0.7214 (mpt) cc_final: 0.6390 (mpt)
REVERT: Q    5 GLN cc_start: 0.9266 (mp10) cc_final: 0.9000 (mp10)
REVERT: Q   46 GLU cc_start: 0.8799 (tt0) cc_final: 0.8405 (pt0)
  outliers start: 20
  outliers final: 11
  residues processed: 154
  average time/residue: 1.1584
  time to fit residues: 197.5600
Evaluate side-chains
  145 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 1.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  396 HIS
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue  188 LEU
Chi-restraints excluded: chain E residue  307 GLU
Chi-restraints excluded: chain E residue  396 HIS
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   23 THR
Chi-restraints excluded: chain H residue   44 GLU
Chi-restraints excluded: chain H residue   87 LYS
Chi-restraints excluded: chain Q residue   23 THR
Chi-restraints excluded: chain Q residue   64 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 118 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 140 optimal weight:    0.9980
   chunk 101 optimal weight:    8.9990
   chunk 96 optimal weight:    0.0980
   chunk 125 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0030
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 544 ASN
** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 544 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.134296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.107689 restraints weight = 79923.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3725 rms_B_bonded: 5.44
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3726
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3726 r_free = 0.3726    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3726 r_free = 0.3726    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3726
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.1592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13754  Z= 0.110
  Angle     :  0.619  12.330  18687  Z= 0.300
  Chirality :  0.041   0.156   2019
  Planarity :  0.004   0.049   2394
  Dihedral  :  5.531  81.923   2386
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 19.71 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.44 (0.21), residues: 1638
  helix:  1.78 (0.23), residues: 524
  sheet: -0.01 (0.31), residues: 284
  loop : -0.54 (0.21), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP E 410 
 HIS   0.005   0.001   HIS A 697 
 PHE   0.013   0.001   PHE Q  68 
 TYR   0.015   0.001   TYR E 299 
 ARG   0.008   0.001   ARG E 190 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00303 (    6)
  link_NAG-ASN         : angle       1.27302 (   18)
  link_ALPHA1-6        : bond        0.00325 (    2)
  link_ALPHA1-6        : angle       1.49311 (    6)
  link_BETA1-4         : bond        0.00366 (   10)
  link_BETA1-4         : angle       1.53287 (   30)
  link_ALPHA1-3        : bond        0.00730 (    2)
  link_ALPHA1-3        : angle       1.38648 (    6)
  hydrogen bonds       : bond        0.03500 (  508)
  hydrogen bonds       : angle       4.74398 ( 1455)
  metal coordination   : bond        0.00164 (    4)
  SS BOND              : bond        0.00570 (    4)
  SS BOND              : angle       0.65724 (    8)
  covalent geometry    : bond        0.00259 (13726)
  covalent geometry    : angle       0.61424 (18619)

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

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

  3276 Ramachandran restraints generated.
    1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3276 Ramachandran restraints generated.
    1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 1.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  537 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7575 (m-80)
REVERT: A  714 ASP cc_start: 0.7377 (t70) cc_final: 0.6785 (t70)
REVERT: E  537 TYR cc_start: 0.7980 (OUTLIER) cc_final: 0.7266 (m-80)
REVERT: E  560 GLU cc_start: 0.8226 (mp0) cc_final: 0.7632 (mp0)
REVERT: E  616 MET cc_start: 0.7877 (mmm) cc_final: 0.7634 (tpp)
REVERT: E  714 ASP cc_start: 0.7218 (t70) cc_final: 0.6708 (t70)
REVERT: H   44 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8726 (mp0)
REVERT: H   79 MET cc_start: 0.7260 (mpt) cc_final: 0.6370 (mpt)
REVERT: Q    5 GLN cc_start: 0.9233 (mp10) cc_final: 0.8959 (mp10)
REVERT: Q   46 GLU cc_start: 0.8754 (tt0) cc_final: 0.8369 (pt0)
  outliers start: 21
  outliers final: 11
  residues processed: 153
  average time/residue: 1.1603
  time to fit residues: 196.1952
Evaluate side-chains
  148 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 134
  time to evaluate  : 1.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  396 HIS
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue  188 LEU
Chi-restraints excluded: chain E residue  396 HIS
Chi-restraints excluded: chain E residue  537 TYR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   23 THR
Chi-restraints excluded: chain H residue   44 GLU
Chi-restraints excluded: chain H residue   87 LYS
Chi-restraints excluded: chain Q residue   20 LEU
Chi-restraints excluded: chain Q residue   23 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9990
   chunk 125 optimal weight:    2.9990
   chunk 157 optimal weight:    9.9990
   chunk 89 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 82 optimal weight:    0.0170
   overall best weight:    0.7824

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 475 HIS
** E 377 HIS ** 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 = 0.4113 r_free = 0.4113 target = 0.134082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.108274 restraints weight = 73983.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 5.24
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3731
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3731 r_free = 0.3731    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3731 r_free = 0.3731    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3731
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  13754  Z= 0.114
  Angle     :  0.624  12.705  18687  Z= 0.302
  Chirality :  0.041   0.155   2019
  Planarity :  0.004   0.049   2394
  Dihedral  :  5.457  81.816   2386
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 20.00 %
    Favored  : 78.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.45 (0.21), residues: 1638
  helix:  1.78 (0.23), residues: 524
  sheet: -0.05 (0.31), residues: 286
  loop : -0.51 (0.21), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP E 410 
 HIS   0.005   0.001   HIS A 475 
 PHE   0.027   0.001   PHE Q  68 
 TYR   0.016   0.001   TYR E 299 
 ARG   0.007   0.000   ARG E 190 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00288 (    6)
  link_NAG-ASN         : angle       1.24567 (   18)
  link_ALPHA1-6        : bond        0.00356 (    2)
  link_ALPHA1-6        : angle       1.51178 (    6)
  link_BETA1-4         : bond        0.00364 (   10)
  link_BETA1-4         : angle       1.50008 (   30)
  link_ALPHA1-3        : bond        0.00696 (    2)
  link_ALPHA1-3        : angle       1.38470 (    6)
  hydrogen bonds       : bond        0.03549 (  508)
  hydrogen bonds       : angle       4.71095 ( 1455)
  metal coordination   : bond        0.00208 (    4)
  SS BOND              : bond        0.00537 (    4)
  SS BOND              : angle       0.58294 (    8)
  covalent geometry    : bond        0.00271 (13726)
  covalent geometry    : angle       0.61937 (18619)

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

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

  3276 Ramachandran restraints generated.
    1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3276 Ramachandran restraints generated.
    1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 1.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 GLU cc_start: 0.8284 (mp0) cc_final: 0.8059 (mp0)
REVERT: A  537 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7591 (m-80)
REVERT: A  648 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7908 (mp0)
REVERT: A  714 ASP cc_start: 0.7435 (t70) cc_final: 0.6830 (t70)
REVERT: E  537 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.7280 (m-80)
REVERT: E  560 GLU cc_start: 0.8232 (mp0) cc_final: 0.7667 (mp0)
REVERT: E  714 ASP cc_start: 0.7269 (t70) cc_final: 0.6756 (t70)
REVERT: H   44 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8698 (mp0)
REVERT: H   79 MET cc_start: 0.7233 (mpt) cc_final: 0.6353 (mpt)
REVERT: Q    5 GLN cc_start: 0.9267 (mp10) cc_final: 0.9016 (mp10)
REVERT: Q   46 GLU cc_start: 0.8792 (tt0) cc_final: 0.8481 (pt0)
  outliers start: 19
  outliers final: 9
  residues processed: 147
  average time/residue: 1.1989
  time to fit residues: 196.9362
Evaluate side-chains
  143 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 1.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  396 HIS
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  648 GLU
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue  396 HIS
Chi-restraints excluded: chain E residue  537 TYR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   23 THR
Chi-restraints excluded: chain H residue   44 GLU
Chi-restraints excluded: chain H residue   87 LYS
Chi-restraints excluded: chain Q residue   20 LEU
Chi-restraints excluded: chain Q residue   23 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 92 optimal weight:    0.0060
   chunk 93 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 143 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0770
   chunk 111 optimal weight:    7.9990
   chunk 139 optimal weight:   20.0000
   chunk 153 optimal weight:    2.9990
   overall best weight:    0.6154

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 544 ASN
** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   1 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.134879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.107822 restraints weight = 93265.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3728 rms_B_bonded: 5.83
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3727
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3727 r_free = 0.3727    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3727 r_free = 0.3727    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3727
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  13754  Z= 0.110
  Angle     :  0.624  11.058  18687  Z= 0.302
  Chirality :  0.041   0.158   2019
  Planarity :  0.004   0.049   2394
  Dihedral  :  5.387  81.649   2386
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 20.29 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.50 (0.21), residues: 1638
  helix:  1.81 (0.23), residues: 524
  sheet:  0.04 (0.31), residues: 284
  loop : -0.50 (0.21), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP E 410 
 HIS   0.005   0.001   HIS E 697 
 PHE   0.028   0.001   PHE Q  68 
 TYR   0.016   0.001   TYR E 299 
 ARG   0.006   0.000   ARG E 190 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00305 (    6)
  link_NAG-ASN         : angle       1.23340 (   18)
  link_ALPHA1-6        : bond        0.00352 (    2)
  link_ALPHA1-6        : angle       1.50081 (    6)
  link_BETA1-4         : bond        0.00372 (   10)
  link_BETA1-4         : angle       1.47606 (   30)
  link_ALPHA1-3        : bond        0.00685 (    2)
  link_ALPHA1-3        : angle       1.39548 (    6)
  hydrogen bonds       : bond        0.03445 (  508)
  hydrogen bonds       : angle       4.65918 ( 1455)
  metal coordination   : bond        0.00160 (    4)
  SS BOND              : bond        0.00595 (    4)
  SS BOND              : angle       0.66298 (    8)
  covalent geometry    : bond        0.00261 (13726)
  covalent geometry    : angle       0.61994 (18619)

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

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

  3276 Ramachandran restraints generated.
    1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3276 Ramachandran restraints generated.
    1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 135
  time to evaluate  : 1.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 GLU cc_start: 0.8301 (mp0) cc_final: 0.8077 (mp0)
REVERT: A  537 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.7581 (m-80)
REVERT: A  648 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7897 (mp0)
REVERT: A  714 ASP cc_start: 0.7469 (t70) cc_final: 0.6847 (t70)
REVERT: E  537 TYR cc_start: 0.7974 (OUTLIER) cc_final: 0.7267 (m-80)
REVERT: E  560 GLU cc_start: 0.8248 (mp0) cc_final: 0.7702 (mp0)
REVERT: E  648 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7987 (mp0)
REVERT: E  669 MET cc_start: 0.8516 (ttm) cc_final: 0.8309 (ttp)
REVERT: E  714 ASP cc_start: 0.7341 (t70) cc_final: 0.6820 (t70)
REVERT: H   44 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8707 (mp0)
REVERT: H   79 MET cc_start: 0.7196 (mpt) cc_final: 0.6274 (mpt)
REVERT: Q    5 GLN cc_start: 0.9318 (mp10) cc_final: 0.9043 (mp10)
REVERT: Q   46 GLU cc_start: 0.8770 (tt0) cc_final: 0.8414 (pt0)
  outliers start: 16
  outliers final: 10
  residues processed: 147
  average time/residue: 1.1265
  time to fit residues: 183.4395
Evaluate side-chains
  143 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 1.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  396 HIS
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  648 GLU
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue  188 LEU
Chi-restraints excluded: chain E residue  396 HIS
Chi-restraints excluded: chain E residue  537 TYR
Chi-restraints excluded: chain E residue  648 GLU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   23 THR
Chi-restraints excluded: chain H residue   44 GLU
Chi-restraints excluded: chain H residue   87 LYS
Chi-restraints excluded: chain Q residue   20 LEU
Chi-restraints excluded: chain Q residue   23 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 162
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 43 optimal weight:    0.2980
   chunk 109 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 128 optimal weight:    6.9990
   chunk 145 optimal weight:    0.0970
   chunk 107 optimal weight:    4.9990
   chunk 123 optimal weight:    0.9990
   chunk 59 optimal weight:    6.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 111 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.135244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.108304 restraints weight = 93910.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 5.80
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3734
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3734 r_free = 0.3734    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3734 r_free = 0.3734    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3734
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13754  Z= 0.111
  Angle     :  0.625  12.707  18687  Z= 0.303
  Chirality :  0.042   0.165   2019
  Planarity :  0.004   0.049   2394
  Dihedral  :  5.332  81.588   2386
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 20.57 %
    Favored  : 78.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.53 (0.21), residues: 1638
  helix:  1.83 (0.23), residues: 524
  sheet:  0.07 (0.31), residues: 284
  loop : -0.48 (0.21), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP E 410 
 HIS   0.005   0.001   HIS E 697 
 PHE   0.029   0.001   PHE Q  68 
 TYR   0.016   0.001   TYR E 299 
 ARG   0.006   0.000   ARG E 190 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00316 (    6)
  link_NAG-ASN         : angle       1.24546 (   18)
  link_ALPHA1-6        : bond        0.00353 (    2)
  link_ALPHA1-6        : angle       1.50603 (    6)
  link_BETA1-4         : bond        0.00374 (   10)
  link_BETA1-4         : angle       1.45783 (   30)
  link_ALPHA1-3        : bond        0.00679 (    2)
  link_ALPHA1-3        : angle       1.40658 (    6)
  hydrogen bonds       : bond        0.03434 (  508)
  hydrogen bonds       : angle       4.65425 ( 1455)
  metal coordination   : bond        0.00163 (    4)
  SS BOND              : bond        0.00577 (    4)
  SS BOND              : angle       0.67894 (    8)
  covalent geometry    : bond        0.00263 (13726)
  covalent geometry    : angle       0.62143 (18619)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8340.60 seconds
wall clock time: 143 minutes 19.74 seconds (8599.74 seconds total)