Starting phenix.real_space_refine
on Wed Mar  4 12:57:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7aip_11801/03_2026/7aip_11801.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7aip_11801/03_2026/7aip_11801.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7aip_11801/03_2026/7aip_11801.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7aip_11801/03_2026/7aip_11801.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7aip_11801/03_2026/7aip_11801.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7aip_11801/03_2026/7aip_11801.cif"
  }
  resolution = 3.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.070
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: 6
    Type Number    sf(0)   Gaussians
     P      10      5.49       5
     Mg      2      5.21       5
     S      96      5.16       5
     C    8769      2.51       5
     N    2216      2.21       5
     O    2442      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13535
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 6670
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 867, 6663
          Classifications: {'peptide': 867}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 37, 'TRANS': 829}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 75
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 66
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 35
      Conformer: "B"
        Number of residues, atoms: 867, 6663
          Classifications: {'peptide': 867}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 37, 'TRANS': 829}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 75
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 66
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 35
          bond proxies already assigned to first conformer: 6811
    Chain: "B"
      Number of atoms: 6663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 867, 6663
          Classifications: {'peptide': 867}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 37, 'TRANS': 829}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 75
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 66
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 35
    Chain: "C"
      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: 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: "J"
      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: "M"
      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: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.51, per 1000 atoms: 0.33
  Number of scatterers: 13535
  At special positions: 0
  Unit cell: (109.65, 109.65, 150.45, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      96     16.00
     P      10     15.00
     Mg      2     11.99
     O    2442      8.00
     N    2216      7.00
     C    8769      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 163 " - pdb=" SG  CYS A 626 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 308 " - pdb=" SG  CYS A 323 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 343 " - pdb=" SG  CYS A 353 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 163 " - pdb=" SG  CYS B 626 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 308 " - pdb=" SG  CYS B 323 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 343 " - pdb=" SG  CYS B 353 " 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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG J   1 " - " NAG J   2 "
      " NAG J   2 " - " BMA J   3 "
      " NAG M   1 " - " NAG M   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 312 "
      " NAG F   1 " - " ASN A 361 "
      " NAG J   1 " - " ASN B 312 "
      " NAG M   1 " - " ASN B 361 "
  Time building additional restraints: 1.23
  Conformation dependent library (CDL) restraints added in 814.6 milliseconds
  

  3414 Ramachandran restraints generated.
    1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3190

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 8 sheets defined
      60.9% alpha, 6.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 120 through 133
      removed outlier: 5.812A  pdb=" N   LEU A 126 " --> pdb=" O   MET A 122 " (cutoff:3.500A)
      Proline residue:  A 127  - end of helix
    Processing helix  chain 'A' and resid 134 through 177
      removed outlier: 4.708A  pdb=" N   PHE A 138 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
      removed outlier: 5.188A  pdb=" N   THR A 142 " --> pdb=" O   PHE A 138 " (cutoff:3.500A)
      removed outlier: 5.476A  pdb=" N   TRP A 143 " --> pdb=" O   LEU A 139 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   MET A 144 " --> pdb=" O   ARG A 140 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   VAL A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
      removed outlier: 9.270A  pdb=" N   LEU A 151 " --> pdb=" O   THR A 147 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   GLN A 152 " --> pdb=" O   ALA A 148 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   CYS A 163 " --> pdb=" O   ILE A 159 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   THR A 164 " --> pdb=" O   CYS A 160 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ASN A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 227
      removed outlier: 4.101A  pdb=" N   ILE A 189 " --> pdb=" O   SER A 185 " (cutoff:3.500A)
      Proline residue:  A 195  - end of helix
      removed outlier: 3.544A  pdb=" N   CYS A 204 " --> pdb=" O   ALA A 200 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   TYR A 227 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 269
    Processing helix  chain 'A' and resid 269 through 301
      removed outlier: 5.487A  pdb=" N   SER A 278 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
      removed outlier: 5.711A  pdb=" N   LEU A 279 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   PHE A 280 " --> pdb=" O   PHE A 276 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LEU A 281 " --> pdb=" O   ALA A 277 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   PHE A 300 " --> pdb=" O   ILE A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 343
    Processing helix  chain 'A' and resid 354 through 360
      removed outlier: 3.917A  pdb=" N   MET A 358 " --> pdb=" O   ASP A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 379
    Processing helix  chain 'A' and resid 407 through 411
    Processing helix  chain 'A' and resid 419 through 428
      removed outlier: 3.878A  pdb=" N   LEU A 423 " --> pdb=" O   SER A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 431
      No H-bonds generated for 'chain 'A' and resid 429 through 431'
    Processing helix  chain 'A' and resid 446 through 477
      Proline residue:  A 452  - end of helix
    Processing helix  chain 'A' and resid 494 through 498
    Processing helix  chain 'A' and resid 504 through 536
      removed outlier: 3.842A  pdb=" N   VAL A 508 " --> pdb=" O   PRO A 504 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE A 509 " --> pdb=" O   TRP A 505 " (cutoff:3.500A)
      Proline residue:  A 527  - end of helix
    Processing helix  chain 'A' and resid 543 through 547
    Processing helix  chain 'A' and resid 557 through 570
    Processing helix  chain 'A' and resid 573 through 602
      Proline residue:  A 579  - end of helix
    Processing helix  chain 'A' and resid 615 through 634
      removed outlier: 3.582A  pdb=" N   SER A 619 " --> pdb=" O   HIS A 615 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   SER A 634 " --> pdb=" O   MET A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 661
    Processing helix  chain 'A' and resid 664 through 682
      removed outlier: 4.121A  pdb=" N   GLU A 682 " --> pdb=" O   LEU A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 720
      removed outlier: 3.800A  pdb=" N   THR A 713 " --> pdb=" O   PRO A 709 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 734 through 738
    Processing helix  chain 'A' and resid 739 through 756
    Processing helix  chain 'A' and resid 769 through 780
    Processing helix  chain 'A' and resid 805 through 820
      removed outlier: 3.800A  pdb=" N   LYS A 809 " --> pdb=" O   PRO A 805 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR A 810 " --> pdb=" O   ARG A 806 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   PHE A 811 " --> pdb=" O   ALA A 807 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 830 through 834
      removed outlier: 3.622A  pdb=" N   TYR A 834 " --> pdb=" O   ILE A 831 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 854 through 867
      Proline residue:  A 862  - end of helix
    Processing helix  chain 'A' and resid 868 through 872
    Processing helix  chain 'A' and resid 888 through 903
      removed outlier: 3.797A  pdb=" N   HIS A 901 " --> pdb=" O   VAL A 897 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU A 902 " --> pdb=" O   PHE A 898 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 918 through 926
    Processing helix  chain 'A' and resid 1015 through 1033
    Processing helix  chain 'A' and resid 1052 through 1064
      removed outlier: 3.810A  pdb=" N   THR A1064 " --> pdb=" O   LEU A1060 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 133
      removed outlier: 5.812A  pdb=" N   LEU B 126 " --> pdb=" O   MET B 122 " (cutoff:3.500A)
      Proline residue:  B 127  - end of helix
    Processing helix  chain 'B' and resid 134 through 177
      removed outlier: 4.708A  pdb=" N   PHE B 138 " --> pdb=" O   GLY B 134 " (cutoff:3.500A)
      removed outlier: 5.188A  pdb=" N   THR B 142 " --> pdb=" O   PHE B 138 " (cutoff:3.500A)
      removed outlier: 5.477A  pdb=" N   TRP B 143 " --> pdb=" O   LEU B 139 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   MET B 144 " --> pdb=" O   ARG B 140 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   VAL B 150 " --> pdb=" O   GLY B 146 " (cutoff:3.500A)
      removed outlier: 9.270A  pdb=" N   LEU B 151 " --> pdb=" O   THR B 147 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   GLN B 152 " --> pdb=" O   ALA B 148 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   CYS B 163 " --> pdb=" O   ILE B 159 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   THR B 164 " --> pdb=" O   CYS B 160 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ASN B 177 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 227
      removed outlier: 4.101A  pdb=" N   ILE B 189 " --> pdb=" O   SER B 185 " (cutoff:3.500A)
      Proline residue:  B 195  - end of helix
      removed outlier: 3.545A  pdb=" N   CYS B 204 " --> pdb=" O   ALA B 200 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   TYR B 227 " --> pdb=" O   ILE B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 269
    Processing helix  chain 'B' and resid 269 through 301
      removed outlier: 5.486A  pdb=" N   SER B 278 " --> pdb=" O   ASN B 274 " (cutoff:3.500A)
      removed outlier: 5.711A  pdb=" N   LEU B 279 " --> pdb=" O   LYS B 275 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   PHE B 280 " --> pdb=" O   PHE B 276 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LEU B 281 " --> pdb=" O   ALA B 277 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   PHE B 300 " --> pdb=" O   ILE B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 336 through 343
    Processing helix  chain 'B' and resid 354 through 360
      removed outlier: 3.918A  pdb=" N   MET B 358 " --> pdb=" O   ASP B 354 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 374 through 379
    Processing helix  chain 'B' and resid 407 through 411
    Processing helix  chain 'B' and resid 419 through 428
      removed outlier: 3.877A  pdb=" N   LEU B 423 " --> pdb=" O   SER B 419 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 431
      No H-bonds generated for 'chain 'B' and resid 429 through 431'
    Processing helix  chain 'B' and resid 446 through 477
      Proline residue:  B 452  - end of helix
    Processing helix  chain 'B' and resid 494 through 498
    Processing helix  chain 'B' and resid 504 through 536
      removed outlier: 3.841A  pdb=" N   VAL B 508 " --> pdb=" O   PRO B 504 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE B 509 " --> pdb=" O   TRP B 505 " (cutoff:3.500A)
      Proline residue:  B 527  - end of helix
    Processing helix  chain 'B' and resid 543 through 547
    Processing helix  chain 'B' and resid 557 through 570
    Processing helix  chain 'B' and resid 573 through 602
      Proline residue:  B 579  - end of helix
    Processing helix  chain 'B' and resid 615 through 634
      removed outlier: 3.582A  pdb=" N   SER B 619 " --> pdb=" O   HIS B 615 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   SER B 634 " --> pdb=" O   MET B 630 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 634 through 661
    Processing helix  chain 'B' and resid 664 through 682
      removed outlier: 4.122A  pdb=" N   GLU B 682 " --> pdb=" O   LEU B 678 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 709 through 720
      removed outlier: 3.800A  pdb=" N   THR B 713 " --> pdb=" O   PRO B 709 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 734 through 738
    Processing helix  chain 'B' and resid 739 through 756
    Processing helix  chain 'B' and resid 769 through 780
    Processing helix  chain 'B' and resid 805 through 820
      removed outlier: 3.800A  pdb=" N   LYS B 809 " --> pdb=" O   PRO B 805 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   THR B 810 " --> pdb=" O   ARG B 806 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   PHE B 811 " --> pdb=" O   ALA B 807 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 830 through 834
      removed outlier: 3.622A  pdb=" N   TYR B 834 " --> pdb=" O   ILE B 831 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 854 through 867
      Proline residue:  B 862  - end of helix
    Processing helix  chain 'B' and resid 868 through 872
    Processing helix  chain 'B' and resid 888 through 903
      removed outlier: 3.797A  pdb=" N   HIS B 901 " --> pdb=" O   VAL B 897 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU B 902 " --> pdb=" O   PHE B 898 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 918 through 926
    Processing helix  chain 'B' and resid 1015 through 1033
    Processing helix  chain 'B' and resid 1052 through 1064
      removed outlier: 3.811A  pdb=" N   THR B1064 " --> pdb=" O   LEU B1060 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314
    Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 329
    Processing sheet with id=AA3, first strand: chain 'A' and resid 761 through 767
      removed outlier: 6.331A  pdb=" N   LEU A 695 " --> pdb=" O   VAL A 792 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   VAL A 791 " --> pdb=" O   LEU A 826 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LEU A1072 " --> pdb=" O   VAL A 827 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   VAL A1070 " --> pdb=" O   LYS A 829 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   VAL A1039 " --> pdb=" O   LEU A1071 " (cutoff:3.500A)
      removed outlier: 7.673A  pdb=" N   VAL A1073 " --> pdb=" O   VAL A1039 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   LEU A1041 " --> pdb=" O   VAL A1073 " (cutoff:3.500A)
      removed outlier: 8.502A  pdb=" N   LEU A1040 " --> pdb=" O   HIS A 845 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ASP A 847 " --> pdb=" O   LEU A1040 " (cutoff:3.500A)
      removed outlier: 8.873A  pdb=" N   ASN A1042 " --> pdb=" O   ASP A 847 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   ILE A 846 " --> pdb=" O   ARG A 877 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   PHE A 879 " --> pdb=" O   ILE A 846 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   VAL A 848 " --> pdb=" O   PHE A 879 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLU A 907 " --> pdb=" O   MET A 876 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 782 through 783
      removed outlier: 3.639A  pdb=" N   LEU A 783 " --> pdb=" O   MET A 786 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 313 through 314
    Processing sheet with id=AA6, first strand: chain 'B' and resid 326 through 329
    Processing sheet with id=AA7, first strand: chain 'B' and resid 761 through 767
      removed outlier: 6.331A  pdb=" N   LEU B 695 " --> pdb=" O   VAL B 792 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   VAL B 791 " --> pdb=" O   LEU B 826 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LEU B1072 " --> pdb=" O   VAL B 827 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   VAL B1070 " --> pdb=" O   LYS B 829 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   VAL B1039 " --> pdb=" O   LEU B1071 " (cutoff:3.500A)
      removed outlier: 7.673A  pdb=" N   VAL B1073 " --> pdb=" O   VAL B1039 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   LEU B1041 " --> pdb=" O   VAL B1073 " (cutoff:3.500A)
      removed outlier: 8.502A  pdb=" N   LEU B1040 " --> pdb=" O   HIS B 845 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ASP B 847 " --> pdb=" O   LEU B1040 " (cutoff:3.500A)
      removed outlier: 8.873A  pdb=" N   ASN B1042 " --> pdb=" O   ASP B 847 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   ILE B 846 " --> pdb=" O   ARG B 877 " (cutoff:3.500A)
      removed outlier: 7.535A  pdb=" N   PHE B 879 " --> pdb=" O   ILE B 846 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   VAL B 848 " --> pdb=" O   PHE B 879 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   GLU B 907 " --> pdb=" O   MET B 876 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 782 through 783
      removed outlier: 3.639A  pdb=" N   LEU B 783 " --> pdb=" O   MET B 786 " (cutoff:3.500A)

    766 hydrogen bonds defined for protein.
    2201 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.18

  Time building geometry restraints manager: 1.59 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: 4213
        1.34 -     1.47: 3483
        1.47 -     1.59: 5975
        1.59 -     1.72: 26
        1.72 -     1.84: 152
  Bond restraints: 13849
  Sorted by residual:
  bond pdb=" C4  ATP B1201 "
       pdb=" C5  ATP B1201 "
    ideal  model  delta    sigma   weight residual
    1.388  1.465 -0.077 1.00e-02 1.00e+04 5.91e+01
  bond pdb=" C4  ATP A1201 "
       pdb=" C5  ATP A1201 "
    ideal  model  delta    sigma   weight residual
    1.388  1.464 -0.076 1.00e-02 1.00e+04 5.81e+01
  bond pdb=" C5  ATP A1201 "
       pdb=" C6  ATP A1201 "
    ideal  model  delta    sigma   weight residual
    1.409  1.479 -0.070 1.00e-02 1.00e+04 4.89e+01
  bond pdb=" C5  ATP B1201 "
       pdb=" C6  ATP B1201 "
    ideal  model  delta    sigma   weight residual
    1.409  1.478 -0.069 1.00e-02 1.00e+04 4.75e+01
  bond pdb=" C8  ATP A1201 "
       pdb=" N7  ATP A1201 "
    ideal  model  delta    sigma   weight residual
    1.310  1.355 -0.045 1.00e-02 1.00e+04 1.99e+01
  ... (remaining 13844 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.97: 18627
        2.97 -     5.94: 207
        5.94 -     8.91: 36
        8.91 -    11.89: 4
       11.89 -    14.86: 4
  Bond angle restraints: 18878
  Sorted by residual:
  angle pdb=" PB  ATP A1201 "
        pdb=" O3B ATP A1201 "
        pdb=" PG  ATP A1201 "
      ideal   model   delta    sigma   weight residual
     139.87  125.01   14.86 1.00e+00 1.00e+00 2.21e+02
  angle pdb=" PB  ATP B1201 "
        pdb=" O3B ATP B1201 "
        pdb=" PG  ATP B1201 "
      ideal   model   delta    sigma   weight residual
     139.87  125.02   14.85 1.00e+00 1.00e+00 2.21e+02
  angle pdb=" PA  ATP B1201 "
        pdb=" O3A ATP B1201 "
        pdb=" PB  ATP B1201 "
      ideal   model   delta    sigma   weight residual
     136.83  123.66   13.17 1.00e+00 1.00e+00 1.73e+02
  angle pdb=" PA  ATP A1201 "
        pdb=" O3A ATP A1201 "
        pdb=" PB  ATP A1201 "
      ideal   model   delta    sigma   weight residual
     136.83  123.69   13.14 1.00e+00 1.00e+00 1.73e+02
  angle pdb=" C5  ATP B1201 "
        pdb=" C4  ATP B1201 "
        pdb=" N3  ATP B1201 "
      ideal   model   delta    sigma   weight residual
     126.80  118.62    8.18 1.00e+00 1.00e+00 6.69e+01
  ... (remaining 18873 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.43: 7388
       21.43 -    42.85: 725
       42.85 -    64.28: 131
       64.28 -    85.71: 28
       85.71 -   107.13: 12
  Dihedral angle restraints: 8284
    sinusoidal: 3302
      harmonic: 4982
  Sorted by residual:
  dihedral pdb=" CB  CYS B 343 "
           pdb=" SG  CYS B 343 "
           pdb=" SG  CYS B 353 "
           pdb=" CB  CYS B 353 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  141.07  -48.07     1      1.00e+01 1.00e-02 3.18e+01
  dihedral pdb=" CB  CYS A 343 "
           pdb=" SG  CYS A 343 "
           pdb=" SG  CYS A 353 "
           pdb=" CB  CYS A 353 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  141.04  -48.04     1      1.00e+01 1.00e-02 3.18e+01
  dihedral pdb=" O4  BMA J   3 "
           pdb=" C4  BMA J   3 "
           pdb=" C5  BMA J   3 "
           pdb=" O5  BMA J   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -178.42  107.13     1      3.00e+01 1.11e-03 1.38e+01
  ... (remaining 8281 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1910
       0.068 -    0.136: 296
       0.136 -    0.203: 15
       0.203 -    0.271: 8
       0.271 -    0.339: 2
  Chirality restraints: 2231
  Sorted by residual:
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN A 361 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.74    0.34 2.00e-01 2.50e+01 2.87e+00
  chirality pdb=" C1  NAG M   1 "
            pdb=" ND2 ASN B 361 "
            pdb=" C2  NAG M   1 "
            pdb=" O5  NAG M   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.74    0.34 2.00e-01 2.50e+01 2.83e+00
  chirality pdb=" C4  NAG M   1 "
            pdb=" C3  NAG M   1 "
            pdb=" C5  NAG M   1 "
            pdb=" O4  NAG M   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.27   -0.26 2.00e-01 2.50e+01 1.73e+00
  ... (remaining 2228 not shown)

  Planarity restraints: 2324
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP B 808 "   -0.014 2.00e-02 2.50e+03   2.75e-02 7.59e+00
        pdb=" C   TRP B 808 "    0.048 2.00e-02 2.50e+03
        pdb=" O   TRP B 808 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   LYS B 809 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 808 "   -0.014 2.00e-02 2.50e+03   2.75e-02 7.58e+00
        pdb=" C   TRP A 808 "    0.048 2.00e-02 2.50e+03
        pdb=" O   TRP A 808 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   LYS A 809 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 137 "    0.012 2.00e-02 2.50e+03   2.44e-02 5.96e+00
        pdb=" C   LEU A 137 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   LEU A 137 "    0.016 2.00e-02 2.50e+03
        pdb=" N   PHE A 138 "    0.014 2.00e-02 2.50e+03
  ... (remaining 2321 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 2065
        2.75 -     3.29: 12937
        3.29 -     3.83: 21296
        3.83 -     4.36: 23646
        4.36 -     4.90: 43608
  Nonbonded interactions: 103552
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B 809 "
            pdb=" OD2 ASP B 813 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" NZ  LYS A 809 "
            pdb=" OD2 ASP A 813 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" OG1 THR B 713 "
            pdb=" OE1 GLU B 756 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OG1 THR A 713 "
            pdb=" OE1 GLU A 756 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   ARG B 806 "
            pdb="MG    MG B1202 "
     model   vdw
     2.256 2.170
  ... (remaining 103547 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 116 through 775 or resid 777 through 1202))
  selection = (chain 'B' and (resid 116 through 775 or resid 777 through 1202))
}
ncs_group {
  reference = chain 'C'
  selection = chain 'J'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'M'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.930
  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:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     14.760
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.077  13865  Z= 0.323
  Angle     :  0.868  14.857  18920  Z= 0.490
  Chirality :  0.050   0.339   2231
  Planarity :  0.005   0.046   2320
  Dihedral  : 17.389 107.133   5076
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 21.40 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.49 (0.19), residues: 1707
  helix:  0.28 (0.16), residues: 943
  sheet: -2.10 (0.40), residues: 136
  loop : -2.72 (0.22), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 866 
 TYR   0.011   0.001   TYR A 739 
 PHE   0.020   0.002   PHE B 541 
 TRP   0.029   0.002   TRP A 143 
 HIS   0.008   0.001   HIS A 853 

Details of bonding type rmsd
  covalent geometry    : bond        0.00685 (13849)
  covalent geometry    : angle       0.83431 (18878)
  SS BOND              : bond        0.00561 (    6)
  SS BOND              : angle       3.83462 (   12)
  hydrogen bonds       : bond        0.15333 (  766)
  hydrogen bonds       : angle       5.41242 ( 2201)
  link_BETA1-4         : bond        0.00503 (    6)
  link_BETA1-4         : angle       4.01190 (   18)
  link_NAG-ASN         : bond        0.00328 (    4)
  link_NAG-ASN         : angle       7.27737 (   12)

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

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

  3414 Ramachandran restraints generated.
    1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3414 Ramachandran restraints generated.
    1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 200
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  443 ASP cc_start: 0.7243 (m-30) cc_final: 0.6872 (t0)
REVERT: A  583 MET cc_start: 0.8014 (mmp) cc_final: 0.7741 (mmp)
REVERT: A  903 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.5280 (pmt170)
REVERT: B  443 ASP cc_start: 0.7219 (m-30) cc_final: 0.6844 (t0)
REVERT: B  903 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.5205 (pmt170)
  outliers start: 10
  outliers final: 6
  residues processed: 210
  average time/residue: 0.1442
  time to fit residues: 41.6684
Evaluate side-chains
  167 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 159
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  879 PHE
Chi-restraints excluded: chain A residue  903 ARG
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  353 CYS
Chi-restraints excluded: chain B residue  879 PHE
Chi-restraints excluded: chain B residue  903 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    0.0070
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    0.7980
   chunk 149 optimal weight:    3.9990
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
A 152 GLN
A 344 HIS
A 547 HIS
A 593 ASN
A 599 GLN
A 655 GLN
A 717 GLN
A 747 GLN
A 751 ASN
A 776 HIS    B
** A 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1026 ASN
B 152 GLN
B 344 HIS
B 547 HIS
B 593 ASN
B 599 GLN
B 655 GLN
B 717 GLN
B 747 GLN
B 751 ASN
B 853 HIS
B1026 ASN

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.170159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.125071 restraints weight = 20523.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.76
r_work: 0.3303 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3304
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3304 r_free = 0.3304    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3304 r_free = 0.3304    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3304
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13865  Z= 0.125
  Angle     :  0.627   9.524  18920  Z= 0.304
  Chirality :  0.042   0.248   2231
  Planarity :  0.004   0.035   2320
  Dihedral  : 10.345  87.061   2170
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 22.32 %
    Favored  : 75.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.20), residues: 1707
  helix:  1.54 (0.17), residues: 949
  sheet: -1.33 (0.40), residues: 136
  loop : -2.24 (0.22), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 317 
 TYR   0.010   0.001   TYR A1056 
 PHE   0.014   0.001   PHE B 541 
 TRP   0.015   0.001   TRP A 143 
 HIS   0.013   0.001   HIS A 853 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (13849)
  covalent geometry    : angle       0.61247 (18878)
  SS BOND              : bond        0.00371 (    6)
  SS BOND              : angle       1.77706 (   12)
  hydrogen bonds       : bond        0.04908 (  766)
  hydrogen bonds       : angle       4.05442 ( 2201)
  link_BETA1-4         : bond        0.00682 (    6)
  link_BETA1-4         : angle       3.22939 (   18)
  link_NAG-ASN         : bond        0.00256 (    4)
  link_NAG-ASN         : angle       3.24434 (   12)

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

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

  3414 Ramachandran restraints generated.
    1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3414 Ramachandran restraints generated.
    1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 174
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 CYS cc_start: 0.5860 (OUTLIER) cc_final: 0.5584 (m)
REVERT: A  443 ASP cc_start: 0.7869 (m-30) cc_final: 0.6701 (t0)
REVERT: A  543 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7050 (ttp80)
REVERT: A 1061 GLU cc_start: 0.7974 (tp30) cc_final: 0.7696 (tp30)
REVERT: B  171 MET cc_start: 0.7628 (tpt) cc_final: 0.7422 (tpt)
REVERT: B  353 CYS cc_start: 0.5884 (OUTLIER) cc_final: 0.5605 (m)
REVERT: B  380 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8903 (tt)
REVERT: B  443 ASP cc_start: 0.7833 (m-30) cc_final: 0.6704 (t0)
REVERT: B  543 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7017 (ttp80)
REVERT: B  591 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7708 (m-80)
REVERT: B 1061 GLU cc_start: 0.7998 (tp30) cc_final: 0.7731 (tp30)
  outliers start: 32
  outliers final: 18
  residues processed: 194
  average time/residue: 0.1058
  time to fit residues: 30.3663
Evaluate side-chains
  178 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 154
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  353 CYS
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  543 ARG
Chi-restraints excluded: chain A residue  879 PHE
Chi-restraints excluded: chain A residue 1073 VAL
Chi-restraints excluded: chain A residue 1081 ILE
Chi-restraints excluded: chain B residue  159 ILE
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  322 ILE
Chi-restraints excluded: chain B residue  353 CYS
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  413 VAL
Chi-restraints excluded: chain B residue  543 ARG
Chi-restraints excluded: chain B residue  569 ILE
Chi-restraints excluded: chain B residue  591 PHE
Chi-restraints excluded: chain B residue  879 PHE
Chi-restraints excluded: chain B residue 1073 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 161 optimal weight:    9.9990
   chunk 2 optimal weight:    2.9990
   chunk 78 optimal weight:    7.9990
   chunk 48 optimal weight:    5.9990
   chunk 129 optimal weight:    0.4980
   chunk 165 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 152 optimal weight:    5.9990
   chunk 62 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
A 547 HIS
A 853 HIS
A 868 HIS
B 547 HIS
B 853 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.168500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.122970 restraints weight = 23835.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 3.22
r_work: 0.3274 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3260
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3260
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.1450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13865  Z= 0.153
  Angle     :  0.620   9.727  18920  Z= 0.297
  Chirality :  0.043   0.269   2231
  Planarity :  0.004   0.035   2320
  Dihedral  :  9.130  89.966   2162
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 22.32 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.21), residues: 1707
  helix:  1.95 (0.17), residues: 937
  sheet: -0.83 (0.42), residues: 136
  loop : -2.04 (0.22), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 317 
 TYR   0.008   0.001   TYR B 654 
 PHE   0.023   0.001   PHE B1059 
 TRP   0.014   0.001   TRP A 143 
 HIS   0.009   0.001   HIS A 853 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (13849)
  covalent geometry    : angle       0.60711 (18878)
  SS BOND              : bond        0.00431 (    6)
  SS BOND              : angle       1.53902 (   12)
  hydrogen bonds       : bond        0.05005 (  766)
  hydrogen bonds       : angle       3.82762 ( 2201)
  link_BETA1-4         : bond        0.00575 (    6)
  link_BETA1-4         : angle       3.01377 (   18)
  link_NAG-ASN         : bond        0.00099 (    4)
  link_NAG-ASN         : angle       3.28446 (   12)

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

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

  3414 Ramachandran restraints generated.
    1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3414 Ramachandran restraints generated.
    1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 170
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 MET cc_start: 0.7857 (mmm) cc_final: 0.7514 (tpt)
REVERT: A  380 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8921 (tt)
REVERT: A  443 ASP cc_start: 0.7919 (m-30) cc_final: 0.6775 (t0)
REVERT: A  543 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7080 (ttp80)
REVERT: A 1061 GLU cc_start: 0.8030 (tp30) cc_final: 0.7748 (tp30)
REVERT: B  380 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8968 (tt)
REVERT: B  443 ASP cc_start: 0.7915 (m-30) cc_final: 0.6735 (t0)
REVERT: B  543 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7046 (ttp80)
REVERT: B  591 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7850 (m-10)
REVERT: B 1061 GLU cc_start: 0.8077 (tp30) cc_final: 0.7807 (tp30)
  outliers start: 39
  outliers final: 25
  residues processed: 194
  average time/residue: 0.1175
  time to fit residues: 33.8353
Evaluate side-chains
  191 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 161
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  543 ARG
Chi-restraints excluded: chain A residue  591 PHE
Chi-restraints excluded: chain A residue  772 GLU
Chi-restraints excluded: chain A residue  879 PHE
Chi-restraints excluded: chain A residue 1081 ILE
Chi-restraints excluded: chain B residue  159 ILE
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  322 ILE
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  413 VAL
Chi-restraints excluded: chain B residue  418 THR
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  543 ARG
Chi-restraints excluded: chain B residue  591 PHE
Chi-restraints excluded: chain B residue  630 MET
Chi-restraints excluded: chain B residue  792 VAL
Chi-restraints excluded: chain B residue  879 PHE
Chi-restraints excluded: chain B residue 1073 VAL
Chi-restraints excluded: chain B residue 1080 VAL
Chi-restraints excluded: chain B residue 1081 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 160 optimal weight:    0.9980
   chunk 134 optimal weight:    3.9990
   chunk 127 optimal weight:    0.8980
   chunk 126 optimal weight:    0.9980
   chunk 116 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 115 optimal weight:    4.9990
   chunk 167 optimal weight:    9.9990
   chunk 119 optimal weight:    0.7980
   chunk 108 optimal weight:    0.1980
   chunk 149 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 547 HIS
B 547 HIS
B 853 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.171294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.126934 restraints weight = 18011.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.56
r_work: 0.3328 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3186
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3186
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  13865  Z= 0.111
  Angle     :  0.562   9.581  18920  Z= 0.269
  Chirality :  0.041   0.267   2231
  Planarity :  0.003   0.037   2320
  Dihedral  :  8.150  88.118   2160
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 21.90 %
    Favored  : 74.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.21), residues: 1707
  helix:  2.21 (0.17), residues: 951
  sheet: -0.42 (0.43), residues: 136
  loop : -1.78 (0.23), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 317 
 TYR   0.009   0.001   TYR A1056 
 PHE   0.020   0.001   PHE B1059 
 TRP   0.014   0.001   TRP A 850 
 HIS   0.007   0.001   HIS B 853 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (13849)
  covalent geometry    : angle       0.54930 (18878)
  SS BOND              : bond        0.00397 (    6)
  SS BOND              : angle       1.37788 (   12)
  hydrogen bonds       : bond        0.04201 (  766)
  hydrogen bonds       : angle       3.61399 ( 2201)
  link_BETA1-4         : bond        0.00574 (    6)
  link_BETA1-4         : angle       2.69796 (   18)
  link_NAG-ASN         : bond        0.00231 (    4)
  link_NAG-ASN         : angle       3.34344 (   12)

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

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

  3414 Ramachandran restraints generated.
    1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3414 Ramachandran restraints generated.
    1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 167
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8888 (tt)
REVERT: A  443 ASP cc_start: 0.7996 (m-30) cc_final: 0.6706 (t0)
REVERT: A  543 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7203 (ttp80)
REVERT: A  591 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.7952 (m-80)
REVERT: A  850 TRP cc_start: 0.8158 (t60) cc_final: 0.7875 (t60)
REVERT: A  867 GLN cc_start: 0.7859 (tt0) cc_final: 0.7651 (mt0)
REVERT: A 1061 GLU cc_start: 0.8077 (tp30) cc_final: 0.7765 (tp30)
REVERT: B  380 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8905 (tt)
REVERT: B  443 ASP cc_start: 0.7948 (m-30) cc_final: 0.6660 (t0)
REVERT: B  543 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7138 (ttp80)
REVERT: B  591 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.7872 (m-80)
REVERT: B  850 TRP cc_start: 0.8208 (t60) cc_final: 0.7869 (t60)
REVERT: B 1061 GLU cc_start: 0.8068 (tp30) cc_final: 0.7779 (tp30)
  outliers start: 44
  outliers final: 27
  residues processed: 200
  average time/residue: 0.1157
  time to fit residues: 34.4012
Evaluate side-chains
  191 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 158
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  543 ARG
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  591 PHE
Chi-restraints excluded: chain A residue  630 MET
Chi-restraints excluded: chain A residue  772 GLU
Chi-restraints excluded: chain A residue  879 PHE
Chi-restraints excluded: chain A residue 1073 VAL
Chi-restraints excluded: chain B residue  159 ILE
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  322 ILE
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  413 VAL
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  543 ARG
Chi-restraints excluded: chain B residue  569 ILE
Chi-restraints excluded: chain B residue  591 PHE
Chi-restraints excluded: chain B residue  772 GLU
Chi-restraints excluded: chain B residue  792 VAL
Chi-restraints excluded: chain B residue  879 PHE
Chi-restraints excluded: chain B residue 1073 VAL
Chi-restraints excluded: chain B residue 1080 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 144 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0050
   chunk 49 optimal weight:    5.9990
   chunk 38 optimal weight:    0.7980
   chunk 95 optimal weight:    0.5980
   chunk 147 optimal weight:    0.7980
   chunk 138 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   chunk 118 optimal weight:    3.9990
   chunk 146 optimal weight:    3.9990
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
A 547 HIS
B 547 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.172082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.126053 restraints weight = 23713.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 2.96
r_work: 0.3319 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3317
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3317 r_free = 0.3317    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3317 r_free = 0.3317    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3317
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  13865  Z= 0.106
  Angle     :  0.549   9.666  18920  Z= 0.262
  Chirality :  0.040   0.269   2231
  Planarity :  0.003   0.038   2320
  Dihedral  :  7.779  87.020   2160
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 22.25 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.21), residues: 1707
  helix:  2.36 (0.17), residues: 963
  sheet: -0.23 (0.43), residues: 136
  loop : -1.65 (0.23), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 317 
 TYR   0.008   0.001   TYR A1056 
 PHE   0.017   0.001   PHE B1059 
 TRP   0.010   0.001   TRP A 850 
 HIS   0.004   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (13849)
  covalent geometry    : angle       0.53630 (18878)
  SS BOND              : bond        0.00377 (    6)
  SS BOND              : angle       1.32932 (   12)
  hydrogen bonds       : bond        0.04007 (  766)
  hydrogen bonds       : angle       3.49867 ( 2201)
  link_BETA1-4         : bond        0.00506 (    6)
  link_BETA1-4         : angle       2.44526 (   18)
  link_NAG-ASN         : bond        0.00244 (    4)
  link_NAG-ASN         : angle       3.36002 (   12)

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

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

  3414 Ramachandran restraints generated.
    1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3414 Ramachandran restraints generated.
    1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 168
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8895 (tt)
REVERT: A  443 ASP cc_start: 0.7839 (m-30) cc_final: 0.6740 (t0)
REVERT: A  543 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7309 (ttp80)
REVERT: A  591 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7950 (m-80)
REVERT: A  850 TRP cc_start: 0.8172 (t60) cc_final: 0.7850 (t60)
REVERT: A  879 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.5894 (m-80)
REVERT: A 1061 GLU cc_start: 0.8018 (tp30) cc_final: 0.7738 (tp30)
REVERT: B  152 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7703 (mt0)
REVERT: B  264 LEU cc_start: 0.7674 (tp) cc_final: 0.7085 (mm)
REVERT: B  380 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8902 (tt)
REVERT: B  443 ASP cc_start: 0.7884 (m-30) cc_final: 0.6750 (t0)
REVERT: B  543 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7125 (ttp80)
REVERT: B 1061 GLU cc_start: 0.8024 (tp30) cc_final: 0.7804 (tp30)
  outliers start: 42
  outliers final: 27
  residues processed: 198
  average time/residue: 0.1135
  time to fit residues: 33.6523
Evaluate side-chains
  195 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 161
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  543 ARG
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  591 PHE
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue  772 GLU
Chi-restraints excluded: chain A residue  879 PHE
Chi-restraints excluded: chain A residue 1073 VAL
Chi-restraints excluded: chain A residue 1081 ILE
Chi-restraints excluded: chain B residue  152 GLN
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  322 ILE
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  413 VAL
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  543 ARG
Chi-restraints excluded: chain B residue  591 PHE
Chi-restraints excluded: chain B residue  772 GLU
Chi-restraints excluded: chain B residue  792 VAL
Chi-restraints excluded: chain B residue  879 PHE
Chi-restraints excluded: chain B residue 1073 VAL
Chi-restraints excluded: chain B residue 1080 VAL
Chi-restraints excluded: chain B residue 1081 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 121 optimal weight:    3.9990
   chunk 135 optimal weight:    5.9990
   chunk 32 optimal weight:    7.9990
   chunk 48 optimal weight:    4.9990
   chunk 60 optimal weight:    4.9990
   chunk 53 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 101 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 163 optimal weight:    7.9990
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
A 547 HIS
A 822 HIS
B 547 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.162410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.117751 restraints weight = 23674.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 3.04
r_work: 0.3252 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3259
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3259
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.1843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  13865  Z= 0.205
  Angle     :  0.635   9.875  18920  Z= 0.308
  Chirality :  0.044   0.275   2231
  Planarity :  0.004   0.039   2320
  Dihedral  :  8.027  86.555   2160
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 22.82 %
    Favored  : 74.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.93 (0.21), residues: 1707
  helix:  2.22 (0.17), residues: 933
  sheet: -0.46 (0.41), residues: 136
  loop : -1.68 (0.22), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 140 
 TYR   0.013   0.001   TYR A 654 
 PHE   0.017   0.002   PHE B 541 
 TRP   0.012   0.001   TRP B 850 
 HIS   0.003   0.001   HIS A 845 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 (13849)
  covalent geometry    : angle       0.62389 (18878)
  SS BOND              : bond        0.00543 (    6)
  SS BOND              : angle       1.76478 (   12)
  hydrogen bonds       : bond        0.05536 (  766)
  hydrogen bonds       : angle       3.74534 ( 2201)
  link_BETA1-4         : bond        0.00467 (    6)
  link_BETA1-4         : angle       2.53466 (   18)
  link_NAG-ASN         : bond        0.00027 (    4)
  link_NAG-ASN         : angle       3.18097 (   12)

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

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

  3414 Ramachandran restraints generated.
    1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3414 Ramachandran restraints generated.
    1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 171
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
REVERT: A  380 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8980 (tt)
REVERT: A  443 ASP cc_start: 0.7955 (m-30) cc_final: 0.6897 (t0)
REVERT: A  543 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7390 (ttp80)
REVERT: A  591 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.8214 (m-10)
REVERT: A  753 MET cc_start: 0.8596 (mtp) cc_final: 0.8390 (mtp)
REVERT: A  879 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.6164 (m-80)
REVERT: A 1061 GLU cc_start: 0.8081 (tp30) cc_final: 0.7793 (tp30)
REVERT: B  380 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8990 (tt)
REVERT: B  443 ASP cc_start: 0.7982 (m-30) cc_final: 0.6920 (t0)
REVERT: B  543 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7347 (ttp80)
REVERT: B  591 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8007 (m-10)
REVERT: B  850 TRP cc_start: 0.8341 (t60) cc_final: 0.8092 (t60)
REVERT: B 1061 GLU cc_start: 0.8072 (tp30) cc_final: 0.7836 (tp30)
  outliers start: 43
  outliers final: 30
  residues processed: 202
  average time/residue: 0.1137
  time to fit residues: 34.1609
Evaluate side-chains
  201 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 164
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  543 ARG
Chi-restraints excluded: chain A residue  591 PHE
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue  772 GLU
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue  879 PHE
Chi-restraints excluded: chain A residue 1062 VAL
Chi-restraints excluded: chain A residue 1073 VAL
Chi-restraints excluded: chain A residue 1081 ILE
Chi-restraints excluded: chain B residue  159 ILE
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  322 ILE
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  413 VAL
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  543 ARG
Chi-restraints excluded: chain B residue  591 PHE
Chi-restraints excluded: chain B residue  630 MET
Chi-restraints excluded: chain B residue  632 VAL
Chi-restraints excluded: chain B residue  772 GLU
Chi-restraints excluded: chain B residue  792 VAL
Chi-restraints excluded: chain B residue  879 PHE
Chi-restraints excluded: chain B residue 1080 VAL
Chi-restraints excluded: chain B residue 1081 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 121 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0270
   chunk 69 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 86 optimal weight:    6.9990
   chunk 118 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 74 optimal weight:    0.4980
   chunk 127 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
A 547 HIS
B 547 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.171133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.128188 restraints weight = 16068.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 2.38
r_work: 0.3330 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3197
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3197
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.2058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  13865  Z= 0.108
  Angle     :  0.558   9.563  18920  Z= 0.268
  Chirality :  0.041   0.260   2231
  Planarity :  0.003   0.038   2320
  Dihedral  :  7.717  85.489   2160
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 23.32 %
    Favored  : 73.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.34 (0.21), residues: 1707
  helix:  2.33 (0.17), residues: 973
  sheet: -0.05 (0.42), residues: 136
  loop : -1.41 (0.23), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 317 
 TYR   0.009   0.001   TYR B 636 
 PHE   0.023   0.001   PHE B1059 
 TRP   0.017   0.001   TRP A 850 
 HIS   0.004   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 (13849)
  covalent geometry    : angle       0.54681 (18878)
  SS BOND              : bond        0.00330 (    6)
  SS BOND              : angle       1.40780 (   12)
  hydrogen bonds       : bond        0.04169 (  766)
  hydrogen bonds       : angle       3.53481 ( 2201)
  link_BETA1-4         : bond        0.00565 (    6)
  link_BETA1-4         : angle       2.35963 (   18)
  link_NAG-ASN         : bond        0.00231 (    4)
  link_NAG-ASN         : angle       3.32011 (   12)

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

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

  3414 Ramachandran restraints generated.
    1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3414 Ramachandran restraints generated.
    1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 166
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
REVERT: A  380 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8885 (tt)
REVERT: A  443 ASP cc_start: 0.8018 (m-30) cc_final: 0.6729 (t0)
REVERT: A  543 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7302 (ttp80)
REVERT: A  591 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.8017 (m-10)
REVERT: A  850 TRP cc_start: 0.8144 (t60) cc_final: 0.7924 (t60)
REVERT: A  879 PHE cc_start: 0.6611 (OUTLIER) cc_final: 0.5956 (m-80)
REVERT: A 1061 GLU cc_start: 0.8055 (tp30) cc_final: 0.7757 (tp30)
REVERT: B  332 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8021 (pp20)
REVERT: B  380 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8851 (tt)
REVERT: B  443 ASP cc_start: 0.8058 (m-30) cc_final: 0.6762 (t0)
REVERT: B  543 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7194 (ttp80)
REVERT: B  591 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7979 (m-80)
REVERT: B  879 PHE cc_start: 0.6586 (OUTLIER) cc_final: 0.5982 (m-80)
REVERT: B 1061 GLU cc_start: 0.8061 (tp30) cc_final: 0.7807 (tp30)
  outliers start: 43
  outliers final: 28
  residues processed: 195
  average time/residue: 0.1095
  time to fit residues: 32.0902
Evaluate side-chains
  200 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 163
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  543 ARG
Chi-restraints excluded: chain A residue  591 PHE
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue  772 GLU
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue  879 PHE
Chi-restraints excluded: chain A residue 1062 VAL
Chi-restraints excluded: chain A residue 1073 VAL
Chi-restraints excluded: chain A residue 1080 VAL
Chi-restraints excluded: chain A residue 1081 ILE
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  322 ILE
Chi-restraints excluded: chain B residue  332 GLU
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  413 VAL
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  543 ARG
Chi-restraints excluded: chain B residue  569 ILE
Chi-restraints excluded: chain B residue  591 PHE
Chi-restraints excluded: chain B residue  630 MET
Chi-restraints excluded: chain B residue  739 TYR
Chi-restraints excluded: chain B residue  772 GLU
Chi-restraints excluded: chain B residue  792 VAL
Chi-restraints excluded: chain B residue  879 PHE
Chi-restraints excluded: chain B residue 1080 VAL
Chi-restraints excluded: chain B residue 1081 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 123 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 161 optimal weight:    9.9990
   chunk 101 optimal weight:    6.9990
   chunk 145 optimal weight:    0.6980
   chunk 93 optimal weight:    0.7980
   chunk 120 optimal weight:    0.6980
   chunk 86 optimal weight:    7.9990
   chunk 150 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 547 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.170899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.125416 restraints weight = 20233.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 2.73
r_work: 0.3314 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3315
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3315 r_free = 0.3315    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3315 r_free = 0.3315    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3315
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  13865  Z= 0.111
  Angle     :  0.554   9.707  18920  Z= 0.266
  Chirality :  0.041   0.266   2231
  Planarity :  0.003   0.040   2320
  Dihedral  :  7.646  84.782   2160
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 23.60 %
    Favored  : 73.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.21), residues: 1707
  helix:  2.44 (0.17), residues: 971
  sheet:  0.11 (0.43), residues: 136
  loop : -1.31 (0.24), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 317 
 TYR   0.008   0.001   TYR A1056 
 PHE   0.021   0.001   PHE B1059 
 TRP   0.028   0.001   TRP B 850 
 HIS   0.003   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (13849)
  covalent geometry    : angle       0.54308 (18878)
  SS BOND              : bond        0.00331 (    6)
  SS BOND              : angle       1.34297 (   12)
  hydrogen bonds       : bond        0.04103 (  766)
  hydrogen bonds       : angle       3.48087 ( 2201)
  link_BETA1-4         : bond        0.00482 (    6)
  link_BETA1-4         : angle       2.33291 (   18)
  link_NAG-ASN         : bond        0.00177 (    4)
  link_NAG-ASN         : angle       3.22816 (   12)

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

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

  3414 Ramachandran restraints generated.
    1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3414 Ramachandran restraints generated.
    1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 166
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8908 (tt)
REVERT: A  443 ASP cc_start: 0.7848 (m-30) cc_final: 0.6786 (t0)
REVERT: A  543 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7240 (ttp80)
REVERT: A  587 MET cc_start: 0.8156 (tpt) cc_final: 0.7915 (tpt)
REVERT: A  591 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7988 (m-10)
REVERT: A  850 TRP cc_start: 0.8104 (t60) cc_final: 0.7899 (t60)
REVERT: A  879 PHE cc_start: 0.6564 (OUTLIER) cc_final: 0.5879 (m-80)
REVERT: A 1061 GLU cc_start: 0.8021 (tp30) cc_final: 0.7768 (tp30)
REVERT: B  332 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8043 (pp20)
REVERT: B  380 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8924 (tt)
REVERT: B  443 ASP cc_start: 0.7945 (m-30) cc_final: 0.6825 (t0)
REVERT: B  543 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7249 (ttp80)
REVERT: B  879 PHE cc_start: 0.6477 (OUTLIER) cc_final: 0.5860 (m-80)
REVERT: B 1061 GLU cc_start: 0.8068 (tp30) cc_final: 0.7846 (tp30)
  outliers start: 40
  outliers final: 31
  residues processed: 195
  average time/residue: 0.1154
  time to fit residues: 33.5987
Evaluate side-chains
  202 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 163
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  543 ARG
Chi-restraints excluded: chain A residue  591 PHE
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue  772 GLU
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue  879 PHE
Chi-restraints excluded: chain A residue 1062 VAL
Chi-restraints excluded: chain A residue 1073 VAL
Chi-restraints excluded: chain A residue 1080 VAL
Chi-restraints excluded: chain A residue 1081 ILE
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  322 ILE
Chi-restraints excluded: chain B residue  332 GLU
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  413 VAL
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  543 ARG
Chi-restraints excluded: chain B residue  569 ILE
Chi-restraints excluded: chain B residue  591 PHE
Chi-restraints excluded: chain B residue  630 MET
Chi-restraints excluded: chain B residue  632 VAL
Chi-restraints excluded: chain B residue  739 TYR
Chi-restraints excluded: chain B residue  772 GLU
Chi-restraints excluded: chain B residue  792 VAL
Chi-restraints excluded: chain B residue  879 PHE
Chi-restraints excluded: chain B residue 1080 VAL
Chi-restraints excluded: chain B residue 1081 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 145 optimal weight:    0.4980
   chunk 67 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   chunk 96 optimal weight:    1.9990
   chunk 126 optimal weight:    1.9990
   chunk 27 optimal weight:    0.4980
   chunk 146 optimal weight:    4.9990
   chunk 90 optimal weight:    0.8980
   chunk 114 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 547 HIS
B 868 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.171440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.127014 restraints weight = 16259.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 2.49
r_work: 0.3338 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3186
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3186
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  13865  Z= 0.109
  Angle     :  0.549   9.683  18920  Z= 0.263
  Chirality :  0.040   0.265   2231
  Planarity :  0.003   0.058   2320
  Dihedral  :  7.570  83.921   2160
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 23.25 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.61 (0.21), residues: 1707
  helix:  2.50 (0.17), residues: 969
  sheet:  0.22 (0.43), residues: 136
  loop : -1.23 (0.23), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 317 
 TYR   0.008   0.001   TYR A1056 
 PHE   0.023   0.001   PHE B1059 
 TRP   0.010   0.001   TRP A 850 
 HIS   0.003   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (13849)
  covalent geometry    : angle       0.53837 (18878)
  SS BOND              : bond        0.00295 (    6)
  SS BOND              : angle       1.31383 (   12)
  hydrogen bonds       : bond        0.03993 (  766)
  hydrogen bonds       : angle       3.43639 ( 2201)
  link_BETA1-4         : bond        0.00482 (    6)
  link_BETA1-4         : angle       2.27971 (   18)
  link_NAG-ASN         : bond        0.00188 (    4)
  link_NAG-ASN         : angle       3.18748 (   12)

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

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

  3414 Ramachandran restraints generated.
    1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3414 Ramachandran restraints generated.
    1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 163
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
REVERT: A  380 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8843 (tt)
REVERT: A  443 ASP cc_start: 0.7949 (m-30) cc_final: 0.6650 (t0)
REVERT: A  543 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7248 (ttp80)
REVERT: A  591 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7893 (m-10)
REVERT: A  850 TRP cc_start: 0.8084 (t60) cc_final: 0.7815 (t60)
REVERT: A  879 PHE cc_start: 0.6661 (OUTLIER) cc_final: 0.5916 (m-80)
REVERT: A 1061 GLU cc_start: 0.8043 (tp30) cc_final: 0.7748 (tp30)
REVERT: B  320 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7447 (p90)
REVERT: B  332 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7991 (pp20)
REVERT: B  380 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8818 (tt)
REVERT: B  443 ASP cc_start: 0.8068 (m-30) cc_final: 0.6709 (t0)
REVERT: B  543 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7227 (ttp80)
REVERT: B  591 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.7935 (m-10)
REVERT: B  879 PHE cc_start: 0.6555 (OUTLIER) cc_final: 0.5869 (m-80)
REVERT: B 1061 GLU cc_start: 0.8085 (tp30) cc_final: 0.7839 (tp30)
  outliers start: 42
  outliers final: 29
  residues processed: 193
  average time/residue: 0.1126
  time to fit residues: 32.5623
Evaluate side-chains
  201 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 162
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  543 ARG
Chi-restraints excluded: chain A residue  591 PHE
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue  772 GLU
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue  879 PHE
Chi-restraints excluded: chain A residue 1073 VAL
Chi-restraints excluded: chain A residue 1080 VAL
Chi-restraints excluded: chain A residue 1081 ILE
Chi-restraints excluded: chain B residue  159 ILE
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  332 GLU
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  413 VAL
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  543 ARG
Chi-restraints excluded: chain B residue  569 ILE
Chi-restraints excluded: chain B residue  591 PHE
Chi-restraints excluded: chain B residue  630 MET
Chi-restraints excluded: chain B residue  632 VAL
Chi-restraints excluded: chain B residue  739 TYR
Chi-restraints excluded: chain B residue  772 GLU
Chi-restraints excluded: chain B residue  792 VAL
Chi-restraints excluded: chain B residue  879 PHE
Chi-restraints excluded: chain B residue 1080 VAL
Chi-restraints excluded: chain B residue 1081 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 87 optimal weight:    0.0970
   chunk 103 optimal weight:    0.9980
   chunk 156 optimal weight:    3.9990
   chunk 148 optimal weight:    0.7980
   chunk 52 optimal weight:    0.7980
   chunk 64 optimal weight:    7.9990
   chunk 59 optimal weight:    0.0870
   chunk 60 optimal weight:    0.2980
   chunk 62 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.4156

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.173835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.127458 restraints weight = 23778.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 3.22
r_work: 0.3321 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3327
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3327 r_free = 0.3327    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3327 r_free = 0.3327    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3327
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  13865  Z= 0.098
  Angle     :  0.541   9.653  18920  Z= 0.259
  Chirality :  0.040   0.265   2231
  Planarity :  0.003   0.054   2320
  Dihedral  :  7.402  82.816   2160
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 24.03 %
    Favored  : 73.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.21), residues: 1707
  helix:  2.61 (0.17), residues: 969
  sheet:  0.34 (0.43), residues: 136
  loop : -1.13 (0.24), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1078 
 TYR   0.008   0.001   TYR A1056 
 PHE   0.023   0.001   PHE B1059 
 TRP   0.010   0.001   TRP A 850 
 HIS   0.003   0.000   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 (13849)
  covalent geometry    : angle       0.53048 (18878)
  SS BOND              : bond        0.00254 (    6)
  SS BOND              : angle       1.16308 (   12)
  hydrogen bonds       : bond        0.03585 (  766)
  hydrogen bonds       : angle       3.36747 ( 2201)
  link_BETA1-4         : bond        0.00485 (    6)
  link_BETA1-4         : angle       2.21831 (   18)
  link_NAG-ASN         : bond        0.00220 (    4)
  link_NAG-ASN         : angle       3.16558 (   12)

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

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

  3414 Ramachandran restraints generated.
    1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3414 Ramachandran restraints generated.
    1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 164
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  320 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7492 (p90)
REVERT: A  380 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8856 (tt)
REVERT: A  443 ASP cc_start: 0.7827 (m-30) cc_final: 0.6717 (t0)
REVERT: A  543 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7210 (ttp80)
REVERT: A  591 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.8000 (m-80)
REVERT: A  850 TRP cc_start: 0.8042 (t60) cc_final: 0.7814 (t60)
REVERT: A  879 PHE cc_start: 0.6503 (OUTLIER) cc_final: 0.5732 (m-80)
REVERT: A 1061 GLU cc_start: 0.8002 (tp30) cc_final: 0.7743 (tp30)
REVERT: B  264 LEU cc_start: 0.7694 (tp) cc_final: 0.7185 (mm)
REVERT: B  320 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7869 (p90)
REVERT: B  380 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8847 (tt)
REVERT: B  443 ASP cc_start: 0.7958 (m-30) cc_final: 0.6785 (t0)
REVERT: B  543 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7194 (ttp80)
REVERT: B  549 LYS cc_start: 0.7695 (mtmt) cc_final: 0.7433 (mtpt)
REVERT: B  859 MET cc_start: 0.7501 (mmt) cc_final: 0.7232 (mmm)
REVERT: B  879 PHE cc_start: 0.6533 (OUTLIER) cc_final: 0.5819 (m-80)
REVERT: B 1025 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7421 (tt)
REVERT: B 1061 GLU cc_start: 0.8083 (tp30) cc_final: 0.7853 (tp30)
  outliers start: 37
  outliers final: 24
  residues processed: 193
  average time/residue: 0.1102
  time to fit residues: 32.0075
Evaluate side-chains
  196 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 162
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  363 THR
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  543 ARG
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  591 PHE
Chi-restraints excluded: chain A residue  739 TYR
Chi-restraints excluded: chain A residue  772 GLU
Chi-restraints excluded: chain A residue  792 VAL
Chi-restraints excluded: chain A residue  879 PHE
Chi-restraints excluded: chain A residue 1073 VAL
Chi-restraints excluded: chain A residue 1080 VAL
Chi-restraints excluded: chain A residue 1081 ILE
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  221 ILE
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  363 THR
Chi-restraints excluded: chain B residue  380 LEU
Chi-restraints excluded: chain B residue  413 VAL
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  543 ARG
Chi-restraints excluded: chain B residue  591 PHE
Chi-restraints excluded: chain B residue  632 VAL
Chi-restraints excluded: chain B residue  792 VAL
Chi-restraints excluded: chain B residue  879 PHE
Chi-restraints excluded: chain B residue 1025 LEU
Chi-restraints excluded: chain B residue 1030 VAL
Chi-restraints excluded: chain B residue 1080 VAL
Chi-restraints excluded: chain B residue 1081 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 107 optimal weight:    8.9990
   chunk 15 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   chunk 119 optimal weight:    0.9990
   chunk 135 optimal weight:    5.9990
   chunk 111 optimal weight:    3.9990
   chunk 168 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0270
   chunk 143 optimal weight:    4.9990
   overall best weight:    1.3842

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.169663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.123628 restraints weight = 20450.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 2.79
r_work: 0.3291 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3300
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3300 r_free = 0.3300    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3300 r_free = 0.3300    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3300
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.2282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  13865  Z= 0.144
  Angle     :  0.573   9.801  18920  Z= 0.276
  Chirality :  0.042   0.269   2231
  Planarity :  0.004   0.049   2320
  Dihedral  :  7.517  82.638   2160
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 23.74 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.59 (0.21), residues: 1707
  helix:  2.47 (0.17), residues: 969
  sheet:  0.20 (0.42), residues: 136
  loop : -1.20 (0.23), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 317 
 TYR   0.009   0.001   TYR A 654 
 PHE   0.023   0.001   PHE B1059 
 TRP   0.008   0.001   TRP A 850 
 HIS   0.003   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (13849)
  covalent geometry    : angle       0.56301 (18878)
  SS BOND              : bond        0.00362 (    6)
  SS BOND              : angle       1.43462 (   12)
  hydrogen bonds       : bond        0.04441 (  766)
  hydrogen bonds       : angle       3.47303 ( 2201)
  link_BETA1-4         : bond        0.00457 (    6)
  link_BETA1-4         : angle       2.28429 (   18)
  link_NAG-ASN         : bond        0.00102 (    4)
  link_NAG-ASN         : angle       3.03137 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3843.02 seconds
wall clock time: 66 minutes 18.38 seconds (3978.38 seconds total)