Starting phenix.real_space_refine
on Wed Mar  4 05:48:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dtt_30853/03_2026/7dtt_30853.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dtt_30853/03_2026/7dtt_30853.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dtt_30853/03_2026/7dtt_30853.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dtt_30853/03_2026/7dtt_30853.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dtt_30853/03_2026/7dtt_30853.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dtt_30853/03_2026/7dtt_30853.cif"
  }
  resolution = 3.8
  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=   0.000 sd=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     Ca      4      9.91       5
     S      46      5.16       5
     C    7072      2.51       5
     N    1936      2.21       5
     O    2146      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 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: 11204
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5474
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 779, 5474
          Classifications: {'peptide': 779}
          Incomplete info: {'truncation_to_alanine': 213}
          Link IDs: {'PTRANS': 29, 'TRANS': 749}
          Chain breaks: 3
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 775
          Unresolved non-hydrogen angles: 997
          Unresolved non-hydrogen dihedrals: 656
          Unresolved non-hydrogen chiralities: 77
          Planarities with less than four sites: {'ASP:plan': 10, 'ASN:plan1': 8, 'GLU:plan': 18, 'PHE:plan': 31, 'HIS:plan': 2, 'ARG:plan': 5, 'TYR:plan': 6, 'TRP:plan': 2, 'GLN:plan1': 5}
          Unresolved non-hydrogen planarities: 427
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          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: "A"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 58
          Unusual residues: {' CA': 2, 'NAG': 4}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Restraints were copied for chains:
    B, E, F
  Time building chain proxies: 4.10, per 1000 atoms: 0.37
  Number of scatterers: 11204
  At special positions: 0
  Unit cell: (90.246, 94.302, 179.478, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      4     19.99
     S      46     16.00
     O    2146      8.00
     N    1936      7.00
     C    7072      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS A 101 " distance=2.07
    Simple disulfide: pdb=" SG  CYS A 236 " - pdb=" SG  CYS A 561 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 358 " - pdb=" SG  CYS A 395 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 437 " - pdb=" SG  CYS A 449 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 542 " - pdb=" SG  CYS A 562 " distance=2.25
    Simple disulfide: pdb=" SG  CYS A 546 " - pdb=" SG  CYS A 565 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 568 " - pdb=" SG  CYS A 582 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 585 " - pdb=" SG  CYS A 598 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 677 " - pdb=" SG  CYS A 765 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  60 " - pdb=" SG  CYS B 101 " distance=2.07
    Simple disulfide: pdb=" SG  CYS B 236 " - pdb=" SG  CYS B 561 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 358 " - pdb=" SG  CYS B 395 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 437 " - pdb=" SG  CYS B 449 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 542 " - pdb=" SG  CYS B 562 " distance=2.25
    Simple disulfide: pdb=" SG  CYS B 546 " - pdb=" SG  CYS B 565 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 568 " - pdb=" SG  CYS B 582 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 585 " - pdb=" SG  CYS B 598 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 677 " - pdb=" SG  CYS B 765 " 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 D   1 " - " NAG D   2 "
      " NAG D   2 " - " NAG D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " NAG F   3 "
    NAG-ASN
      " NAG A1103 " - " ASN A 261 "
      " NAG A1104 " - " ASN A 287 "
      " NAG A1105 " - " ASN A 446 "
      " NAG A1106 " - " ASN A 468 "
      " NAG B1103 " - " ASN B 261 "
      " NAG B1104 " - " ASN B 287 "
      " NAG B1105 " - " ASN B 446 "
      " NAG B1106 " - " ASN B 468 "
      " NAG C   1 " - " ASN A 488 "
      " NAG D   1 " - " ASN A 541 "
      " NAG E   1 " - " ASN B 488 "
      " NAG F   1 " - " ASN B 541 "
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 462.6 milliseconds
  

  3084 Ramachandran restraints generated.
    1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2928

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 14 sheets defined
      43.4% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 64 through 84
    Processing helix  chain 'A' and resid 103 through 115
      removed outlier: 3.583A  pdb=" N   ALA A 110 " --> pdb=" O   LYS A 106 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   SER A 113 " --> pdb=" O   GLU A 109 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   VAL A 115 " --> pdb=" O   THR A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 157
      removed outlier: 3.526A  pdb=" N   ALA A 152 " --> pdb=" O   GLY A 148 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ASN A 155 " --> pdb=" O   THR A 151 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LEU A 156 " --> pdb=" O   ALA A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 205
      removed outlier: 3.954A  pdb=" N   ILE A 201 " --> pdb=" O   MET A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 229
      removed outlier: 3.600A  pdb=" N   GLU A 224 " --> pdb=" O   ARG A 220 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LYS A 225 " --> pdb=" O   PRO A 221 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   PHE A 226 " --> pdb=" O   GLY A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 262
    Processing helix  chain 'A' and resid 272 through 287
      removed outlier: 3.692A  pdb=" N   LEU A 276 " --> pdb=" O   SER A 272 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   GLU A 277 " --> pdb=" O   GLY A 273 " (cutoff:3.500A)
      Proline residue:  A 278  - end of helix
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 329 through 336
      removed outlier: 3.634A  pdb=" N   LYS A 335 " --> pdb=" O   ARG A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 357
    Processing helix  chain 'A' and resid 415 through 436
      removed outlier: 3.523A  pdb=" N   ASN A 419 " --> pdb=" O   ARG A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 448
    Processing helix  chain 'A' and resid 456 through 466
      removed outlier: 3.536A  pdb=" N   VAL A 460 " --> pdb=" O   GLU A 456 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   HIS A 466 " --> pdb=" O   LYS A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 533
      removed outlier: 3.573A  pdb=" N   PHE A 533 " --> pdb=" O   TRP A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 637
      removed outlier: 4.055A  pdb=" N   ALA A 615 " --> pdb=" O   PRO A 611 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   LEU A 616 " --> pdb=" O   PHE A 612 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL A 630 " --> pdb=" O   LEU A 626 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 664
      removed outlier: 4.381A  pdb=" N   LEU A 658 " --> pdb=" O   LEU A 654 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   PHE A 662 " --> pdb=" O   LEU A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 669
      removed outlier: 3.895A  pdb=" N   PHE A 668 " --> pdb=" O   SER A 665 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ILE A 669 " --> pdb=" O   LEU A 666 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 665 through 669'
    Processing helix  chain 'A' and resid 673 through 679
    Processing helix  chain 'A' and resid 681 through 691
      removed outlier: 4.599A  pdb=" N   SER A 687 " --> pdb=" O   ALA A 683 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 692 through 697
    Processing helix  chain 'A' and resid 727 through 730
    Processing helix  chain 'A' and resid 731 through 746
      removed outlier: 4.027A  pdb=" N   TYR A 744 " --> pdb=" O   VAL A 740 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   THR A 745 " --> pdb=" O   ILE A 741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 770 through 792
      removed outlier: 4.512A  pdb=" N   CYS A 781 " --> pdb=" O   ILE A 777 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   LEU A 782 " --> pdb=" O   GLY A 778 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ALA A 784 " --> pdb=" O   THR A 780 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   ALA A 785 " --> pdb=" O   CYS A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 827
      removed outlier: 3.823A  pdb=" N   ILE A 822 " --> pdb=" O   TRP A 818 " (cutoff:3.500A)
      Proline residue:  A 823  - end of helix
    Processing helix  chain 'A' and resid 830 through 859
      removed outlier: 4.029A  pdb=" N   SER A 834 " --> pdb=" O   GLY A 830 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ALA A 835 " --> pdb=" O   LYS A 831 " (cutoff:3.500A)
      removed outlier: 4.866A  pdb=" N   VAL A 836 " --> pdb=" O   PHE A 832 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   GLU A 837 " --> pdb=" O   VAL A 833 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LEU A 849 " --> pdb=" O   SER A 845 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ILE A 852 " --> pdb=" O   LEU A 848 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   PHE A 854 " --> pdb=" O   ALA A 850 " (cutoff:3.500A)
      removed outlier: 5.064A  pdb=" N   ASN A 855 " --> pdb=" O   CYS A 851 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ILE A 859 " --> pdb=" O   ASN A 855 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 64 through 84
    Processing helix  chain 'B' and resid 103 through 115
      removed outlier: 3.583A  pdb=" N   ALA B 110 " --> pdb=" O   LYS B 106 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   SER B 113 " --> pdb=" O   GLU B 109 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   VAL B 115 " --> pdb=" O   THR B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 157
      removed outlier: 3.526A  pdb=" N   ALA B 152 " --> pdb=" O   GLY B 148 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ASN B 155 " --> pdb=" O   THR B 151 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LEU B 156 " --> pdb=" O   ALA B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 205
      removed outlier: 3.954A  pdb=" N   ILE B 201 " --> pdb=" O   MET B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 229
      removed outlier: 3.601A  pdb=" N   GLU B 224 " --> pdb=" O   ARG B 220 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LYS B 225 " --> pdb=" O   PRO B 221 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   PHE B 226 " --> pdb=" O   GLY B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 262
    Processing helix  chain 'B' and resid 272 through 287
      removed outlier: 3.692A  pdb=" N   LEU B 276 " --> pdb=" O   SER B 272 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   GLU B 277 " --> pdb=" O   GLY B 273 " (cutoff:3.500A)
      Proline residue:  B 278  - end of helix
    Processing helix  chain 'B' and resid 307 through 311
    Processing helix  chain 'B' and resid 329 through 336
      removed outlier: 3.634A  pdb=" N   LYS B 335 " --> pdb=" O   ARG B 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 357
    Processing helix  chain 'B' and resid 415 through 436
      removed outlier: 3.523A  pdb=" N   ASN B 419 " --> pdb=" O   ARG B 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 448
    Processing helix  chain 'B' and resid 456 through 466
      removed outlier: 3.535A  pdb=" N   VAL B 460 " --> pdb=" O   GLU B 456 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   HIS B 466 " --> pdb=" O   LYS B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 529 through 533
      removed outlier: 3.572A  pdb=" N   PHE B 533 " --> pdb=" O   TRP B 530 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 610 through 637
      removed outlier: 4.055A  pdb=" N   ALA B 615 " --> pdb=" O   PRO B 611 " (cutoff:3.500A)
      removed outlier: 4.863A  pdb=" N   LEU B 616 " --> pdb=" O   PHE B 612 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL B 630 " --> pdb=" O   LEU B 626 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 652 through 664
      removed outlier: 4.380A  pdb=" N   LEU B 658 " --> pdb=" O   LEU B 654 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   PHE B 662 " --> pdb=" O   LEU B 658 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 665 through 669
      removed outlier: 3.896A  pdb=" N   PHE B 668 " --> pdb=" O   SER B 665 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ILE B 669 " --> pdb=" O   LEU B 666 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 665 through 669'
    Processing helix  chain 'B' and resid 673 through 679
    Processing helix  chain 'B' and resid 681 through 691
      removed outlier: 4.600A  pdb=" N   SER B 687 " --> pdb=" O   ALA B 683 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 692 through 697
    Processing helix  chain 'B' and resid 727 through 730
    Processing helix  chain 'B' and resid 731 through 746
      removed outlier: 4.026A  pdb=" N   TYR B 744 " --> pdb=" O   VAL B 740 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   THR B 745 " --> pdb=" O   ILE B 741 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 770 through 792
      removed outlier: 4.513A  pdb=" N   CYS B 781 " --> pdb=" O   ILE B 777 " (cutoff:3.500A)
      removed outlier: 5.052A  pdb=" N   LEU B 782 " --> pdb=" O   GLY B 778 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ALA B 784 " --> pdb=" O   THR B 780 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   ALA B 785 " --> pdb=" O   CYS B 781 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 802 through 827
      removed outlier: 3.823A  pdb=" N   ILE B 822 " --> pdb=" O   TRP B 818 " (cutoff:3.500A)
      Proline residue:  B 823  - end of helix
    Processing helix  chain 'B' and resid 830 through 859
      removed outlier: 4.029A  pdb=" N   SER B 834 " --> pdb=" O   GLY B 830 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ALA B 835 " --> pdb=" O   LYS B 831 " (cutoff:3.500A)
      removed outlier: 4.866A  pdb=" N   VAL B 836 " --> pdb=" O   PHE B 832 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   GLU B 837 " --> pdb=" O   VAL B 833 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LEU B 849 " --> pdb=" O   SER B 845 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ILE B 852 " --> pdb=" O   LEU B 848 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   PHE B 854 " --> pdb=" O   ALA B 850 " (cutoff:3.500A)
      removed outlier: 5.064A  pdb=" N   ASN B 855 " --> pdb=" O   CYS B 851 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ILE B 859 " --> pdb=" O   ASN B 855 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28
      removed outlier: 6.303A  pdb=" N   ILE A  32 " --> pdb=" O   GLY A  94 " (cutoff:3.500A)
      removed outlier: 7.811A  pdb=" N   ARG A  96 " --> pdb=" O   ILE A  32 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 166
      removed outlier: 5.932A  pdb=" N   GLN A 164 " --> pdb=" O   LEU A 184 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 243
      removed outlier: 7.759A  pdb=" N   VAL A 209 " --> pdb=" O   ASP A 238 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   SER A 240 " --> pdb=" O   VAL A 209 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   THR A 211 " --> pdb=" O   SER A 240 " (cutoff:3.500A)
      removed outlier: 5.958A  pdb=" N   LEU A 242 " --> pdb=" O   THR A 211 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   ALA A 213 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   TRP A 208 " --> pdb=" O   VAL A 266 " (cutoff:3.500A)
      removed outlier: 8.372A  pdb=" N   VAL A 268 " --> pdb=" O   TRP A 208 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   GLY A 210 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   PHE A 270 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   ILE A 212 " --> pdb=" O   PHE A 270 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   ILE A 267 " --> pdb=" O   LEU A 294 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 469 through 470
    Processing sheet with id=AA5, first strand: chain 'A' and resid 492 through 495
    Processing sheet with id=AA6, first strand: chain 'A' and resid 509 through 511
      removed outlier: 3.841A  pdb=" N   PHE A 522 " --> pdb=" O   TYR A 510 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 589 through 590
      removed outlier: 3.977A  pdb=" N   ALA A 600 " --> pdb=" O   TRP A 590 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 28
      removed outlier: 6.302A  pdb=" N   ILE B  32 " --> pdb=" O   GLY B  94 " (cutoff:3.500A)
      removed outlier: 7.811A  pdb=" N   ARG B  96 " --> pdb=" O   ILE B  32 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 164 through 166
      removed outlier: 5.932A  pdb=" N   GLN B 164 " --> pdb=" O   LEU B 184 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 236 through 243
      removed outlier: 7.759A  pdb=" N   VAL B 209 " --> pdb=" O   ASP B 238 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   SER B 240 " --> pdb=" O   VAL B 209 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   THR B 211 " --> pdb=" O   SER B 240 " (cutoff:3.500A)
      removed outlier: 5.957A  pdb=" N   LEU B 242 " --> pdb=" O   THR B 211 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   ALA B 213 " --> pdb=" O   LEU B 242 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   TRP B 208 " --> pdb=" O   VAL B 266 " (cutoff:3.500A)
      removed outlier: 8.371A  pdb=" N   VAL B 268 " --> pdb=" O   TRP B 208 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   GLY B 210 " --> pdb=" O   VAL B 268 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   PHE B 270 " --> pdb=" O   GLY B 210 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ILE B 212 " --> pdb=" O   PHE B 270 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   ILE B 267 " --> pdb=" O   LEU B 294 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 469 through 470
    Processing sheet with id=AB3, first strand: chain 'B' and resid 492 through 495
    Processing sheet with id=AB4, first strand: chain 'B' and resid 509 through 511
      removed outlier: 3.841A  pdb=" N   PHE B 522 " --> pdb=" O   TYR B 510 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 589 through 590
      removed outlier: 3.977A  pdb=" N   ALA B 600 " --> pdb=" O   TRP B 590 " (cutoff:3.500A)

    416 hydrogen bonds defined for protein.
    1194 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.87

  Time building geometry restraints manager: 1.05 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: 3687
        1.34 -     1.46: 2750
        1.46 -     1.58: 4931
        1.58 -     1.71: 0
        1.71 -     1.83: 54
  Bond restraints: 11422
  Sorted by residual:
  bond pdb=" CA  PHE B 270 "
       pdb=" CB  PHE B 270 "
    ideal  model  delta    sigma   weight residual
    1.528  1.445  0.084 2.61e-02 1.47e+03 1.03e+01
  bond pdb=" CA  PHE A 270 "
       pdb=" CB  PHE A 270 "
    ideal  model  delta    sigma   weight residual
    1.528  1.445  0.083 2.61e-02 1.47e+03 1.02e+01
  bond pdb=" CA  ASP B 217 "
       pdb=" C   ASP B 217 "
    ideal  model  delta    sigma   weight residual
    1.523  1.475  0.048 1.80e-02 3.09e+03 7.11e+00
  bond pdb=" CA  ASP A 217 "
       pdb=" C   ASP A 217 "
    ideal  model  delta    sigma   weight residual
    1.523  1.476  0.048 1.80e-02 3.09e+03 7.04e+00
  bond pdb=" C1  NAG A1105 "
       pdb=" O5  NAG A1105 "
    ideal  model  delta    sigma   weight residual
    1.406  1.459 -0.053 2.00e-02 2.50e+03 7.03e+00
  ... (remaining 11417 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 14459
        1.79 -     3.58: 964
        3.58 -     5.37: 120
        5.37 -     7.17: 35
        7.17 -     8.96: 12
  Bond angle restraints: 15590
  Sorted by residual:
  angle pdb=" N   THR A 145 "
        pdb=" CA  THR A 145 "
        pdb=" C   THR A 145 "
      ideal   model   delta    sigma   weight residual
     111.33  116.10   -4.77 1.21e+00 6.83e-01 1.56e+01
  angle pdb=" N   THR B 145 "
        pdb=" CA  THR B 145 "
        pdb=" C   THR B 145 "
      ideal   model   delta    sigma   weight residual
     111.33  116.10   -4.77 1.21e+00 6.83e-01 1.55e+01
  angle pdb=" N   CYS A  60 "
        pdb=" CA  CYS A  60 "
        pdb=" C   CYS A  60 "
      ideal   model   delta    sigma   weight residual
     110.53  105.54    4.99 1.29e+00 6.01e-01 1.50e+01
  angle pdb=" N   CYS B  60 "
        pdb=" CA  CYS B  60 "
        pdb=" C   CYS B  60 "
      ideal   model   delta    sigma   weight residual
     110.53  105.54    4.99 1.29e+00 6.01e-01 1.49e+01
  angle pdb=" N   GLY A 830 "
        pdb=" CA  GLY A 830 "
        pdb=" C   GLY A 830 "
      ideal   model   delta    sigma   weight residual
     110.77  118.06   -7.29 1.93e+00 2.68e-01 1.43e+01
  ... (remaining 15585 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.10: 6302
       18.10 -    36.20: 544
       36.20 -    54.30: 92
       54.30 -    72.40: 36
       72.40 -    90.50: 12
  Dihedral angle restraints: 6986
    sinusoidal: 2466
      harmonic: 4520
  Sorted by residual:
  dihedral pdb=" CB  CYS A 236 "
           pdb=" SG  CYS A 236 "
           pdb=" SG  CYS A 561 "
           pdb=" CB  CYS A 561 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -176.50   90.50     1      1.00e+01 1.00e-02 9.68e+01
  dihedral pdb=" CB  CYS B 236 "
           pdb=" SG  CYS B 236 "
           pdb=" SG  CYS B 561 "
           pdb=" CB  CYS B 561 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -176.51  -90.49     1      1.00e+01 1.00e-02 9.68e+01
  dihedral pdb=" CB  CYS A 677 "
           pdb=" SG  CYS A 677 "
           pdb=" SG  CYS A 765 "
           pdb=" CB  CYS A 765 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -169.73   83.73     1      1.00e+01 1.00e-02 8.55e+01
  ... (remaining 6983 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.232: 1834
       0.232 -    0.464: 8
       0.464 -    0.696: 0
       0.696 -    0.928: 0
       0.928 -    1.159: 2
  Chirality restraints: 1844
  Sorted by residual:
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 488 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.24   -1.16 2.00e-01 2.50e+01 3.36e+01
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN B 488 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.24   -1.16 2.00e-01 2.50e+01 3.35e+01
  chirality pdb=" C1  NAG B1105 "
            pdb=" ND2 ASN B 446 "
            pdb=" C2  NAG B1105 "
            pdb=" O5  NAG B1105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.11e+00
  ... (remaining 1841 not shown)

  Planarity restraints: 2042
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 187 "   -0.036 5.00e-02 4.00e+02   5.52e-02 4.88e+00
        pdb=" N   PRO B 188 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO B 188 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 188 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 187 "    0.036 5.00e-02 4.00e+02   5.50e-02 4.84e+00
        pdb=" N   PRO A 188 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 188 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 188 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 135 "    0.011 2.00e-02 2.50e+03   2.14e-02 4.60e+00
        pdb=" C   ILE B 135 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   ILE B 135 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PRO B 136 "    0.013 2.00e-02 2.50e+03
  ... (remaining 2039 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 2373
        2.76 -     3.30: 10268
        3.30 -     3.83: 18312
        3.83 -     4.37: 20223
        4.37 -     4.90: 35429
  Nonbonded interactions: 86605
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 144 "
            pdb=" OG  SER A 150 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   ALA B 144 "
            pdb=" OG  SER B 150 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   SER B 540 "
            pdb=" OG  SER B 540 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   SER A 540 "
            pdb=" OG  SER A 540 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OG1 THR B 396 "
            pdb=" OD1 ASP B 398 "
     model   vdw
     2.268 3.040
  ... (remaining 86600 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
}

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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.590
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
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      :  0.011   0.224  11458  Z= 0.508
  Angle     :  1.171  39.818  15680  Z= 0.628
  Chirality :  0.072   1.159   1844
  Planarity :  0.006   0.055   2030
  Dihedral  : 14.406  86.830   4004
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.73 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.21 %
    Favored  : 88.79 %
  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: -4.29 (0.17), residues: 1542
  helix: -2.71 (0.14), residues: 612
  sheet: -2.59 (0.46), residues: 108
  loop : -3.05 (0.18), residues: 822

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 172 
 TYR   0.028   0.003   TYR B 421 
 PHE   0.018   0.002   PHE B 539 
 TRP   0.011   0.002   TRP A 208 
 HIS   0.005   0.002   HIS B 595 

Details of bonding type rmsd
  covalent geometry    : bond        0.01062 (11422)
  covalent geometry    : angle       1.00093 (15590)
  SS BOND              : bond        0.07586 (   18)
  SS BOND              : angle      10.56164 (   36)
  hydrogen bonds       : bond        0.14244 (  416)
  hydrogen bonds       : angle       5.97561 ( 1194)
  link_BETA1-4         : bond        0.01096 (    6)
  link_BETA1-4         : angle       2.25214 (   18)
  link_NAG-ASN         : bond        0.01027 (   12)
  link_NAG-ASN         : angle       7.03886 (   36)

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

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

  3084 Ramachandran restraints generated.
    1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3084 Ramachandran restraints generated.
    1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.418 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.1009
  time to fit residues: 4.7583
Evaluate side-chains
  18 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:    0.0000
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    0.0970
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    0.0970
   chunk 149 optimal weight:   30.0000
   overall best weight:    0.3982

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

Flipped N/Q/H residues before XYZ refinement:
A 117 GLN
A 193 GLN
A 253 GLN
A 338 HIS
A 344 HIS
A 413 HIS
A 466 HIS
A 476 GLN
A 524 ASN
A 595 HIS
B 117 GLN
B 193 GLN
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 344 HIS
B 413 HIS
B 466 HIS
B 476 GLN
B 524 ASN
B 595 HIS

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.080551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.056070 restraints weight = 39664.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.057575 restraints weight = 24038.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.058493 restraints weight = 18044.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.059110 restraints weight = 15241.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.059307 restraints weight = 13802.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.1181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  11458  Z= 0.107
  Angle     :  0.629  16.001  15680  Z= 0.318
  Chirality :  0.050   0.707   1844
  Planarity :  0.004   0.051   2030
  Dihedral  :  7.700  56.673   2018
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.38 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 11.64 %
    Favored  : 86.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.88 (0.19), residues: 1542
  helix: -1.10 (0.19), residues: 604
  sheet: -2.22 (0.47), residues: 116
  loop : -2.56 (0.19), residues: 822

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 286 
 TYR   0.020   0.001   TYR B 421 
 PHE   0.011   0.001   PHE B 333 
 TRP   0.008   0.001   TRP B 352 
 HIS   0.002   0.001   HIS A 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 (11422)
  covalent geometry    : angle       0.56826 (15590)
  SS BOND              : bond        0.00284 (   18)
  SS BOND              : angle       2.01251 (   36)
  hydrogen bonds       : bond        0.03801 (  416)
  hydrogen bonds       : angle       4.25126 ( 1194)
  link_BETA1-4         : bond        0.00380 (    6)
  link_BETA1-4         : angle       1.56301 (   18)
  link_NAG-ASN         : bond        0.00787 (   12)
  link_NAG-ASN         : angle       5.21701 (   36)

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

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

  3084 Ramachandran restraints generated.
    1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3084 Ramachandran restraints generated.
    1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 26
  time to evaluate  : 0.405 
Fit side-chains
REVERT: A  818 TRP cc_start: 0.6708 (OUTLIER) cc_final: 0.6149 (m-90)
REVERT: B  818 TRP cc_start: 0.6886 (OUTLIER) cc_final: 0.5856 (m-90)
  outliers start: 19
  outliers final: 9
  residues processed: 43
  average time/residue: 0.0641
  time to fit residues: 5.1356
Evaluate side-chains
  29 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 18
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  818 TRP
Chi-restraints excluded: chain B residue   79 GLU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  486 VAL
Chi-restraints excluded: chain B residue  818 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 53 optimal weight:   40.0000
   chunk 112 optimal weight:    9.9990
   chunk 95 optimal weight:    1.9990
   chunk 137 optimal weight:   30.0000
   chunk 86 optimal weight:    0.8980
   chunk 89 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 111 optimal weight:   10.0000
   chunk 99 optimal weight:    0.0870
   chunk 97 optimal weight:    0.5980
   overall best weight:    0.8960

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

Flipped N/Q/H residues before XYZ refinement:
A  27 GLN
B  27 GLN
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.080483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.055805 restraints weight = 39701.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.057288 restraints weight = 24272.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.058248 restraints weight = 18237.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.058822 restraints weight = 15410.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.059122 restraints weight = 13972.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11458  Z= 0.116
  Angle     :  0.572  15.020  15680  Z= 0.287
  Chirality :  0.048   0.641   1844
  Planarity :  0.003   0.044   2030
  Dihedral  :  6.767  55.346   2018
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 13.58 %
    Favored  : 84.91 %
  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: -2.05 (0.20), residues: 1542
  helix: -0.23 (0.20), residues: 624
  sheet: -1.80 (0.48), residues: 118
  loop : -2.29 (0.20), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 286 
 TYR   0.015   0.001   TYR A 421 
 PHE   0.010   0.001   PHE B 333 
 TRP   0.009   0.001   TRP A 352 
 HIS   0.002   0.001   HIS B 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (11422)
  covalent geometry    : angle       0.51486 (15590)
  SS BOND              : bond        0.00898 (   18)
  SS BOND              : angle       1.59130 (   36)
  hydrogen bonds       : bond        0.03407 (  416)
  hydrogen bonds       : angle       3.76856 ( 1194)
  link_BETA1-4         : bond        0.00362 (    6)
  link_BETA1-4         : angle       1.65893 (   18)
  link_NAG-ASN         : bond        0.00721 (   12)
  link_NAG-ASN         : angle       4.86837 (   36)

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

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

  3084 Ramachandran restraints generated.
    1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3084 Ramachandran restraints generated.
    1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 20
  time to evaluate  : 0.402 
Fit side-chains
REVERT: A  818 TRP cc_start: 0.6726 (OUTLIER) cc_final: 0.6170 (m-90)
REVERT: B  818 TRP cc_start: 0.6981 (OUTLIER) cc_final: 0.5990 (m-90)
  outliers start: 14
  outliers final: 6
  residues processed: 32
  average time/residue: 0.0646
  time to fit residues: 3.9843
Evaluate side-chains
  27 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 19
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  818 TRP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  425 TYR
Chi-restraints excluded: chain B residue  818 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 50 optimal weight:    9.9990
   chunk 140 optimal weight:   40.0000
   chunk 28 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 142 optimal weight:    0.9990
   chunk 71 optimal weight:   40.0000
   chunk 149 optimal weight:    6.9990
   chunk 120 optimal weight:    5.9990
   chunk 17 optimal weight:    0.5980
   chunk 148 optimal weight:   30.0000
   chunk 13 optimal weight:    3.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
B 253 GLN
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.079109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.054297 restraints weight = 40112.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.055641 restraints weight = 24664.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.056553 restraints weight = 18862.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.057117 restraints weight = 15998.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 15)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.057233 restraints weight = 14502.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  11458  Z= 0.221
  Angle     :  0.618  15.976  15680  Z= 0.312
  Chirality :  0.050   0.673   1844
  Planarity :  0.003   0.041   2030
  Dihedral  :  6.518  59.351   2018
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 15.30 %
    Favored  : 82.33 %
  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: -1.74 (0.21), residues: 1542
  helix:  0.26 (0.21), residues: 616
  sheet: -2.11 (0.42), residues: 136
  loop : -2.20 (0.20), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 185 
 TYR   0.024   0.001   TYR B 435 
 PHE   0.009   0.001   PHE B 539 
 TRP   0.006   0.001   TRP B 458 
 HIS   0.004   0.001   HIS B 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 (11422)
  covalent geometry    : angle       0.56025 (15590)
  SS BOND              : bond        0.00441 (   18)
  SS BOND              : angle       1.82528 (   36)
  hydrogen bonds       : bond        0.03705 (  416)
  hydrogen bonds       : angle       3.83562 ( 1194)
  link_BETA1-4         : bond        0.00342 (    6)
  link_BETA1-4         : angle       1.53556 (   18)
  link_NAG-ASN         : bond        0.00651 (   12)
  link_NAG-ASN         : angle       5.10669 (   36)

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

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

  3084 Ramachandran restraints generated.
    1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3084 Ramachandran restraints generated.
    1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 20
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A  818 TRP cc_start: 0.6919 (OUTLIER) cc_final: 0.6495 (m-90)
REVERT: B  818 TRP cc_start: 0.7066 (OUTLIER) cc_final: 0.6196 (m-90)
  outliers start: 22
  outliers final: 13
  residues processed: 40
  average time/residue: 0.0596
  time to fit residues: 4.4513
Evaluate side-chains
  35 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 20
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  425 TYR
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  818 TRP
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  425 TYR
Chi-restraints excluded: chain B residue  818 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 110 optimal weight:    4.9990
   chunk 72 optimal weight:   20.0000
   chunk 5 optimal weight:    0.8980
   chunk 88 optimal weight:    0.0770
   chunk 10 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9980
   chunk 141 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 76 optimal weight:    5.9990
   chunk 32 optimal weight:    7.9990
   overall best weight:    0.7938

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

Flipped N/Q/H residues before XYZ refinement:
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.080816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.056123 restraints weight = 39729.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.057634 restraints weight = 24143.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.058557 restraints weight = 18085.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.059140 restraints weight = 15387.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.059371 restraints weight = 13941.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  11458  Z= 0.099
  Angle     :  0.544  14.543  15680  Z= 0.272
  Chirality :  0.047   0.634   1844
  Planarity :  0.003   0.042   2030
  Dihedral  :  5.893  55.701   2018
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 15.73 %
    Favored  : 81.25 %
  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: -1.31 (0.21), residues: 1542
  helix:  0.62 (0.21), residues: 618
  sheet: -1.67 (0.49), residues: 118
  loop : -2.01 (0.21), residues: 806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 185 
 TYR   0.030   0.001   TYR A 435 
 PHE   0.011   0.001   PHE B 469 
 TRP   0.007   0.001   TRP B 352 
 HIS   0.002   0.000   HIS B 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 (11422)
  covalent geometry    : angle       0.48701 (15590)
  SS BOND              : bond        0.00213 (   18)
  SS BOND              : angle       1.56532 (   36)
  hydrogen bonds       : bond        0.03081 (  416)
  hydrogen bonds       : angle       3.58844 ( 1194)
  link_BETA1-4         : bond        0.00351 (    6)
  link_BETA1-4         : angle       1.51666 (   18)
  link_NAG-ASN         : bond        0.00752 (   12)
  link_NAG-ASN         : angle       4.73532 (   36)

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

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

  3084 Ramachandran restraints generated.
    1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3084 Ramachandran restraints generated.
    1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 19
  time to evaluate  : 0.377 
Fit side-chains
REVERT: A  818 TRP cc_start: 0.6894 (OUTLIER) cc_final: 0.6495 (m-90)
REVERT: B  818 TRP cc_start: 0.7028 (OUTLIER) cc_final: 0.6133 (m-90)
  outliers start: 28
  outliers final: 15
  residues processed: 45
  average time/residue: 0.0599
  time to fit residues: 5.0773
Evaluate side-chains
  36 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 19
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  425 TYR
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  818 TRP
Chi-restraints excluded: chain B residue   79 GLU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  404 VAL
Chi-restraints excluded: chain B residue  425 TYR
Chi-restraints excluded: chain B residue  818 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 98 optimal weight:    0.0970
   chunk 79 optimal weight:    1.9990
   chunk 68 optimal weight:   30.0000
   chunk 19 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 62 optimal weight:   30.0000
   chunk 149 optimal weight:   20.0000
   chunk 35 optimal weight:    6.9990
   chunk 109 optimal weight:    7.9990
   chunk 106 optimal weight:    0.6980
   chunk 134 optimal weight:   40.0000
   overall best weight:    2.1584

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

Flipped N/Q/H residues before XYZ refinement:
** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.079468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.054794 restraints weight = 40277.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.056161 restraints weight = 24458.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.057089 restraints weight = 18610.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.057614 restraints weight = 15743.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.057980 restraints weight = 14326.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11458  Z= 0.193
  Angle     :  0.601  15.349  15680  Z= 0.301
  Chirality :  0.049   0.652   1844
  Planarity :  0.003   0.037   2030
  Dihedral  :  5.853  58.802   2018
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.87 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.92 %
    Favored  : 80.50 %
  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: -1.14 (0.21), residues: 1542
  helix:  0.82 (0.22), residues: 618
  sheet: -1.96 (0.48), residues: 118
  loop : -1.90 (0.21), residues: 806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 185 
 TYR   0.020   0.001   TYR B 435 
 PHE   0.010   0.001   PHE B 469 
 TRP   0.013   0.001   TRP B 675 
 HIS   0.003   0.001   HIS B 463 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 (11422)
  covalent geometry    : angle       0.54254 (15590)
  SS BOND              : bond        0.00341 (   18)
  SS BOND              : angle       2.05023 (   36)
  hydrogen bonds       : bond        0.03397 (  416)
  hydrogen bonds       : angle       3.62370 ( 1194)
  link_BETA1-4         : bond        0.00293 (    6)
  link_BETA1-4         : angle       1.53402 (   18)
  link_NAG-ASN         : bond        0.00674 (   12)
  link_NAG-ASN         : angle       4.93529 (   36)

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

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

  3084 Ramachandran restraints generated.
    1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3084 Ramachandran restraints generated.
    1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 21
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A  818 TRP cc_start: 0.7052 (OUTLIER) cc_final: 0.6696 (m-90)
REVERT: B  818 TRP cc_start: 0.7203 (OUTLIER) cc_final: 0.6514 (m-90)
  outliers start: 24
  outliers final: 14
  residues processed: 43
  average time/residue: 0.0858
  time to fit residues: 5.9049
Evaluate side-chains
  36 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 20
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  425 TYR
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  818 TRP
Chi-restraints excluded: chain B residue   79 GLU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  404 VAL
Chi-restraints excluded: chain B residue  425 TYR
Chi-restraints excluded: chain B residue  818 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 128 optimal weight:    6.9990
   chunk 11 optimal weight:    5.9990
   chunk 60 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 34 optimal weight:    8.9990
   chunk 140 optimal weight:   40.0000
   chunk 40 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 112 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.078192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.053527 restraints weight = 40437.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.054906 restraints weight = 24760.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.055751 restraints weight = 18733.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.056074 restraints weight = 16008.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.056533 restraints weight = 14858.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  11458  Z= 0.278
  Angle     :  0.672  16.466  15680  Z= 0.338
  Chirality :  0.051   0.697   1844
  Planarity :  0.004   0.037   2030
  Dihedral  :  6.141  58.315   2018
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.30 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 18.53 %
    Favored  : 79.53 %
  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: -1.16 (0.21), residues: 1542
  helix:  0.85 (0.22), residues: 614
  sheet: -2.20 (0.43), residues: 136
  loop : -1.88 (0.21), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 285 
 TYR   0.024   0.002   TYR A 435 
 PHE   0.012   0.001   PHE A 469 
 TRP   0.010   0.001   TRP A 675 
 HIS   0.005   0.001   HIS A 463 

Details of bonding type rmsd
  covalent geometry    : bond        0.00635 (11422)
  covalent geometry    : angle       0.61329 (15590)
  SS BOND              : bond        0.00467 (   18)
  SS BOND              : angle       2.29983 (   36)
  hydrogen bonds       : bond        0.03870 (  416)
  hydrogen bonds       : angle       3.84492 ( 1194)
  link_BETA1-4         : bond        0.00426 (    6)
  link_BETA1-4         : angle       1.57085 (   18)
  link_NAG-ASN         : bond        0.00645 (   12)
  link_NAG-ASN         : angle       5.21920 (   36)

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

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

  3084 Ramachandran restraints generated.
    1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3084 Ramachandran restraints generated.
    1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 20
  time to evaluate  : 0.338 
Fit side-chains
  outliers start: 18
  outliers final: 15
  residues processed: 38
  average time/residue: 0.0656
  time to fit residues: 4.5650
Evaluate side-chains
  35 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 20
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  425 TYR
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain B residue   79 GLU
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  404 VAL
Chi-restraints excluded: chain B residue  425 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 74 optimal weight:    9.9990
   chunk 9 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 102 optimal weight:    2.9990
   chunk 140 optimal weight:   40.0000
   chunk 143 optimal weight:   20.0000
   chunk 103 optimal weight:    2.9990
   chunk 126 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 108 optimal weight:    0.7980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.079401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.054552 restraints weight = 40338.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.056006 restraints weight = 24736.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.056922 restraints weight = 18615.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.057330 restraints weight = 15801.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.057792 restraints weight = 14508.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11458  Z= 0.164
  Angle     :  0.586  15.423  15680  Z= 0.294
  Chirality :  0.048   0.657   1844
  Planarity :  0.003   0.040   2030
  Dihedral  :  5.891  59.633   2018
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 18.75 %
    Favored  : 79.42 %
  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: -0.95 (0.22), residues: 1542
  helix:  1.03 (0.22), residues: 614
  sheet: -2.09 (0.43), residues: 136
  loop : -1.77 (0.22), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 285 
 TYR   0.020   0.001   TYR A 435 
 PHE   0.012   0.001   PHE B 469 
 TRP   0.005   0.001   TRP B 352 
 HIS   0.002   0.001   HIS B 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (11422)
  covalent geometry    : angle       0.52864 (15590)
  SS BOND              : bond        0.00314 (   18)
  SS BOND              : angle       1.77877 (   36)
  hydrogen bonds       : bond        0.03368 (  416)
  hydrogen bonds       : angle       3.64978 ( 1194)
  link_BETA1-4         : bond        0.00274 (    6)
  link_BETA1-4         : angle       1.41940 (   18)
  link_NAG-ASN         : bond        0.00694 (   12)
  link_NAG-ASN         : angle       4.94050 (   36)

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

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

  3084 Ramachandran restraints generated.
    1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3084 Ramachandran restraints generated.
    1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 20
  time to evaluate  : 0.414 
Fit side-chains
  outliers start: 17
  outliers final: 13
  residues processed: 37
  average time/residue: 0.0595
  time to fit residues: 4.0804
Evaluate side-chains
  33 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 20
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  425 TYR
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  404 VAL
Chi-restraints excluded: chain B residue  425 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 75 optimal weight:   10.0000
   chunk 132 optimal weight:    7.9990
   chunk 112 optimal weight:    9.9990
   chunk 76 optimal weight:    5.9990
   chunk 85 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 57 optimal weight:   30.0000
   chunk 50 optimal weight:    5.9990
   chunk 105 optimal weight:    0.6980
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.078937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.054167 restraints weight = 39977.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.055551 restraints weight = 25044.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.056418 restraints weight = 19049.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.056937 restraints weight = 16327.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.057225 restraints weight = 14914.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  11458  Z= 0.204
  Angle     :  0.611  15.676  15680  Z= 0.306
  Chirality :  0.049   0.662   1844
  Planarity :  0.003   0.038   2030
  Dihedral  :  5.914  59.818   2018
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 18.75 %
    Favored  : 79.53 %
  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 (0.22), residues: 1542
  helix:  1.06 (0.22), residues: 614
  sheet: -2.12 (0.43), residues: 136
  loop : -1.76 (0.22), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 285 
 TYR   0.020   0.001   TYR A 435 
 PHE   0.011   0.001   PHE A 469 
 TRP   0.005   0.001   TRP A 458 
 HIS   0.003   0.001   HIS B 463 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 (11422)
  covalent geometry    : angle       0.55314 (15590)
  SS BOND              : bond        0.00322 (   18)
  SS BOND              : angle       2.05682 (   36)
  hydrogen bonds       : bond        0.03483 (  416)
  hydrogen bonds       : angle       3.68801 ( 1194)
  link_BETA1-4         : bond        0.00278 (    6)
  link_BETA1-4         : angle       1.50096 (   18)
  link_NAG-ASN         : bond        0.00660 (   12)
  link_NAG-ASN         : angle       4.99726 (   36)

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

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

  3084 Ramachandran restraints generated.
    1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3084 Ramachandran restraints generated.
    1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 20
  time to evaluate  : 0.410 
Fit side-chains
  outliers start: 16
  outliers final: 14
  residues processed: 36
  average time/residue: 0.0639
  time to fit residues: 4.3590
Evaluate side-chains
  34 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 20
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  425 TYR
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  404 VAL
Chi-restraints excluded: chain B residue  425 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9990
   chunk 151 optimal weight:    8.9990
   chunk 14 optimal weight:    2.9990
   chunk 142 optimal weight:    5.9990
   chunk 137 optimal weight:    6.9990
   chunk 74 optimal weight:    9.9990
   chunk 108 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 63 optimal weight:   20.0000
   chunk 114 optimal weight:    0.6980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.079851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.057940 restraints weight = 39987.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.058091 restraints weight = 31978.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.058471 restraints weight = 24317.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.058971 restraints weight = 20692.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.059024 restraints weight = 18787.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.2529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  11458  Z= 0.108
  Angle     :  0.549  14.481  15680  Z= 0.274
  Chirality :  0.047   0.619   1844
  Planarity :  0.003   0.042   2030
  Dihedral  :  5.590  56.663   2018
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 19.29 %
    Favored  : 79.53 %
  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: -0.68 (0.22), residues: 1542
  helix:  1.28 (0.22), residues: 612
  sheet: -1.68 (0.50), residues: 114
  loop : -1.70 (0.21), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 285 
 TYR   0.018   0.001   TYR A 435 
 PHE   0.012   0.001   PHE B 469 
 TRP   0.008   0.001   TRP B 352 
 HIS   0.002   0.000   HIS B 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (11422)
  covalent geometry    : angle       0.49236 (15590)
  SS BOND              : bond        0.00234 (   18)
  SS BOND              : angle       1.68477 (   36)
  hydrogen bonds       : bond        0.03030 (  416)
  hydrogen bonds       : angle       3.48891 ( 1194)
  link_BETA1-4         : bond        0.00383 (    6)
  link_BETA1-4         : angle       1.49501 (   18)
  link_NAG-ASN         : bond        0.00737 (   12)
  link_NAG-ASN         : angle       4.71399 (   36)

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

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

  3084 Ramachandran restraints generated.
    1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3084 Ramachandran restraints generated.
    1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 22
  time to evaluate  : 0.396 
Fit side-chains
  outliers start: 11
  outliers final: 11
  residues processed: 33
  average time/residue: 0.0595
  time to fit residues: 3.7901
Evaluate side-chains
  31 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 20
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  425 TYR
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  404 VAL
Chi-restraints excluded: chain B residue  425 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 83 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9980
   chunk 107 optimal weight:    4.9990
   chunk 150 optimal weight:    5.9990
   chunk 60 optimal weight:    8.9990
   chunk 108 optimal weight:    3.9990
   chunk 147 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0470
   chunk 17 optimal weight:    0.9980
   overall best weight:    1.3680

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

Flipped N/Q/H residues before XYZ refinement:
** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.079400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.055019 restraints weight = 40134.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.056472 restraints weight = 24298.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.057377 restraints weight = 18283.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.057787 restraints weight = 15481.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.058247 restraints weight = 14188.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11458  Z= 0.137
  Angle     :  0.556  14.668  15680  Z= 0.277
  Chirality :  0.048   0.624   1844
  Planarity :  0.003   0.040   2030
  Dihedral  :  5.531  57.435   2018
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 18.97 %
    Favored  : 79.74 %
  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: -0.61 (0.22), residues: 1542
  helix:  1.34 (0.22), residues: 612
  sheet: -1.83 (0.49), residues: 116
  loop : -1.62 (0.22), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 285 
 TYR   0.022   0.001   TYR A 435 
 PHE   0.011   0.001   PHE B 469 
 TRP   0.008   0.001   TRP A 208 
 HIS   0.002   0.001   HIS B 463 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (11422)
  covalent geometry    : angle       0.49944 (15590)
  SS BOND              : bond        0.00298 (   18)
  SS BOND              : angle       1.73963 (   36)
  hydrogen bonds       : bond        0.03082 (  416)
  hydrogen bonds       : angle       3.48805 ( 1194)
  link_BETA1-4         : bond        0.00282 (    6)
  link_BETA1-4         : angle       1.54208 (   18)
  link_NAG-ASN         : bond        0.00706 (   12)
  link_NAG-ASN         : angle       4.74217 (   36)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1548.92 seconds
wall clock time: 27 minutes 31.49 seconds (1651.49 seconds total)