Starting phenix.real_space_refine
on Wed Mar  4 02:51:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wih_32530/03_2026/7wih_32530.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wih_32530/03_2026/7wih_32530.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wih_32530/03_2026/7wih_32530.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wih_32530/03_2026/7wih_32530.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wih_32530/03_2026/7wih_32530.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wih_32530/03_2026/7wih_32530.cif"
  }
  resolution = 3.68
  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=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 104 atoms to isotropic.
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: 4
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    6320      2.51       5
     N    1740      2.21       5
     O    1876      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 10002
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4963
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 741, 4963
          Classifications: {'peptide': 741}
          Incomplete info: {'truncation_to_alanine': 235}
          Link IDs: {'PTRANS': 28, 'TRANS': 712}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 953
          Unresolved non-hydrogen angles: 1211
          Unresolved non-hydrogen dihedrals: 815
          Unresolved non-hydrogen chiralities: 67
          Planarities with less than four sites: {'GLU:plan': 27, 'ASP:plan': 14, 'ARG:plan': 21, 'GLN:plan1': 10, 'TYR:plan': 15, 'HIS:plan': 4, 'ASN:plan1': 9, 'PHE:plan': 16, 'TRP:plan': 5}
          Unresolved non-hydrogen planarities: 588
    Chain: "A"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 38
          Unusual residues: {'CWY': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 3.62, per 1000 atoms: 0.36
  Number of scatterers: 10002
  At special positions: 0
  Unit cell: (104.442, 84.162, 179.478, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      66     16.00
     O    1876      8.00
     N    1740      7.00
     C    6320      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=16, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 240 " - pdb=" SG  CYS A 527 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 361 " - pdb=" SG  CYS A 373 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 412 " - pdb=" SG  CYS A 419 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 509 " - pdb=" SG  CYS A 528 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 513 " - pdb=" SG  CYS A 531 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 534 " - pdb=" SG  CYS A 546 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 549 " - pdb=" SG  CYS A 562 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 641 " - pdb=" SG  CYS A 730 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 240 " - pdb=" SG  CYS B 527 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 361 " - pdb=" SG  CYS B 373 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 412 " - pdb=" SG  CYS B 419 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 509 " - pdb=" SG  CYS B 528 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 513 " - pdb=" SG  CYS B 531 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 534 " - pdb=" SG  CYS B 546 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 549 " - pdb=" SG  CYS B 562 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 641 " - pdb=" SG  CYS B 730 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 901 " - " ASN A 209 "
      " NAG B 901 " - " ASN B 209 "
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 510.6 milliseconds
  

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2800

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 14 sheets defined
      34.8% alpha, 6.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 78
      removed outlier: 4.559A  pdb=" N   ALA A  71 " --> pdb=" O   GLN A  67 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   PHE A  74 " --> pdb=" O   GLU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 114
      removed outlier: 3.508A  pdb=" N   ALA A 105 " --> pdb=" O   ARG A 101 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU A 106 " --> pdb=" O   ASP A 102 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   GLU A 107 " --> pdb=" O   THR A 103 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU A 110 " --> pdb=" O   LEU A 106 " (cutoff:3.500A)
      removed outlier: 4.845A  pdb=" N   GLU A 111 " --> pdb=" O   GLU A 107 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   PHE A 112 " --> pdb=" O   GLN A 108 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   VAL A 113 " --> pdb=" O   SER A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 156
      removed outlier: 4.017A  pdb=" N   GLN A 156 " --> pdb=" O   SER A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 180
      removed outlier: 3.721A  pdb=" N   SER A 179 " --> pdb=" O   ALA A 176 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ASP A 180 " --> pdb=" O   LYS A 177 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 176 through 180'
    Processing helix  chain 'A' and resid 194 through 203
      removed outlier: 4.266A  pdb=" N   ALA A 200 " --> pdb=" O   TYR A 196 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLU A 203 " --> pdb=" O   LYS A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 235
    Processing helix  chain 'A' and resid 256 through 261
    Processing helix  chain 'A' and resid 261 through 266
      removed outlier: 4.074A  pdb=" N   LYS A 266 " --> pdb=" O   GLU A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 340
      removed outlier: 3.719A  pdb=" N   LEU A 340 " --> pdb=" O   PHE A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 359
    Processing helix  chain 'A' and resid 387 through 389
      No H-bonds generated for 'chain 'A' and resid 387 through 389'
    Processing helix  chain 'A' and resid 390 through 407
      removed outlier: 3.744A  pdb=" N   TYR A 398 " --> pdb=" O   VAL A 394 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   MET A 400 " --> pdb=" O   ALA A 396 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   HIS A 405 " --> pdb=" O   ALA A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 412
      removed outlier: 3.546A  pdb=" N   CYS A 412 " --> pdb=" O   GLN A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 431
    Processing helix  chain 'A' and resid 499 through 503
      removed outlier: 3.518A  pdb=" N   ASN A 502 " --> pdb=" O   TRP A 499 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   SER A 503 " --> pdb=" O   SER A 500 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 499 through 503'
    Processing helix  chain 'A' and resid 578 through 586
      removed outlier: 3.525A  pdb=" N   THR A 582 " --> pdb=" O   ILE A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 594
      removed outlier: 4.227A  pdb=" N   THR A 591 " --> pdb=" O   GLY A 587 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   CYS A 592 " --> pdb=" O   PHE A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 599
    Processing helix  chain 'A' and resid 604 through 609
    Processing helix  chain 'A' and resid 614 through 619
    Processing helix  chain 'A' and resid 619 through 626
    Processing helix  chain 'A' and resid 640 through 652
      removed outlier: 3.508A  pdb=" N   ARG A 645 " --> pdb=" O   CYS A 641 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLY A 649 " --> pdb=" O   ARG A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 666
      removed outlier: 3.897A  pdb=" N   ASN A 664 " --> pdb=" O   LEU A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 690 through 696
    Processing helix  chain 'A' and resid 701 through 709
    Processing helix  chain 'A' and resid 733 through 750
      removed outlier: 3.922A  pdb=" N   ASP A 744 " --> pdb=" O   SER A 740 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ILE A 746 " --> pdb=" O   THR A 742 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   LEU A 747 " --> pdb=" O   TYR A 743 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU A 750 " --> pdb=" O   ILE A 746 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 750 through 755
    Processing helix  chain 'A' and resid 766 through 783
      removed outlier: 4.886A  pdb=" N   GLY A 772 " --> pdb=" O   ALA A 768 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   PHE A 773 " --> pdb=" O   LYS A 769 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   THR A 778 " --> pdb=" O   THR A 774 " (cutoff:3.500A)
      removed outlier: 4.822A  pdb=" N   CYS A 779 " --> pdb=" O   MET A 775 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ILE A 781 " --> pdb=" O   THR A 777 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TRP A 782 " --> pdb=" O   THR A 778 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 789
    Processing helix  chain 'A' and resid 799 through 813
      removed outlier: 3.681A  pdb=" N   MET A 803 " --> pdb=" O   GLN A 799 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   CYS A 804 " --> pdb=" O   THR A 800 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   VAL A 807 " --> pdb=" O   MET A 803 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   SER A 808 " --> pdb=" O   CYS A 804 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   LEU A 809 " --> pdb=" O   ILE A 805 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   SER A 810 " --> pdb=" O   SER A 806 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 78
      removed outlier: 4.560A  pdb=" N   ALA B  71 " --> pdb=" O   GLN B  67 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   PHE B  74 " --> pdb=" O   GLU B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 114
      removed outlier: 3.508A  pdb=" N   ALA B 105 " --> pdb=" O   ARG B 101 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU B 106 " --> pdb=" O   ASP B 102 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLU B 107 " --> pdb=" O   THR B 103 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU B 110 " --> pdb=" O   LEU B 106 " (cutoff:3.500A)
      removed outlier: 4.845A  pdb=" N   GLU B 111 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   PHE B 112 " --> pdb=" O   GLN B 108 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   VAL B 113 " --> pdb=" O   SER B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 156
      removed outlier: 4.017A  pdb=" N   GLN B 156 " --> pdb=" O   SER B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 180
      removed outlier: 3.720A  pdb=" N   SER B 179 " --> pdb=" O   ALA B 176 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ASP B 180 " --> pdb=" O   LYS B 177 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 176 through 180'
    Processing helix  chain 'B' and resid 194 through 203
      removed outlier: 4.266A  pdb=" N   ALA B 200 " --> pdb=" O   TYR B 196 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLU B 203 " --> pdb=" O   LYS B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 235
    Processing helix  chain 'B' and resid 256 through 261
    Processing helix  chain 'B' and resid 261 through 266
      removed outlier: 4.075A  pdb=" N   LYS B 266 " --> pdb=" O   GLU B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 336 through 340
      removed outlier: 3.720A  pdb=" N   LEU B 340 " --> pdb=" O   PHE B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 359
    Processing helix  chain 'B' and resid 387 through 389
      No H-bonds generated for 'chain 'B' and resid 387 through 389'
    Processing helix  chain 'B' and resid 390 through 407
      removed outlier: 3.744A  pdb=" N   TYR B 398 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   MET B 400 " --> pdb=" O   ALA B 396 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   HIS B 405 " --> pdb=" O   ALA B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 412
      removed outlier: 3.546A  pdb=" N   CYS B 412 " --> pdb=" O   GLN B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 431
    Processing helix  chain 'B' and resid 499 through 503
      removed outlier: 3.518A  pdb=" N   ASN B 502 " --> pdb=" O   TRP B 499 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   SER B 503 " --> pdb=" O   SER B 500 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 499 through 503'
    Processing helix  chain 'B' and resid 578 through 586
      removed outlier: 3.524A  pdb=" N   THR B 582 " --> pdb=" O   ILE B 578 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 594
      removed outlier: 4.226A  pdb=" N   THR B 591 " --> pdb=" O   GLY B 587 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   CYS B 592 " --> pdb=" O   PHE B 588 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 594 through 599
    Processing helix  chain 'B' and resid 604 through 609
    Processing helix  chain 'B' and resid 614 through 619
    Processing helix  chain 'B' and resid 619 through 626
    Processing helix  chain 'B' and resid 640 through 652
      removed outlier: 3.508A  pdb=" N   ARG B 645 " --> pdb=" O   CYS B 641 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLY B 649 " --> pdb=" O   ARG B 645 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 666
      removed outlier: 3.896A  pdb=" N   ASN B 664 " --> pdb=" O   LEU B 660 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 690 through 696
    Processing helix  chain 'B' and resid 701 through 709
    Processing helix  chain 'B' and resid 733 through 750
      removed outlier: 3.922A  pdb=" N   ASP B 744 " --> pdb=" O   SER B 740 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ILE B 746 " --> pdb=" O   THR B 742 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   LEU B 747 " --> pdb=" O   TYR B 743 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU B 750 " --> pdb=" O   ILE B 746 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 750 through 755
    Processing helix  chain 'B' and resid 766 through 783
      removed outlier: 4.887A  pdb=" N   GLY B 772 " --> pdb=" O   ALA B 768 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   PHE B 773 " --> pdb=" O   LYS B 769 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   THR B 778 " --> pdb=" O   THR B 774 " (cutoff:3.500A)
      removed outlier: 4.823A  pdb=" N   CYS B 779 " --> pdb=" O   MET B 775 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ILE B 781 " --> pdb=" O   THR B 777 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TRP B 782 " --> pdb=" O   THR B 778 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 785 through 789
    Processing helix  chain 'B' and resid 799 through 813
      removed outlier: 3.683A  pdb=" N   MET B 803 " --> pdb=" O   GLN B 799 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   CYS B 804 " --> pdb=" O   THR B 800 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   VAL B 807 " --> pdb=" O   MET B 803 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   SER B 808 " --> pdb=" O   CYS B 804 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   LEU B 809 " --> pdb=" O   ILE B 805 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   SER B 810 " --> pdb=" O   SER B 806 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34
    Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 34
    Processing sheet with id=AA3, first strand: chain 'A' and resid 240 through 241
      removed outlier: 6.352A  pdb=" N   CYS A 240 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   THR A 215 " --> pdb=" O   CYS A 240 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   GLU A 245 " --> pdb=" O   THR A 215 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 241
      removed outlier: 6.352A  pdb=" N   CYS A 240 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   THR A 215 " --> pdb=" O   CYS A 240 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   VAL A 271 " --> pdb=" O   TYR A 212 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL A 272 " --> pdb=" O   THR A 296 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   TRP A 297 " --> pdb=" O   ILE A 321 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 469 through 470
    Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 539
    Processing sheet with id=AA7, first strand: chain 'A' and resid 553 through 555
    Processing sheet with id=AA8, first strand: chain 'B' and resid 33 through 34
    Processing sheet with id=AA9, first strand: chain 'B' and resid 33 through 34
    Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 241
      removed outlier: 6.352A  pdb=" N   CYS B 240 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   THR B 215 " --> pdb=" O   CYS B 240 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   GLU B 245 " --> pdb=" O   THR B 215 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 240 through 241
      removed outlier: 6.352A  pdb=" N   CYS B 240 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   THR B 215 " --> pdb=" O   CYS B 240 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   VAL B 271 " --> pdb=" O   TYR B 212 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL B 272 " --> pdb=" O   THR B 296 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   TRP B 297 " --> pdb=" O   ILE B 321 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 469 through 470
    Processing sheet with id=AB4, first strand: chain 'B' and resid 538 through 539
    Processing sheet with id=AB5, first strand: chain 'B' and resid 553 through 555

    238 hydrogen bonds defined for protein.
    672 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: 1.43

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1700
        1.31 -     1.44: 2573
        1.44 -     1.57: 5821
        1.57 -     1.70: 4
        1.70 -     1.83: 82
  Bond restraints: 10180
  Sorted by residual:
  bond pdb=" C   CWY A 902 "
       pdb=" C7  CWY A 902 "
    ideal  model  delta    sigma   weight residual
    1.537  1.315  0.222 2.00e-02 2.50e+03 1.23e+02
  bond pdb=" C   CWY B 902 "
       pdb=" C7  CWY B 902 "
    ideal  model  delta    sigma   weight residual
    1.537  1.316  0.221 2.00e-02 2.50e+03 1.22e+02
  bond pdb=" C1  CWY A 902 "
       pdb=" C3  CWY A 902 "
    ideal  model  delta    sigma   weight residual
    1.533  1.355  0.178 2.00e-02 2.50e+03 7.94e+01
  bond pdb=" C1  CWY B 902 "
       pdb=" C3  CWY B 902 "
    ideal  model  delta    sigma   weight residual
    1.533  1.355  0.178 2.00e-02 2.50e+03 7.92e+01
  bond pdb=" C8  CWY A 902 "
       pdb=" N1  CWY A 902 "
    ideal  model  delta    sigma   weight residual
    1.342  1.461 -0.119 2.00e-02 2.50e+03 3.53e+01
  ... (remaining 10175 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.66: 13910
        5.66 -    11.31: 50
       11.31 -    16.97: 6
       16.97 -    22.63: 0
       22.63 -    28.28: 2
  Bond angle restraints: 13968
  Sorted by residual:
  angle pdb=" C4  CWY A 902 "
        pdb=" C6  CWY A 902 "
        pdb=" C7  CWY A 902 "
      ideal   model   delta    sigma   weight residual
     116.66  144.94  -28.28 3.00e+00 1.11e-01 8.89e+01
  angle pdb=" C4  CWY B 902 "
        pdb=" C6  CWY B 902 "
        pdb=" C7  CWY B 902 "
      ideal   model   delta    sigma   weight residual
     116.66  144.92  -28.26 3.00e+00 1.11e-01 8.87e+01
  angle pdb=" C   TRP B 486 "
        pdb=" N   ALA B 487 "
        pdb=" CA  ALA B 487 "
      ideal   model   delta    sigma   weight residual
     121.54  133.51  -11.97 1.91e+00 2.74e-01 3.93e+01
  angle pdb=" C   TRP A 486 "
        pdb=" N   ALA A 487 "
        pdb=" CA  ALA A 487 "
      ideal   model   delta    sigma   weight residual
     121.54  133.49  -11.95 1.91e+00 2.74e-01 3.92e+01
  angle pdb=" C   VAL A 247 "
        pdb=" CA  VAL A 247 "
        pdb=" CB  VAL A 247 "
      ideal   model   delta    sigma   weight residual
     110.70  116.28   -5.58 9.90e-01 1.02e+00 3.18e+01
  ... (remaining 13963 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 5550
       17.78 -    35.57: 459
       35.57 -    53.35: 83
       53.35 -    71.13: 28
       71.13 -    88.91: 12
  Dihedral angle restraints: 6132
    sinusoidal: 1824
      harmonic: 4308
  Sorted by residual:
  dihedral pdb=" CB  CYS A 240 "
           pdb=" SG  CYS A 240 "
           pdb=" SG  CYS A 527 "
           pdb=" CB  CYS A 527 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -3.62  -82.38     1      1.00e+01 1.00e-02 8.33e+01
  dihedral pdb=" CB  CYS B 240 "
           pdb=" SG  CYS B 240 "
           pdb=" SG  CYS B 527 "
           pdb=" CB  CYS B 527 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -3.63  -82.37     1      1.00e+01 1.00e-02 8.32e+01
  dihedral pdb=" CB  CYS B 361 "
           pdb=" SG  CYS B 361 "
           pdb=" SG  CYS B 373 "
           pdb=" CB  CYS B 373 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -143.20   57.20     1      1.00e+01 1.00e-02 4.40e+01
  ... (remaining 6129 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.165: 1698
       0.165 -    0.329: 8
       0.329 -    0.494: 2
       0.494 -    0.659: 2
       0.659 -    0.823: 2
  Chirality restraints: 1712
  Sorted by residual:
  chirality pdb=" C6  CWY A 902 "
            pdb=" C3  CWY A 902 "
            pdb=" C4  CWY A 902 "
            pdb=" C7  CWY A 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.64    1.81    0.82 2.00e-01 2.50e+01 1.70e+01
  chirality pdb=" C6  CWY B 902 "
            pdb=" C3  CWY B 902 "
            pdb=" C4  CWY B 902 "
            pdb=" C7  CWY B 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.64    1.82    0.82 2.00e-01 2.50e+01 1.69e+01
  chirality pdb=" C3  CWY A 902 "
            pdb=" C1  CWY A 902 "
            pdb=" C4  CWY A 902 "
            pdb=" C6  CWY A 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.61    2.03    0.58 2.00e-01 2.50e+01 8.33e+00
  ... (remaining 1709 not shown)

  Planarity restraints: 1828
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 247 "    0.017 2.00e-02 2.50e+03   3.49e-02 1.22e+01
        pdb=" C   VAL B 247 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   VAL B 247 "    0.023 2.00e-02 2.50e+03
        pdb=" N   GLY B 248 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 247 "   -0.017 2.00e-02 2.50e+03   3.48e-02 1.21e+01
        pdb=" C   VAL A 247 "    0.060 2.00e-02 2.50e+03
        pdb=" O   VAL A 247 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   GLY A 248 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 637 "    0.041 5.00e-02 4.00e+02   6.23e-02 6.20e+00
        pdb=" N   PRO B 638 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO B 638 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 638 "    0.035 5.00e-02 4.00e+02
  ... (remaining 1825 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 3429
        2.83 -     3.35: 8448
        3.35 -     3.87: 15395
        3.87 -     4.38: 16830
        4.38 -     4.90: 28536
  Nonbonded interactions: 72638
  Sorted by model distance:
  nonbonded pdb=" O   SER A 250 "
            pdb=" OG  SER A 250 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" O   SER B 250 "
            pdb=" OG  SER B 250 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" OG  SER B 149 "
            pdb=" O2  CWY B 902 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" OG  SER A 149 "
            pdb=" O2  CWY A 902 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" O   SER B 100 "
            pdb=" OG  SER B 100 "
     model   vdw
     2.327 3.040
  ... (remaining 72633 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'
}

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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.280
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
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      :  0.006   0.222  10198  Z= 0.316
  Angle     :  1.036  28.282  14006  Z= 0.544
  Chirality :  0.064   0.823   1712
  Planarity :  0.006   0.062   1826
  Dihedral  : 14.904  88.913   3284
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  : 10.81 %
    Favored  : 88.92 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  7.56 %
    Favored  : 91.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -6.08 (0.15), residues: 1462
  helix: -4.83 (0.07), residues: 508
  sheet: -4.23 (0.29), residues: 164
  loop : -3.46 (0.18), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 253 
 TYR   0.012   0.001   TYR B 539 
 PHE   0.015   0.001   PHE B  45 
 TRP   0.015   0.002   TRP A 486 
 HIS   0.006   0.001   HIS B  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00625 (10180)
  covalent geometry    : angle       1.03282 (13968)
  SS BOND              : bond        0.00407 (   16)
  SS BOND              : angle       0.69368 (   32)
  hydrogen bonds       : bond        0.31768 (  234)
  hydrogen bonds       : angle      10.77039 (  672)
  link_NAG-ASN         : bond        0.00406 (    2)
  link_NAG-ASN         : angle       4.15082 (    6)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 139
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  630 PHE cc_start: 0.8383 (m-10) cc_final: 0.7977 (m-80)
REVERT: B  630 PHE cc_start: 0.8335 (m-10) cc_final: 0.7912 (m-80)
  outliers start: 6
  outliers final: 0
  residues processed: 143
  average time/residue: 0.0818
  time to fit residues: 17.4649
Evaluate side-chains
  105 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    0.5980
   chunk 55 optimal weight:    9.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  80 ASN
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 238 ASN
A 467 ASN
B  80 ASN
** B  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 238 ASN
B 467 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4712 r_free = 0.4712 target = 0.230338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.165047 restraints weight = 15094.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.167266 restraints weight = 11250.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.168663 restraints weight = 9095.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.169831 restraints weight = 7904.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.170145 restraints weight = 7165.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.4177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  10198  Z= 0.152
  Angle     :  0.670   9.263  14006  Z= 0.358
  Chirality :  0.043   0.132   1712
  Planarity :  0.005   0.052   1826
  Dihedral  :  9.676  84.486   1654
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 10.40 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 13.54 %
    Favored  : 84.27 %
  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: -5.36 (0.17), residues: 1462
  helix: -3.99 (0.13), residues: 526
  sheet: -3.74 (0.33), residues: 168
  loop : -3.20 (0.20), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 335 
 TYR   0.009   0.001   TYR A 256 
 PHE   0.009   0.001   PHE B 652 
 TRP   0.011   0.001   TRP B 297 
 HIS   0.002   0.001   HIS B 485 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (10180)
  covalent geometry    : angle       0.66540 (13968)
  SS BOND              : bond        0.00278 (   16)
  SS BOND              : angle       0.81469 (   32)
  hydrogen bonds       : bond        0.05173 (  234)
  hydrogen bonds       : angle       6.64181 (  672)
  link_NAG-ASN         : bond        0.00072 (    2)
  link_NAG-ASN         : angle       3.58695 (    6)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A  194 ASP cc_start: 0.8020 (m-30) cc_final: 0.7807 (m-30)
REVERT: A  630 PHE cc_start: 0.8446 (m-10) cc_final: 0.8035 (m-80)
REVERT: B  194 ASP cc_start: 0.8016 (m-30) cc_final: 0.7797 (m-30)
REVERT: B  630 PHE cc_start: 0.8403 (m-10) cc_final: 0.7977 (m-80)
  outliers start: 18
  outliers final: 10
  residues processed: 124
  average time/residue: 0.0794
  time to fit residues: 15.1121
Evaluate side-chains
  113 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  391 MET
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  454 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 78 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 124 optimal weight:   20.0000
   chunk 120 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0370
   chunk 145 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   chunk 88 optimal weight:    0.0470
   overall best weight:    0.4356

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 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 = 0.4733 r_free = 0.4733 target = 0.227407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.169399 restraints weight = 14723.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.168083 restraints weight = 10622.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.167871 restraints weight = 7677.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.168008 restraints weight = 7071.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.168202 restraints weight = 7559.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.4069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10198  Z= 0.114
  Angle     :  0.609   7.749  14006  Z= 0.323
  Chirality :  0.042   0.138   1712
  Planarity :  0.004   0.050   1826
  Dihedral  :  8.248  78.884   1654
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.99 %
    Favored  : 90.01 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.34 %
    Favored  : 81.22 %
  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: -4.61 (0.19), residues: 1462
  helix: -3.35 (0.16), residues: 532
  sheet: -3.32 (0.36), residues: 170
  loop : -2.75 (0.21), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 189 
 TYR   0.019   0.001   TYR B 537 
 PHE   0.008   0.001   PHE B 295 
 TRP   0.020   0.002   TRP A 297 
 HIS   0.005   0.001   HIS B  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (10180)
  covalent geometry    : angle       0.60559 (13968)
  SS BOND              : bond        0.00243 (   16)
  SS BOND              : angle       0.72450 (   32)
  hydrogen bonds       : bond        0.04061 (  234)
  hydrogen bonds       : angle       5.67557 (  672)
  link_NAG-ASN         : bond        0.00215 (    2)
  link_NAG-ASN         : angle       2.89233 (    6)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A  630 PHE cc_start: 0.8442 (m-10) cc_final: 0.8051 (m-80)
REVERT: B  156 GLN cc_start: 0.7135 (tp-100) cc_final: 0.6738 (tp40)
REVERT: B  630 PHE cc_start: 0.8385 (m-10) cc_final: 0.8002 (m-80)
  outliers start: 20
  outliers final: 20
  residues processed: 127
  average time/residue: 0.0772
  time to fit residues: 15.3309
Evaluate side-chains
  120 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  391 MET
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  660 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 142 optimal weight:    3.9990
   chunk 65 optimal weight:    8.9990
   chunk 85 optimal weight:    2.9990
   chunk 128 optimal weight:   50.0000
   chunk 83 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0170
   overall best weight:    0.8620

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 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 = 0.4613 r_free = 0.4613 target = 0.212552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.145351 restraints weight = 14456.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.147686 restraints weight = 12546.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.148422 restraints weight = 9486.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.148270 restraints weight = 8164.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.148384 restraints weight = 8172.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.4128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10198  Z= 0.149
  Angle     :  0.617   8.184  14006  Z= 0.325
  Chirality :  0.042   0.138   1712
  Planarity :  0.004   0.050   1826
  Dihedral  :  8.003  77.893   1654
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.26 %
    Favored  : 89.74 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 17.32 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.27 (0.20), residues: 1462
  helix: -2.85 (0.18), residues: 554
  sheet: -3.11 (0.39), residues: 168
  loop : -2.72 (0.22), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 183 
 TYR   0.012   0.001   TYR A 539 
 PHE   0.020   0.002   PHE B 598 
 TRP   0.027   0.002   TRP B 529 
 HIS   0.003   0.001   HIS B  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (10180)
  covalent geometry    : angle       0.61472 (13968)
  SS BOND              : bond        0.00213 (   16)
  SS BOND              : angle       0.63126 (   32)
  hydrogen bonds       : bond        0.03774 (  234)
  hydrogen bonds       : angle       5.39825 (  672)
  link_NAG-ASN         : bond        0.00073 (    2)
  link_NAG-ASN         : angle       2.87060 (    6)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 113
  time to evaluate  : 0.385 
Fit side-chains
REVERT: A  104 TYR cc_start: 0.8046 (t80) cc_final: 0.7691 (t80)
REVERT: A  194 ASP cc_start: 0.8078 (m-30) cc_final: 0.7801 (m-30)
REVERT: A  204 ILE cc_start: 0.8846 (tp) cc_final: 0.8532 (tp)
REVERT: A  630 PHE cc_start: 0.8423 (m-10) cc_final: 0.8022 (m-80)
REVERT: B  104 TYR cc_start: 0.8005 (t80) cc_final: 0.7731 (t80)
REVERT: B  204 ILE cc_start: 0.8865 (tp) cc_final: 0.8533 (tp)
REVERT: B  630 PHE cc_start: 0.8429 (m-10) cc_final: 0.8011 (m-80)
  outliers start: 32
  outliers final: 23
  residues processed: 136
  average time/residue: 0.0686
  time to fit residues: 14.5866
Evaluate side-chains
  135 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  485 HIS
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   79 ILE
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  391 MET
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  485 HIS
Chi-restraints excluded: chain B residue  771 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 51 optimal weight:    9.9990
   chunk 89 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 68 optimal weight:    0.4980
   chunk 128 optimal weight:   30.0000
   chunk 84 optimal weight:    0.5980
   chunk 96 optimal weight:    0.6980
   chunk 57 optimal weight:   10.0000
   chunk 101 optimal weight:    0.9980
   chunk 63 optimal weight:   30.0000
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 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 = 0.4609 r_free = 0.4609 target = 0.211953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 94)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.152034 restraints weight = 14445.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.148645 restraints weight = 11399.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.149016 restraints weight = 10655.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.149378 restraints weight = 10915.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.149796 restraints weight = 9564.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.4151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  10198  Z= 0.157
  Angle     :  0.609   7.461  14006  Z= 0.320
  Chirality :  0.042   0.139   1712
  Planarity :  0.004   0.048   1826
  Dihedral  :  7.903  79.105   1654
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 10.74 %
    Favored  : 89.12 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 18.54 %
    Favored  : 76.95 %
  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: -4.00 (0.20), residues: 1462
  helix: -2.56 (0.20), residues: 558
  sheet: -3.01 (0.39), residues: 168
  loop : -2.61 (0.22), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 335 
 TYR   0.010   0.001   TYR B 539 
 PHE   0.014   0.001   PHE A 471 
 TRP   0.025   0.002   TRP A 529 
 HIS   0.003   0.001   HIS B  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (10180)
  covalent geometry    : angle       0.60466 (13968)
  SS BOND              : bond        0.00181 (   16)
  SS BOND              : angle       1.18699 (   32)
  hydrogen bonds       : bond        0.03604 (  234)
  hydrogen bonds       : angle       5.26416 (  672)
  link_NAG-ASN         : bond        0.00057 (    2)
  link_NAG-ASN         : angle       2.87052 (    6)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 110
  time to evaluate  : 0.398 
Fit side-chains
REVERT: A  104 TYR cc_start: 0.8084 (t80) cc_final: 0.7792 (t80)
REVERT: A  194 ASP cc_start: 0.8103 (m-30) cc_final: 0.7797 (m-30)
REVERT: A  204 ILE cc_start: 0.8950 (tp) cc_final: 0.8661 (tp)
REVERT: A  630 PHE cc_start: 0.8323 (m-10) cc_final: 0.7963 (m-80)
REVERT: B  104 TYR cc_start: 0.8016 (t80) cc_final: 0.7738 (t80)
REVERT: B  194 ASP cc_start: 0.8062 (m-30) cc_final: 0.7760 (m-30)
REVERT: B  204 ILE cc_start: 0.8940 (tp) cc_final: 0.8661 (tp)
REVERT: B  630 PHE cc_start: 0.8284 (m-10) cc_final: 0.7925 (m-80)
  outliers start: 37
  outliers final: 30
  residues processed: 137
  average time/residue: 0.0739
  time to fit residues: 15.7525
Evaluate side-chains
  140 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 110
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  391 MET
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  485 HIS
Chi-restraints excluded: chain A residue  518 MET
Chi-restraints excluded: chain A residue  660 LEU
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   79 ILE
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  327 SER
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  391 MET
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  485 HIS
Chi-restraints excluded: chain B residue  518 MET
Chi-restraints excluded: chain B residue  660 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 22 optimal weight:    0.0060
   chunk 70 optimal weight:    0.4980
   chunk 117 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 145 optimal weight:    0.0070
   chunk 147 optimal weight:    0.2980
   chunk 19 optimal weight:    0.0010
   chunk 141 optimal weight:   30.0000
   chunk 36 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 86 optimal weight:    0.5980
   overall best weight:    0.1620

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 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 = 0.4731 r_free = 0.4731 target = 0.226982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.169632 restraints weight = 14702.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.166397 restraints weight = 10990.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.168190 restraints weight = 9827.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.168138 restraints weight = 8122.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.168958 restraints weight = 7227.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.4221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  10198  Z= 0.091
  Angle     :  0.571   6.296  14006  Z= 0.299
  Chirality :  0.041   0.146   1712
  Planarity :  0.003   0.047   1826
  Dihedral  :  7.278  78.833   1654
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.58 %
    Favored  : 90.42 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 21.95 %
    Favored  : 75.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.73 (0.21), residues: 1462
  helix: -2.30 (0.20), residues: 558
  sheet: -2.81 (0.40), residues: 170
  loop : -2.49 (0.22), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 189 
 TYR   0.008   0.001   TYR A 539 
 PHE   0.021   0.001   PHE B 598 
 TRP   0.029   0.002   TRP B 529 
 HIS   0.004   0.001   HIS B  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 (10180)
  covalent geometry    : angle       0.56757 (13968)
  SS BOND              : bond        0.00196 (   16)
  SS BOND              : angle       1.04128 (   32)
  hydrogen bonds       : bond        0.03076 (  234)
  hydrogen bonds       : angle       4.83498 (  672)
  link_NAG-ASN         : bond        0.00226 (    2)
  link_NAG-ASN         : angle       2.39926 (    6)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 115
  time to evaluate  : 0.377 
Fit side-chains
REVERT: A  104 TYR cc_start: 0.7886 (t80) cc_final: 0.7630 (t80)
REVERT: A  194 ASP cc_start: 0.8059 (m-30) cc_final: 0.7729 (m-30)
REVERT: A  400 MET cc_start: 0.7811 (mmm) cc_final: 0.7584 (mmm)
REVERT: A  630 PHE cc_start: 0.8277 (m-10) cc_final: 0.7911 (m-80)
REVERT: B  104 TYR cc_start: 0.7832 (t80) cc_final: 0.7545 (t80)
REVERT: B  400 MET cc_start: 0.7797 (mmm) cc_final: 0.7572 (mmm)
REVERT: B  630 PHE cc_start: 0.8249 (m-10) cc_final: 0.7914 (m-80)
  outliers start: 21
  outliers final: 17
  residues processed: 126
  average time/residue: 0.0734
  time to fit residues: 14.4713
Evaluate side-chains
  128 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  518 MET
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  434 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 126 optimal weight:    6.9990
   chunk 129 optimal weight:    9.9990
   chunk 15 optimal weight:    0.7980
   chunk 55 optimal weight:   10.0000
   chunk 132 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 3 optimal weight:    0.6980
   chunk 105 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  61 ASN
** B  94 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 = 0.4630 r_free = 0.4630 target = 0.213893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.158669 restraints weight = 14421.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.157304 restraints weight = 16131.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.158797 restraints weight = 14910.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.159207 restraints weight = 10905.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.158953 restraints weight = 10662.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.4254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.2762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10198  Z= 0.133
  Angle     :  0.587   6.512  14006  Z= 0.305
  Chirality :  0.042   0.125   1712
  Planarity :  0.003   0.050   1826
  Dihedral  :  7.439  79.771   1654
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.53 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 22.56 %
    Favored  : 74.51 %
  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: -3.47 (0.21), residues: 1462
  helix: -2.08 (0.21), residues: 556
  sheet: -2.28 (0.43), residues: 148
  loop : -2.48 (0.22), residues: 758

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 335 
 TYR   0.018   0.001   TYR B 537 
 PHE   0.010   0.001   PHE A 471 
 TRP   0.017   0.001   TRP A 529 
 HIS   0.003   0.001   HIS B  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (10180)
  covalent geometry    : angle       0.58393 (13968)
  SS BOND              : bond        0.00167 (   16)
  SS BOND              : angle       0.91178 (   32)
  hydrogen bonds       : bond        0.03316 (  234)
  hydrogen bonds       : angle       4.87453 (  672)
  link_NAG-ASN         : bond        0.00081 (    2)
  link_NAG-ASN         : angle       2.49830 (    6)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.361 
Fit side-chains
REVERT: A  104 TYR cc_start: 0.7998 (t80) cc_final: 0.7687 (t80)
REVERT: A  194 ASP cc_start: 0.8152 (m-30) cc_final: 0.7815 (m-30)
REVERT: A  400 MET cc_start: 0.8016 (mmm) cc_final: 0.7754 (mmm)
REVERT: A  529 TRP cc_start: 0.7480 (p-90) cc_final: 0.7194 (p-90)
REVERT: A  630 PHE cc_start: 0.7912 (m-10) cc_final: 0.7711 (m-80)
REVERT: B  104 TYR cc_start: 0.7968 (t80) cc_final: 0.7730 (t80)
REVERT: B  194 ASP cc_start: 0.8154 (m-30) cc_final: 0.7805 (m-30)
REVERT: B  400 MET cc_start: 0.7990 (mmm) cc_final: 0.7742 (mmm)
REVERT: B  529 TRP cc_start: 0.7491 (p-90) cc_final: 0.7204 (p-90)
  outliers start: 24
  outliers final: 22
  residues processed: 130
  average time/residue: 0.0733
  time to fit residues: 14.6920
Evaluate side-chains
  133 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 111
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  518 MET
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  518 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 132 optimal weight:    8.9990
   chunk 94 optimal weight:    0.0170
   chunk 66 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9980
   chunk 118 optimal weight:    0.6980
   chunk 46 optimal weight:    0.3980
   chunk 141 optimal weight:    0.0270
   chunk 75 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.3876

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 238 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4751 r_free = 0.4751 target = 0.228838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.165055 restraints weight = 14592.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.167796 restraints weight = 9617.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.168100 restraints weight = 7277.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.168188 restraints weight = 6747.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.168974 restraints weight = 6575.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.4174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10198  Z= 0.099
  Angle     :  0.567   6.006  14006  Z= 0.296
  Chirality :  0.041   0.133   1712
  Planarity :  0.003   0.050   1826
  Dihedral  :  7.190  80.583   1654
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.71 %
    Favored  : 90.29 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 22.56 %
    Favored  : 74.27 %
  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: -3.36 (0.21), residues: 1462
  helix: -1.95 (0.21), residues: 556
  sheet: -2.28 (0.43), residues: 150
  loop : -2.44 (0.22), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 206 
 TYR   0.006   0.001   TYR A 431 
 PHE   0.019   0.001   PHE B 598 
 TRP   0.020   0.001   TRP A 554 
 HIS   0.003   0.001   HIS A  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 (10180)
  covalent geometry    : angle       0.56454 (13968)
  SS BOND              : bond        0.00161 (   16)
  SS BOND              : angle       0.84255 (   32)
  hydrogen bonds       : bond        0.02968 (  234)
  hydrogen bonds       : angle       4.67705 (  672)
  link_NAG-ASN         : bond        0.00159 (    2)
  link_NAG-ASN         : angle       2.34669 (    6)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 116
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A  104 TYR cc_start: 0.7895 (t80) cc_final: 0.7610 (t80)
REVERT: A  194 ASP cc_start: 0.8157 (m-30) cc_final: 0.7809 (m-30)
REVERT: A  400 MET cc_start: 0.7914 (mmm) cc_final: 0.7666 (mmm)
REVERT: A  630 PHE cc_start: 0.8589 (m-10) cc_final: 0.8199 (m-80)
REVERT: B  104 TYR cc_start: 0.7865 (t80) cc_final: 0.7634 (t80)
REVERT: B  194 ASP cc_start: 0.8105 (m-30) cc_final: 0.7764 (m-30)
REVERT: B  400 MET cc_start: 0.7895 (mmm) cc_final: 0.7656 (mmm)
REVERT: B  529 TRP cc_start: 0.7231 (p-90) cc_final: 0.6828 (p-90)
  outliers start: 26
  outliers final: 21
  residues processed: 134
  average time/residue: 0.0732
  time to fit residues: 15.2957
Evaluate side-chains
  134 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  518 MET
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  518 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 85 optimal weight:    0.7980
   chunk 93 optimal weight:    0.8980
   chunk 126 optimal weight:    8.9990
   chunk 44 optimal weight:    6.9990
   chunk 70 optimal weight:    0.2980
   chunk 82 optimal weight:    2.9990
   chunk 91 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 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 = 0.4735 r_free = 0.4735 target = 0.227198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.166155 restraints weight = 14574.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.165260 restraints weight = 11943.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.165674 restraints weight = 9291.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.166289 restraints weight = 8096.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.166546 restraints weight = 8350.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.4154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.3029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10198  Z= 0.120
  Angle     :  0.577   6.033  14006  Z= 0.301
  Chirality :  0.042   0.134   1712
  Planarity :  0.003   0.050   1826
  Dihedral  :  7.278  81.473   1654
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.05 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 22.56 %
    Favored  : 74.27 %
  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: -3.22 (0.21), residues: 1462
  helix: -1.83 (0.22), residues: 556
  sheet: -2.21 (0.43), residues: 148
  loop : -2.35 (0.22), residues: 758

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 335 
 TYR   0.019   0.001   TYR A 537 
 PHE   0.011   0.001   PHE B 630 
 TRP   0.022   0.002   TRP A 529 
 HIS   0.003   0.001   HIS A  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (10180)
  covalent geometry    : angle       0.57426 (13968)
  SS BOND              : bond        0.00152 (   16)
  SS BOND              : angle       0.79293 (   32)
  hydrogen bonds       : bond        0.03147 (  234)
  hydrogen bonds       : angle       4.69659 (  672)
  link_NAG-ASN         : bond        0.00068 (    2)
  link_NAG-ASN         : angle       2.35941 (    6)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: A  104 TYR cc_start: 0.7954 (t80) cc_final: 0.7652 (t80)
REVERT: A  194 ASP cc_start: 0.8159 (m-30) cc_final: 0.7780 (m-30)
REVERT: A  270 ARG cc_start: 0.7290 (mmm-85) cc_final: 0.6841 (mtm180)
REVERT: A  400 MET cc_start: 0.7994 (mmm) cc_final: 0.7729 (mmm)
REVERT: A  529 TRP cc_start: 0.7266 (p-90) cc_final: 0.6640 (p-90)
REVERT: A  630 PHE cc_start: 0.8557 (m-10) cc_final: 0.8185 (m-80)
REVERT: B  104 TYR cc_start: 0.7927 (t80) cc_final: 0.7703 (t80)
REVERT: B  194 ASP cc_start: 0.8139 (m-30) cc_final: 0.7770 (m-30)
REVERT: B  270 ARG cc_start: 0.7265 (mmm-85) cc_final: 0.6817 (mtm180)
REVERT: B  400 MET cc_start: 0.7984 (mmm) cc_final: 0.7729 (mmm)
  outliers start: 26
  outliers final: 23
  residues processed: 130
  average time/residue: 0.0768
  time to fit residues: 15.1076
Evaluate side-chains
  134 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  518 MET
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  518 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 142 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   chunk 113 optimal weight:    0.8980
   chunk 106 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0170
   chunk 76 optimal weight:    0.7980
   chunk 98 optimal weight:    0.0870
   chunk 4 optimal weight:    3.9990
   chunk 108 optimal weight:    0.9990
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 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 = 0.4650 r_free = 0.4650 target = 0.215754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.165863 restraints weight = 14364.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.162375 restraints weight = 18320.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.159082 restraints weight = 14096.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.159352 restraints weight = 14192.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.159238 restraints weight = 11638.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.4246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10198  Z= 0.111
  Angle     :  0.571   6.567  14006  Z= 0.297
  Chirality :  0.041   0.125   1712
  Planarity :  0.003   0.050   1826
  Dihedral  :  7.218  82.958   1654
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.78 %
    Favored  : 90.22 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 23.29 %
    Favored  : 73.90 %
  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: -3.09 (0.22), residues: 1462
  helix: -1.73 (0.22), residues: 552
  sheet: -2.12 (0.43), residues: 148
  loop : -2.29 (0.22), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 206 
 TYR   0.006   0.001   TYR A 431 
 PHE   0.016   0.001   PHE B 598 
 TRP   0.020   0.002   TRP B 529 
 HIS   0.003   0.001   HIS A  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (10180)
  covalent geometry    : angle       0.56830 (13968)
  SS BOND              : bond        0.00170 (   16)
  SS BOND              : angle       0.79048 (   32)
  hydrogen bonds       : bond        0.02996 (  234)
  hydrogen bonds       : angle       4.59021 (  672)
  link_NAG-ASN         : bond        0.00134 (    2)
  link_NAG-ASN         : angle       2.25055 (    6)

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

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

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2924 Ramachandran restraints generated.
    1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 TYR cc_start: 0.7953 (t80) cc_final: 0.7657 (t80)
REVERT: A  194 ASP cc_start: 0.8148 (m-30) cc_final: 0.7778 (m-30)
REVERT: A  400 MET cc_start: 0.7994 (mmm) cc_final: 0.7753 (mmm)
REVERT: A  529 TRP cc_start: 0.7519 (p-90) cc_final: 0.7070 (p-90)
REVERT: A  630 PHE cc_start: 0.8100 (m-10) cc_final: 0.7897 (m-80)
REVERT: B  104 TYR cc_start: 0.7909 (t80) cc_final: 0.7690 (t80)
REVERT: B  194 ASP cc_start: 0.8101 (m-30) cc_final: 0.7754 (m-30)
REVERT: B  400 MET cc_start: 0.7993 (mmm) cc_final: 0.7777 (mmm)
REVERT: B  529 TRP cc_start: 0.7444 (p-90) cc_final: 0.7069 (p-90)
  outliers start: 23
  outliers final: 21
  residues processed: 135
  average time/residue: 0.0811
  time to fit residues: 16.3621
Evaluate side-chains
  133 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  216 VAL
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  434 TYR
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  518 MET
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  434 TYR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  518 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 128 optimal weight:   20.0000
   chunk 14 optimal weight:    0.7980
   chunk 115 optimal weight:    4.9990
   chunk 94 optimal weight:    1.9990
   chunk 30 optimal weight:    7.9990
   chunk 38 optimal weight:    0.7980
   chunk 62 optimal weight:   20.0000
   chunk 139 optimal weight:    5.9990
   chunk 122 optimal weight:    6.9990
   chunk 61 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 HIS
** B  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 601 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4687 r_free = 0.4687 target = 0.221951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.165650 restraints weight = 14675.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.165123 restraints weight = 14601.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.166035 restraints weight = 11935.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.166167 restraints weight = 9224.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.166776 restraints weight = 8284.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.4204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.3227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10198  Z= 0.165
  Angle     :  0.603   6.145  14006  Z= 0.314
  Chirality :  0.043   0.121   1712
  Planarity :  0.004   0.050   1826
  Dihedral  :  7.656  85.136   1654
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.08 %
    Favored  : 88.92 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 23.78 %
    Favored  : 73.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.12 (0.22), residues: 1462
  helix: -1.75 (0.22), residues: 558
  sheet: -2.17 (0.43), residues: 148
  loop : -2.30 (0.23), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 335 
 TYR   0.020   0.001   TYR B 537 
 PHE   0.009   0.001   PHE A 471 
 TRP   0.018   0.002   TRP A 486 
 HIS   0.003   0.001   HIS B  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (10180)
  covalent geometry    : angle       0.60031 (13968)
  SS BOND              : bond        0.00176 (   16)
  SS BOND              : angle       0.77779 (   32)
  hydrogen bonds       : bond        0.03358 (  234)
  hydrogen bonds       : angle       4.75947 (  672)
  link_NAG-ASN         : bond        0.00022 (    2)
  link_NAG-ASN         : angle       2.44976 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1706.70 seconds
wall clock time: 30 minutes 0.55 seconds (1800.55 seconds total)