Starting phenix.real_space_refine
on Tue Jul 29 19:52:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t6j_41069/07_2025/8t6j_41069.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t6j_41069/07_2025/8t6j_41069.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t6j_41069/07_2025/8t6j_41069.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t6j_41069/07_2025/8t6j_41069.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t6j_41069/07_2025/8t6j_41069.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t6j_41069/07_2025/8t6j_41069.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     112      5.16       5
     C    7473      2.51       5
     N    1940      2.21       5
     O    2127      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11652
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 5803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 767, 5803
          Classifications: {'peptide': 767}
          Incomplete info: {'truncation_to_alanine': 60}
          Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 734}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 256
          Unresolved non-hydrogen angles: 317
          Unresolved non-hydrogen dihedrals: 222
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 150
    Chain: "A"
      Number of atoms: 5793
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 767, 5793
          Classifications: {'peptide': 767}
          Incomplete info: {'truncation_to_alanine': 63}
          Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 734}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 266
          Unresolved non-hydrogen angles: 329
          Unresolved non-hydrogen dihedrals: 230
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 156
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'YKU': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'YKU': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 8.10, per 1000 atoms: 0.70
  Number of scatterers: 11652
  At special positions: 0
  Unit cell: (123.555, 82.6537, 188.314, 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     112     16.00
     O    2127      8.00
     N    1940      7.00
     C    7473      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=16, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  57 " - pdb=" SG  CYS B  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 365 " - pdb=" SG  CYS B 381 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 419 " - pdb=" SG  CYS B 426 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 511 " - pdb=" SG  CYS B 531 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 515 " - pdb=" SG  CYS B 534 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 537 " - pdb=" SG  CYS B 549 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 552 " - pdb=" SG  CYS B 565 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 644 " - pdb=" SG  CYS B 733 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  57 " - pdb=" SG  CYS A  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 365 " - pdb=" SG  CYS A 381 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 419 " - pdb=" SG  CYS A 426 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 511 " - pdb=" SG  CYS A 531 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 515 " - pdb=" SG  CYS A 534 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 537 " - pdb=" SG  CYS A 549 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 552 " - pdb=" SG  CYS A 565 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 644 " - pdb=" SG  CYS A 733 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.85
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2864

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 18 sheets defined
      51.9% alpha, 10.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.35
  Creating SS restraints...
    Processing helix  chain 'B' and resid 48 through 52
      removed outlier: 3.670A  pdb=" N   VAL B  52 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 82
    Processing helix  chain 'B' and resid 101 through 117
      removed outlier: 3.500A  pdb=" N   ALA B 105 " --> pdb=" O   HIS B 101 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ILE B 110 " --> pdb=" O   LEU B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 163
      removed outlier: 3.896A  pdb=" N   GLN B 157 " --> pdb=" O   SER B 153 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU B 161 " --> pdb=" O   GLN B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 166
      No H-bonds generated for 'chain 'B' and resid 164 through 166'
    Processing helix  chain 'B' and resid 177 through 181
      removed outlier: 3.889A  pdb=" N   SER B 180 " --> pdb=" O   MET B 177 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ASP B 181 " --> pdb=" O   ASP B 178 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 177 through 181'
    Processing helix  chain 'B' and resid 197 through 209
      removed outlier: 3.588A  pdb=" N   VAL B 203 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 237
      removed outlier: 3.975A  pdb=" N   LYS B 237 " --> pdb=" O   ASP B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 265
    Processing helix  chain 'B' and resid 266 through 268
      No H-bonds generated for 'chain 'B' and resid 266 through 268'
    Processing helix  chain 'B' and resid 281 through 294
      removed outlier: 3.666A  pdb=" N   ARG B 292 " --> pdb=" O   MET B 288 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU B 293 " --> pdb=" O   ALA B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 342
      removed outlier: 4.378A  pdb=" N   ASP B 338 " --> pdb=" O   VAL B 334 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ASP B 339 " --> pdb=" O   LYS B 335 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   TYR B 340 " --> pdb=" O   TRP B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 349
      removed outlier: 3.807A  pdb=" N   ASN B 349 " --> pdb=" O   PRO B 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 364
    Processing helix  chain 'B' and resid 396 through 419
      removed outlier: 3.923A  pdb=" N   VAL B 400 " --> pdb=" O   LYS B 396 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ILE B 401 " --> pdb=" O   MET B 397 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ILE B 404 " --> pdb=" O   VAL B 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 443
      removed outlier: 3.929A  pdb=" N   LEU B 437 " --> pdb=" O   ASP B 433 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   LEU B 438 " --> pdb=" O   GLY B 434 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   GLU B 439 " --> pdb=" O   ARG B 435 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   LYS B 443 " --> pdb=" O   GLU B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 495 through 500
      removed outlier: 3.833A  pdb=" N   VAL B 499 " --> pdb=" O   ASP B 495 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   TRP B 500 " --> pdb=" O   ASP B 496 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 495 through 500'
    Processing helix  chain 'B' and resid 502 through 506
    Processing helix  chain 'B' and resid 577 through 604
      removed outlier: 3.694A  pdb=" N   ILE B 581 " --> pdb=" O   ASP B 577 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 607 through 613
    Processing helix  chain 'B' and resid 614 through 630
    Processing helix  chain 'B' and resid 631 through 637
      removed outlier: 3.723A  pdb=" N   ALA B 637 " --> pdb=" O   PHE B 633 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 640 through 673
      removed outlier: 4.223A  pdb=" N   CYS B 644 " --> pdb=" O   LYS B 640 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   TYR B 645 " --> pdb=" O   GLN B 641 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ILE B 651 " --> pdb=" O   GLN B 647 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   GLY B 652 " --> pdb=" O   ARG B 648 " (cutoff:3.500A)
      Proline residue:  B 655  - end of helix
      removed outlier: 4.272A  pdb=" N   SER B 658 " --> pdb=" O   SER B 654 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   TYR B 659 " --> pdb=" O   PRO B 655 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ALA B 661 " --> pdb=" O   MET B 657 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 689 through 715
      removed outlier: 3.535A  pdb=" N   GLN B 693 " --> pdb=" O   SER B 689 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 737 through 761
      Proline residue:  B 743  - end of helix
      removed outlier: 4.097A  pdb=" N   LEU B 749 " --> pdb=" O   GLY B 745 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   LEU B 750 " --> pdb=" O   TYR B 746 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ILE B 751 " --> pdb=" O   ASN B 747 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 765 through 793
      removed outlier: 3.594A  pdb=" N   ASN B 769 " --> pdb=" O   PRO B 765 " (cutoff:3.500A)
      removed outlier: 5.648A  pdb=" N   ALA B 771 " --> pdb=" O   ASN B 767 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   LYS B 772 " --> pdb=" O   PHE B 768 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   TYR B 773 " --> pdb=" O   ASN B 769 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   MET B 778 " --> pdb=" O   ILE B 774 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   TYR B 779 " --> pdb=" O   ALA B 775 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   THR B 780 " --> pdb=" O   PHE B 776 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   THR B 781 " --> pdb=" O   THR B 777 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   VAL B 789 " --> pdb=" O   TRP B 785 " (cutoff:3.500A)
      Proline residue:  B 790  - end of helix
    Processing helix  chain 'B' and resid 797 through 816
      removed outlier: 3.931A  pdb=" N   VAL B 806 " --> pdb=" O   MET B 802 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   SER B 807 " --> pdb=" O   CYS B 803 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 818 through 827
    Processing helix  chain 'A' and resid 48 through 52
      removed outlier: 3.742A  pdb=" N   VAL A  52 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 82
    Processing helix  chain 'A' and resid 101 through 117
      removed outlier: 3.685A  pdb=" N   ILE A 110 " --> pdb=" O   LEU A 106 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ASP A 115 " --> pdb=" O   GLU A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 163
      removed outlier: 3.883A  pdb=" N   GLN A 157 " --> pdb=" O   SER A 153 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU A 161 " --> pdb=" O   GLN A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 166
      No H-bonds generated for 'chain 'A' and resid 164 through 166'
    Processing helix  chain 'A' and resid 177 through 181
      removed outlier: 3.893A  pdb=" N   SER A 180 " --> pdb=" O   MET A 177 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ASP A 181 " --> pdb=" O   ASP A 178 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 177 through 181'
    Processing helix  chain 'A' and resid 197 through 209
      removed outlier: 3.588A  pdb=" N   VAL A 203 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 236
    Processing helix  chain 'A' and resid 237 through 239
      No H-bonds generated for 'chain 'A' and resid 237 through 239'
    Processing helix  chain 'A' and resid 253 through 266
      removed outlier: 3.729A  pdb=" N   SER A 266 " --> pdb=" O   LYS A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 294
      removed outlier: 3.655A  pdb=" N   ARG A 292 " --> pdb=" O   MET A 288 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LEU A 293 " --> pdb=" O   ALA A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 314
      removed outlier: 3.558A  pdb=" N   VAL A 313 " --> pdb=" O   ARG A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 342
      removed outlier: 4.388A  pdb=" N   ASP A 338 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   ASP A 339 " --> pdb=" O   LYS A 335 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   TYR A 340 " --> pdb=" O   TRP A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 349
      removed outlier: 3.790A  pdb=" N   ASN A 349 " --> pdb=" O   PRO A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 364
    Processing helix  chain 'A' and resid 396 through 419
      removed outlier: 3.930A  pdb=" N   VAL A 400 " --> pdb=" O   LYS A 396 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   ILE A 401 " --> pdb=" O   MET A 397 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ILE A 404 " --> pdb=" O   VAL A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 430
      removed outlier: 4.072A  pdb=" N   LYS A 430 " --> pdb=" O   ASP A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 443
      removed outlier: 3.895A  pdb=" N   LEU A 437 " --> pdb=" O   ASP A 433 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   LEU A 438 " --> pdb=" O   GLY A 434 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   GLU A 439 " --> pdb=" O   ARG A 435 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   LYS A 443 " --> pdb=" O   GLU A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 500
      removed outlier: 3.859A  pdb=" N   VAL A 499 " --> pdb=" O   ASP A 495 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   TRP A 500 " --> pdb=" O   ASP A 496 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 495 through 500'
    Processing helix  chain 'A' and resid 502 through 506
    Processing helix  chain 'A' and resid 577 through 604
      removed outlier: 3.697A  pdb=" N   ILE A 581 " --> pdb=" O   ASP A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 613
    Processing helix  chain 'A' and resid 614 through 630
    Processing helix  chain 'A' and resid 631 through 637
      removed outlier: 3.662A  pdb=" N   ALA A 637 " --> pdb=" O   PHE A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 673
      removed outlier: 4.241A  pdb=" N   CYS A 644 " --> pdb=" O   LYS A 640 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   TYR A 645 " --> pdb=" O   GLN A 641 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ILE A 651 " --> pdb=" O   GLN A 647 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   GLY A 652 " --> pdb=" O   ARG A 648 " (cutoff:3.500A)
      Proline residue:  A 655  - end of helix
      removed outlier: 4.298A  pdb=" N   SER A 658 " --> pdb=" O   SER A 654 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   TYR A 659 " --> pdb=" O   PRO A 655 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ALA A 661 " --> pdb=" O   MET A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 689 through 715
      removed outlier: 3.523A  pdb=" N   GLN A 693 " --> pdb=" O   SER A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 737 through 761
      Proline residue:  A 743  - end of helix
      removed outlier: 4.044A  pdb=" N   LEU A 749 " --> pdb=" O   GLY A 745 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   LEU A 750 " --> pdb=" O   TYR A 746 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ILE A 751 " --> pdb=" O   ASN A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 765 through 793
      removed outlier: 3.582A  pdb=" N   ASN A 769 " --> pdb=" O   PRO A 765 " (cutoff:3.500A)
      removed outlier: 5.647A  pdb=" N   ALA A 771 " --> pdb=" O   ASN A 767 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   LYS A 772 " --> pdb=" O   PHE A 768 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   TYR A 773 " --> pdb=" O   ASN A 769 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   MET A 778 " --> pdb=" O   ILE A 774 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   TYR A 779 " --> pdb=" O   ALA A 775 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   THR A 780 " --> pdb=" O   PHE A 776 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   THR A 781 " --> pdb=" O   THR A 777 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   VAL A 789 " --> pdb=" O   TRP A 785 " (cutoff:3.500A)
      Proline residue:  A 790  - end of helix
    Processing helix  chain 'A' and resid 797 through 816
      removed outlier: 3.927A  pdb=" N   VAL A 806 " --> pdb=" O   MET A 802 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   SER A 807 " --> pdb=" O   CYS A 803 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 818 through 827
    Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 31
      removed outlier: 6.262A  pdb=" N   ILE B  37 " --> pdb=" O   GLU B  94 " (cutoff:3.500A)
      removed outlier: 7.642A  pdb=" N   ARG B  96 " --> pdb=" O   ILE B  37 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   ALA B  39 " --> pdb=" O   ARG B  96 " (cutoff:3.500A)
      removed outlier: 7.284A  pdb=" N   ILE B  36 " --> pdb=" O   ILE B 143 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   GLY B 145 " --> pdb=" O   ILE B  36 " (cutoff:3.500A)
      removed outlier: 8.617A  pdb=" N   ILE B 170 " --> pdb=" O   VAL B 144 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   VAL B 146 " --> pdb=" O   ILE B 170 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 213 through 216
      removed outlier: 7.768A  pdb=" N   VAL B 214 " --> pdb=" O   ALA B 243 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   SER B 245 " --> pdb=" O   VAL B 214 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ALA B 216 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 273 through 276
      removed outlier: 6.291A  pdb=" N   VAL B 274 " --> pdb=" O   LEU B 302 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ILE B 327 " --> pdb=" O   GLY B 303 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE B 468 " --> pdb=" O   GLY B 485 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLY B 485 " --> pdb=" O   ILE B 468 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 445 through 447
    Processing sheet with id=AA5, first strand: chain 'B' and resid 471 through 475
      removed outlier: 3.570A  pdb=" N   LYS B 472 " --> pdb=" O   ASP B 480 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ASP B 480 " --> pdb=" O   LYS B 472 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   TYR B 478 " --> pdb=" O   MET B 474 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 520 through 522
    Processing sheet with id=AA7, first strand: chain 'B' and resid 541 through 543
    Processing sheet with id=AA8, first strand: chain 'B' and resid 556 through 558
    Processing sheet with id=AA9, first strand: chain 'B' and resid 719 through 722
      removed outlier: 3.609A  pdb=" N   ASP B 722 " --> pdb=" O   TYR B 730 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 29 through 31
      removed outlier: 6.258A  pdb=" N   ILE A  37 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
      removed outlier: 7.643A  pdb=" N   ARG A  96 " --> pdb=" O   ILE A  37 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   ALA A  39 " --> pdb=" O   ARG A  96 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   ILE A  36 " --> pdb=" O   ILE A 143 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   GLY A 145 " --> pdb=" O   ILE A  36 " (cutoff:3.500A)
      removed outlier: 8.639A  pdb=" N   ILE A 170 " --> pdb=" O   VAL A 144 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   VAL A 146 " --> pdb=" O   ILE A 170 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 213 through 216
      removed outlier: 7.759A  pdb=" N   VAL A 214 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   SER A 245 " --> pdb=" O   VAL A 214 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ALA A 216 " --> pdb=" O   SER A 245 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'A' and resid 274 through 276
      removed outlier: 3.714A  pdb=" N   ILE A 327 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   THR A 326 " --> pdb=" O   MET A 469 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LYS A 472 " --> pdb=" O   ASP A 480 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ASP A 480 " --> pdb=" O   LYS A 472 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   TYR A 478 " --> pdb=" O   MET A 474 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 274 through 276
      removed outlier: 3.714A  pdb=" N   ILE A 327 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   THR A 326 " --> pdb=" O   MET A 469 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE A 468 " --> pdb=" O   GLY A 485 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLY A 485 " --> pdb=" O   ILE A 468 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 445 through 447
    Processing sheet with id=AB6, first strand: chain 'A' and resid 520 through 522
    Processing sheet with id=AB7, first strand: chain 'A' and resid 541 through 543
    Processing sheet with id=AB8, first strand: chain 'A' and resid 556 through 558
    Processing sheet with id=AB9, first strand: chain 'A' and resid 719 through 722
      removed outlier: 3.606A  pdb=" N   ASP A 722 " --> pdb=" O   TYR A 730 " (cutoff:3.500A)

    534 hydrogen bonds defined for protein.
    1527 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.07

  Time building geometry restraints manager: 3.37 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 1887
        1.27 -     1.41: 3001
        1.41 -     1.55: 6857
        1.55 -     1.68: 11
        1.68 -     1.82: 162
  Bond restraints: 11918
  Sorted by residual:
  bond pdb=" C19 YKU B 901 "
       pdb=" C21 YKU B 901 "
    ideal  model  delta    sigma   weight residual
    1.429  1.527 -0.098 2.00e-02 2.50e+03 2.38e+01
  bond pdb=" C19 YKU A 901 "
       pdb=" C21 YKU A 901 "
    ideal  model  delta    sigma   weight residual
    1.429  1.526 -0.097 2.00e-02 2.50e+03 2.36e+01
  bond pdb=" C13 YKU A 901 "
       pdb=" N12 YKU A 901 "
    ideal  model  delta    sigma   weight residual
    1.359  1.454 -0.095 2.00e-02 2.50e+03 2.24e+01
  bond pdb=" C13 YKU B 901 "
       pdb=" N12 YKU B 901 "
    ideal  model  delta    sigma   weight residual
    1.359  1.453 -0.094 2.00e-02 2.50e+03 2.22e+01
  bond pdb=" C04 YKU B 901 "
       pdb=" C07 YKU B 901 "
    ideal  model  delta    sigma   weight residual
    1.465  1.528 -0.063 2.00e-02 2.50e+03 9.87e+00
  ... (remaining 11913 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 15964
        2.00 -     4.00: 222
        4.00 -     6.00: 19
        6.00 -     7.99: 3
        7.99 -     9.99: 2
  Bond angle restraints: 16210
  Sorted by residual:
  angle pdb=" CB  LYS B  51 "
        pdb=" CG  LYS B  51 "
        pdb=" CD  LYS B  51 "
      ideal   model   delta    sigma   weight residual
     111.30  117.90   -6.60 2.30e+00 1.89e-01 8.23e+00
  angle pdb=" CA  LEU B 295 "
        pdb=" CB  LEU B 295 "
        pdb=" CG  LEU B 295 "
      ideal   model   delta    sigma   weight residual
     116.30  126.29   -9.99 3.50e+00 8.16e-02 8.15e+00
  angle pdb=" CB  ARG B 114 "
        pdb=" CG  ARG B 114 "
        pdb=" CD  ARG B 114 "
      ideal   model   delta    sigma   weight residual
     111.30  104.76    6.54 2.30e+00 1.89e-01 8.09e+00
  angle pdb=" CB  MET A 474 "
        pdb=" CG  MET A 474 "
        pdb=" SD  MET A 474 "
      ideal   model   delta    sigma   weight residual
     112.70  121.19   -8.49 3.00e+00 1.11e-01 8.01e+00
  angle pdb=" CB  LYS A  51 "
        pdb=" CG  LYS A  51 "
        pdb=" CD  LYS A  51 "
      ideal   model   delta    sigma   weight residual
     111.30  117.26   -5.96 2.30e+00 1.89e-01 6.71e+00
  ... (remaining 16205 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 6401
       17.97 -    35.94: 567
       35.94 -    53.91: 105
       53.91 -    71.88: 20
       71.88 -    89.85: 3
  Dihedral angle restraints: 7096
    sinusoidal: 2638
      harmonic: 4458
  Sorted by residual:
  dihedral pdb=" CB  CYS A 511 "
           pdb=" SG  CYS A 511 "
           pdb=" SG  CYS A 531 "
           pdb=" CB  CYS A 531 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  135.61  -42.61     1      1.00e+01 1.00e-02 2.53e+01
  dihedral pdb=" CB  CYS B 419 "
           pdb=" SG  CYS B 419 "
           pdb=" SG  CYS B 426 "
           pdb=" CB  CYS B 426 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -44.07  -41.93     1      1.00e+01 1.00e-02 2.46e+01
  dihedral pdb=" CB  CYS B 511 "
           pdb=" SG  CYS B 511 "
           pdb=" SG  CYS B 531 "
           pdb=" CB  CYS B 531 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.68  -41.68     1      1.00e+01 1.00e-02 2.43e+01
  ... (remaining 7093 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1000
       0.027 -    0.054: 531
       0.054 -    0.082: 203
       0.082 -    0.109: 84
       0.109 -    0.136: 34
  Chirality restraints: 1852
  Sorted by residual:
  chirality pdb=" CA  ILE B 568 "
            pdb=" N   ILE B 568 "
            pdb=" C   ILE B 568 "
            pdb=" CB  ILE B 568 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.63e-01
  chirality pdb=" CA  ILE A 568 "
            pdb=" N   ILE A 568 "
            pdb=" C   ILE A 568 "
            pdb=" CB  ILE A 568 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.53e-01
  chirality pdb=" CA  VAL B 217 "
            pdb=" N   VAL B 217 "
            pdb=" C   VAL B 217 "
            pdb=" CB  VAL B 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.23e-01
  ... (remaining 1849 not shown)

  Planarity restraints: 2058
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 789 "    0.024 5.00e-02 4.00e+02   3.61e-02 2.09e+00
        pdb=" N   PRO A 790 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 790 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 790 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 789 "   -0.023 5.00e-02 4.00e+02   3.49e-02 1.94e+00
        pdb=" N   PRO B 790 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO B 790 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 790 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 764 "    0.020 5.00e-02 4.00e+02   3.06e-02 1.50e+00
        pdb=" N   PRO A 765 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 765 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 765 "    0.017 5.00e-02 4.00e+02
  ... (remaining 2055 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 791
        2.74 -     3.28: 11449
        3.28 -     3.82: 18007
        3.82 -     4.36: 19638
        4.36 -     4.90: 36335
  Nonbonded interactions: 86220
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 152 "
            pdb=" OG  SER B 176 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OG  SER A 152 "
            pdb=" OG  SER A 176 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   ARG B 435 "
            pdb=" NH1 ARG B 435 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" O   ARG A 435 "
            pdb=" NH1 ARG A 435 "
     model   vdw
     2.229 3.120
  nonbonded pdb=" O   GLY A 253 "
            pdb=" OG  SER A 256 "
     model   vdw
     2.274 3.040
  ... (remaining 86215 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 26 through 515 or (resid 516 through 517 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 518 through 827 or resid 901))
  selection = (chain 'B' and (resid 26 through 378 or (resid 379 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 380 through 552 or (resid 553 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 554 through 559 or (resid 5 \ 
60 through 561 and (name N or name CA or name C or name O or name CB )) or resid \ 
 562 through 827 or resid 901))
}

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:             3.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.100
  Set scattering table:                    0.110
  Process input model:                     30.570
  Find NCS groups from input model:        0.570
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
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      :  0.003   0.098  11934  Z= 0.169
  Angle     :  0.564   9.992  16242  Z= 0.290
  Chirality :  0.041   0.136   1852
  Planarity :  0.003   0.036   2058
  Dihedral  : 13.807  89.854   4184
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.00 (0.23), residues: 1522
  helix:  1.52 (0.21), residues: 648
  sheet: -1.22 (0.42), residues: 172
  loop : -1.14 (0.24), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 487 
 HIS   0.004   0.001   HIS B  30 
 PHE   0.013   0.001   PHE B 544 
 TYR   0.010   0.001   TYR B 223 
 ARG   0.013   0.001   ARG B 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14829 (  527)
  hydrogen bonds       : angle       5.56016 ( 1527)
  SS BOND              : bond        0.00179 (   16)
  SS BOND              : angle       1.03347 (   32)
  covalent geometry    : bond        0.00350 (11918)
  covalent geometry    : angle       0.56267 (16210)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 1.168 
Fit side-chains
   revert: symmetry clash
REVERT: B  657 MET cc_start: 0.6699 (ptm) cc_final: 0.6420 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.2045
  time to fit residues: 47.4425
Evaluate side-chains
  124 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    6.9990
   chunk 115 optimal weight:    3.9990
   chunk 63 optimal weight:    9.9990
   chunk 39 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 119 optimal weight:    3.9990
   chunk 46 optimal weight:    6.9990
   chunk 72 optimal weight:    0.9990
   chunk 88 optimal weight:    2.9990
   chunk 138 optimal weight:    9.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 747 ASN
A 747 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.138287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.112875 restraints weight = 21889.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.112329 restraints weight = 17166.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.113158 restraints weight = 16817.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.1400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.060  11934  Z= 0.333
  Angle     :  0.736   6.799  16242  Z= 0.387
  Chirality :  0.049   0.164   1852
  Planarity :  0.005   0.071   2058
  Dihedral  :  5.353  34.235   1662
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 11.23 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.22), residues: 1522
  helix:  1.10 (0.21), residues: 662
  sheet: -1.51 (0.40), residues: 182
  loop : -1.44 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 487 
 HIS   0.006   0.002   HIS B  30 
 PHE   0.020   0.002   PHE A 712 
 TYR   0.020   0.002   TYR B 340 
 ARG   0.009   0.001   ARG B 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06688 (  527)
  hydrogen bonds       : angle       4.70499 ( 1527)
  SS BOND              : bond        0.00406 (   16)
  SS BOND              : angle       1.31531 (   32)
  covalent geometry    : bond        0.00804 (11918)
  covalent geometry    : angle       0.73415 (16210)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 130
  time to evaluate  : 1.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 GLU cc_start: 0.6333 (mt-10) cc_final: 0.6111 (mt-10)
  outliers start: 21
  outliers final: 12
  residues processed: 142
  average time/residue: 0.2201
  time to fit residues: 46.1375
Evaluate side-chains
  136 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 1.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  548 THR
Chi-restraints excluded: chain B residue  554 LEU
Chi-restraints excluded: chain B residue  669 ILE
Chi-restraints excluded: chain B residue  742 THR
Chi-restraints excluded: chain A residue  389 THR
Chi-restraints excluded: chain A residue  547 TYR
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  669 ILE
Chi-restraints excluded: chain A residue  742 THR
Chi-restraints excluded: chain A residue  747 ASN
Chi-restraints excluded: chain A residue  808 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 135 optimal weight:    0.9980
   chunk 56 optimal weight:    8.9990
   chunk 79 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 66 optimal weight:    0.7980
   chunk 74 optimal weight:    0.6980
   chunk 104 optimal weight:    0.2980
   chunk 87 optimal weight:    0.6980
   chunk 101 optimal weight:    0.6980
   chunk 97 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 571 GLN
A 571 GLN
A 747 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.143376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.118338 restraints weight = 22029.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.117837 restraints weight = 15958.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.118889 restraints weight = 14733.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.1239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  11934  Z= 0.108
  Angle     :  0.511   5.486  16242  Z= 0.268
  Chirality :  0.041   0.147   1852
  Planarity :  0.003   0.032   2058
  Dihedral  :  4.616  29.426   1662
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 11.97 %
    Favored  : 85.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.22), residues: 1522
  helix:  1.60 (0.21), residues: 654
  sheet: -1.38 (0.40), residues: 184
  loop : -1.17 (0.24), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 336 
 HIS   0.003   0.001   HIS B  30 
 PHE   0.019   0.001   PHE A 712 
 TYR   0.012   0.001   TYR A 629 
 ARG   0.006   0.000   ARG B 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04090 (  527)
  hydrogen bonds       : angle       4.05722 ( 1527)
  SS BOND              : bond        0.00240 (   16)
  SS BOND              : angle       1.04262 (   32)
  covalent geometry    : bond        0.00236 (11918)
  covalent geometry    : angle       0.50919 (16210)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 1.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  688 MET cc_start: 0.6823 (mmt) cc_final: 0.6484 (mmt)
REVERT: A  416 MET cc_start: 0.7979 (ttp) cc_final: 0.7746 (ttp)
  outliers start: 27
  outliers final: 13
  residues processed: 149
  average time/residue: 0.2098
  time to fit residues: 47.0075
Evaluate side-chains
  139 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 126
  time to evaluate  : 1.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  548 THR
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  669 ILE
Chi-restraints excluded: chain A residue  234 MET
Chi-restraints excluded: chain A residue  389 THR
Chi-restraints excluded: chain A residue  547 TYR
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  669 ILE
Chi-restraints excluded: chain A residue  747 ASN
Chi-restraints excluded: chain A residue  808 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 19 optimal weight:    7.9990
   chunk 130 optimal weight:    3.9990
   chunk 81 optimal weight:    0.1980
   chunk 75 optimal weight:    4.9990
   chunk 95 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 119 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 145 optimal weight:    0.9980
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 747 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.141115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.115721 restraints weight = 22044.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.115029 restraints weight = 17254.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.115893 restraints weight = 16996.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11934  Z= 0.185
  Angle     :  0.566   5.912  16242  Z= 0.295
  Chirality :  0.043   0.150   1852
  Planarity :  0.004   0.037   2058
  Dihedral  :  4.661  25.242   1662
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.28 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.22), residues: 1522
  helix:  1.53 (0.21), residues: 654
  sheet: -1.52 (0.39), residues: 184
  loop : -1.23 (0.24), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 487 
 HIS   0.006   0.001   HIS A 218 
 PHE   0.026   0.002   PHE A 712 
 TYR   0.018   0.001   TYR A 629 
 ARG   0.006   0.000   ARG B 524 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04879 (  527)
  hydrogen bonds       : angle       4.05437 ( 1527)
  SS BOND              : bond        0.00259 (   16)
  SS BOND              : angle       0.92740 (   32)
  covalent geometry    : bond        0.00442 (11918)
  covalent geometry    : angle       0.56551 (16210)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 129
  time to evaluate  : 1.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  657 MET cc_start: 0.7235 (ptm) cc_final: 0.6845 (ptt)
  outliers start: 25
  outliers final: 17
  residues processed: 146
  average time/residue: 0.2003
  time to fit residues: 44.1341
Evaluate side-chains
  144 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 1.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  547 TYR
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  664 THR
Chi-restraints excluded: chain B residue  669 ILE
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  389 THR
Chi-restraints excluded: chain A residue  547 TYR
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  629 TYR
Chi-restraints excluded: chain A residue  657 MET
Chi-restraints excluded: chain A residue  669 ILE
Chi-restraints excluded: chain A residue  747 ASN
Chi-restraints excluded: chain A residue  808 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 132 optimal weight:    9.9990
   chunk 96 optimal weight:    3.9990
   chunk 128 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 119 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 110 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 747 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.139385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.113836 restraints weight = 22032.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.112950 restraints weight = 17305.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.113894 restraints weight = 16998.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051  11934  Z= 0.250
  Angle     :  0.630   8.558  16242  Z= 0.330
  Chirality :  0.045   0.153   1852
  Planarity :  0.004   0.050   2058
  Dihedral  :  4.887  22.669   1662
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 15.94 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.22), residues: 1522
  helix:  1.35 (0.21), residues: 654
  sheet: -1.73 (0.38), residues: 184
  loop : -1.35 (0.23), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 487 
 HIS   0.007   0.002   HIS B 218 
 PHE   0.027   0.002   PHE A 712 
 TYR   0.021   0.002   TYR A 340 
 ARG   0.006   0.001   ARG B 524 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05577 (  527)
  hydrogen bonds       : angle       4.20355 ( 1527)
  SS BOND              : bond        0.00306 (   16)
  SS BOND              : angle       1.03241 (   32)
  covalent geometry    : bond        0.00601 (11918)
  covalent geometry    : angle       0.62885 (16210)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 131
  time to evaluate  : 1.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  474 MET cc_start: 0.8139 (mmp) cc_final: 0.7894 (mmp)
REVERT: A   79 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7732 (tt)
  outliers start: 37
  outliers final: 30
  residues processed: 157
  average time/residue: 0.2006
  time to fit residues: 47.6896
Evaluate side-chains
  160 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 129
  time to evaluate  : 1.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  507 ILE
Chi-restraints excluded: chain B residue  547 TYR
Chi-restraints excluded: chain B residue  548 THR
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  591 LEU
Chi-restraints excluded: chain B residue  629 TYR
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  664 THR
Chi-restraints excluded: chain B residue  669 ILE
Chi-restraints excluded: chain B residue  672 ILE
Chi-restraints excluded: chain B residue  742 THR
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  389 THR
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  547 TYR
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  629 TYR
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  657 MET
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  669 ILE
Chi-restraints excluded: chain A residue  742 THR
Chi-restraints excluded: chain A residue  808 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 56 optimal weight:    9.9990
   chunk 18 optimal weight:    0.4980
   chunk 133 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 85 optimal weight:    0.3980
   chunk 147 optimal weight:    3.9990
   chunk 109 optimal weight:    7.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 571 GLN
A 571 GLN
A 747 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.143239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.117848 restraints weight = 22109.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.117049 restraints weight = 16333.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.117867 restraints weight = 18656.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.1604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11934  Z= 0.112
  Angle     :  0.516   9.313  16242  Z= 0.267
  Chirality :  0.041   0.152   1852
  Planarity :  0.003   0.040   2058
  Dihedral  :  4.356  20.995   1662
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 16.68 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.22), residues: 1522
  helix:  1.57 (0.21), residues: 658
  sheet: -1.38 (0.40), residues: 180
  loop : -1.13 (0.24), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 336 
 HIS   0.003   0.001   HIS A 218 
 PHE   0.023   0.001   PHE A 712 
 TYR   0.019   0.001   TYR A 340 
 ARG   0.007   0.000   ARG B 524 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03808 (  527)
  hydrogen bonds       : angle       3.79410 ( 1527)
  SS BOND              : bond        0.00228 (   16)
  SS BOND              : angle       0.84758 (   32)
  covalent geometry    : bond        0.00256 (11918)
  covalent geometry    : angle       0.51517 (16210)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 140
  time to evaluate  : 1.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  429 MET cc_start: 0.6851 (ttm) cc_final: 0.6556 (ttm)
REVERT: B  474 MET cc_start: 0.8054 (mmp) cc_final: 0.7838 (mmp)
REVERT: B  601 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.6587 (t80)
REVERT: B  688 MET cc_start: 0.6788 (mmt) cc_final: 0.6436 (mmt)
REVERT: A  601 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.6598 (t80)
  outliers start: 36
  outliers final: 26
  residues processed: 166
  average time/residue: 0.2117
  time to fit residues: 52.2744
Evaluate side-chains
  159 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 131
  time to evaluate  : 1.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  249 TYR
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  547 TYR
Chi-restraints excluded: chain B residue  548 THR
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  591 LEU
Chi-restraints excluded: chain B residue  601 PHE
Chi-restraints excluded: chain B residue  629 TYR
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  653 LEU
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  664 THR
Chi-restraints excluded: chain B residue  669 ILE
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  389 THR
Chi-restraints excluded: chain A residue  547 TYR
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  601 PHE
Chi-restraints excluded: chain A residue  629 TYR
Chi-restraints excluded: chain A residue  634 CYS
Chi-restraints excluded: chain A residue  657 MET
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  669 ILE
Chi-restraints excluded: chain A residue  747 ASN
Chi-restraints excluded: chain A residue  777 THR
Chi-restraints excluded: chain A residue  808 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 115 optimal weight:    0.8980
   chunk 34 optimal weight:    5.9990
   chunk 56 optimal weight:   10.0000
   chunk 122 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 110 optimal weight:    0.0030
   chunk 147 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 114 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.6990

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

Flipped N/Q/H residues before XYZ refinement:
B 571 GLN
A 571 GLN
A 747 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.143616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.118521 restraints weight = 22282.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.117927 restraints weight = 16945.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.118952 restraints weight = 15839.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.1640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  11934  Z= 0.112
  Angle     :  0.526  12.423  16242  Z= 0.267
  Chirality :  0.041   0.149   1852
  Planarity :  0.003   0.037   2058
  Dihedral  :  4.196  19.505   1662
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 17.18 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.22), residues: 1522
  helix:  1.61 (0.21), residues: 660
  sheet: -1.28 (0.40), residues: 180
  loop : -1.07 (0.24), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 575 
 HIS   0.003   0.001   HIS A 218 
 PHE   0.029   0.001   PHE A 712 
 TYR   0.018   0.001   TYR A 629 
 ARG   0.009   0.000   ARG B 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03781 (  527)
  hydrogen bonds       : angle       3.69717 ( 1527)
  SS BOND              : bond        0.00205 (   16)
  SS BOND              : angle       0.76163 (   32)
  covalent geometry    : bond        0.00261 (11918)
  covalent geometry    : angle       0.52566 (16210)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 136
  time to evaluate  : 1.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  474 MET cc_start: 0.8061 (mmp) cc_final: 0.7824 (mmp)
REVERT: B  601 PHE cc_start: 0.7566 (OUTLIER) cc_final: 0.6638 (t80)
REVERT: B  657 MET cc_start: 0.7238 (ptm) cc_final: 0.6806 (ptt)
REVERT: B  688 MET cc_start: 0.6733 (mmt) cc_final: 0.6389 (mmt)
REVERT: A   79 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7815 (tt)
REVERT: A  601 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.6603 (t80)
REVERT: A  788 PHE cc_start: 0.6758 (OUTLIER) cc_final: 0.6470 (t80)
  outliers start: 38
  outliers final: 29
  residues processed: 165
  average time/residue: 0.2033
  time to fit residues: 50.7906
Evaluate side-chains
  163 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 130
  time to evaluate  : 1.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  547 TYR
Chi-restraints excluded: chain B residue  548 THR
Chi-restraints excluded: chain B residue  571 GLN
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  601 PHE
Chi-restraints excluded: chain B residue  625 ILE
Chi-restraints excluded: chain B residue  629 TYR
Chi-restraints excluded: chain B residue  653 LEU
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  664 THR
Chi-restraints excluded: chain B residue  669 ILE
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  389 THR
Chi-restraints excluded: chain A residue  547 TYR
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  571 GLN
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  601 PHE
Chi-restraints excluded: chain A residue  629 TYR
Chi-restraints excluded: chain A residue  634 CYS
Chi-restraints excluded: chain A residue  657 MET
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  669 ILE
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  747 ASN
Chi-restraints excluded: chain A residue  777 THR
Chi-restraints excluded: chain A residue  788 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 116 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 132 optimal weight:    0.9980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 747 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.142798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.117478 restraints weight = 22128.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.116525 restraints weight = 16624.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.117374 restraints weight = 17934.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11934  Z= 0.141
  Angle     :  0.550  13.550  16242  Z= 0.279
  Chirality :  0.042   0.148   1852
  Planarity :  0.004   0.042   2058
  Dihedral  :  4.240  18.488   1662
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 17.01 %
    Favored  : 79.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.22), residues: 1522
  helix:  1.58 (0.20), residues: 660
  sheet: -1.30 (0.40), residues: 180
  loop : -1.08 (0.24), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 575 
 HIS   0.004   0.001   HIS B 218 
 PHE   0.027   0.001   PHE A 712 
 TYR   0.018   0.001   TYR A 629 
 ARG   0.008   0.000   ARG B 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04087 (  527)
  hydrogen bonds       : angle       3.72842 ( 1527)
  SS BOND              : bond        0.00227 (   16)
  SS BOND              : angle       0.78378 (   32)
  covalent geometry    : bond        0.00337 (11918)
  covalent geometry    : angle       0.54904 (16210)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 129
  time to evaluate  : 1.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7652 (tt)
REVERT: B  474 MET cc_start: 0.8098 (mmp) cc_final: 0.7848 (mmp)
REVERT: B  601 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.6615 (t80)
REVERT: B  657 MET cc_start: 0.7247 (ptm) cc_final: 0.6972 (ptt)
REVERT: B  688 MET cc_start: 0.6767 (mmt) cc_final: 0.6349 (mmt)
REVERT: A   79 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7811 (tt)
REVERT: A  601 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.6580 (t80)
  outliers start: 41
  outliers final: 29
  residues processed: 161
  average time/residue: 0.2046
  time to fit residues: 49.9764
Evaluate side-chains
  158 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 125
  time to evaluate  : 1.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   79 ILE
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  548 THR
Chi-restraints excluded: chain B residue  554 LEU
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  591 LEU
Chi-restraints excluded: chain B residue  601 PHE
Chi-restraints excluded: chain B residue  625 ILE
Chi-restraints excluded: chain B residue  629 TYR
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  653 LEU
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  664 THR
Chi-restraints excluded: chain B residue  669 ILE
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  389 THR
Chi-restraints excluded: chain A residue  547 TYR
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  601 PHE
Chi-restraints excluded: chain A residue  629 TYR
Chi-restraints excluded: chain A residue  634 CYS
Chi-restraints excluded: chain A residue  657 MET
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  669 ILE
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  747 ASN
Chi-restraints excluded: chain A residue  777 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 148 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 132 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 112 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
A 571 GLN
A 747 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.143382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.118153 restraints weight = 22074.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.117081 restraints weight = 16903.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.117946 restraints weight = 18191.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11934  Z= 0.121
  Angle     :  0.546  14.194  16242  Z= 0.273
  Chirality :  0.041   0.149   1852
  Planarity :  0.004   0.036   2058
  Dihedral  :  4.171  17.965   1662
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 17.01 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.22), residues: 1522
  helix:  1.61 (0.20), residues: 660
  sheet: -1.25 (0.40), residues: 180
  loop : -1.07 (0.24), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 575 
 HIS   0.003   0.001   HIS B 218 
 PHE   0.026   0.001   PHE A 712 
 TYR   0.017   0.001   TYR A 629 
 ARG   0.007   0.000   ARG B 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03889 (  527)
  hydrogen bonds       : angle       3.67071 ( 1527)
  SS BOND              : bond        0.00214 (   16)
  SS BOND              : angle       0.77995 (   32)
  covalent geometry    : bond        0.00285 (11918)
  covalent geometry    : angle       0.54524 (16210)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 131
  time to evaluate  : 1.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7662 (tt)
REVERT: B  474 MET cc_start: 0.8113 (mmp) cc_final: 0.7879 (mmp)
REVERT: B  601 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.6599 (t80)
REVERT: B  688 MET cc_start: 0.6745 (mmt) cc_final: 0.6400 (mmt)
REVERT: A   79 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7826 (tt)
REVERT: A  601 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.6539 (t80)
  outliers start: 40
  outliers final: 32
  residues processed: 161
  average time/residue: 0.2080
  time to fit residues: 51.2764
Evaluate side-chains
  163 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 127
  time to evaluate  : 1.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   79 ILE
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  547 TYR
Chi-restraints excluded: chain B residue  548 THR
Chi-restraints excluded: chain B residue  554 LEU
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  591 LEU
Chi-restraints excluded: chain B residue  601 PHE
Chi-restraints excluded: chain B residue  625 ILE
Chi-restraints excluded: chain B residue  629 TYR
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  653 LEU
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  664 THR
Chi-restraints excluded: chain B residue  669 ILE
Chi-restraints excluded: chain B residue  672 ILE
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  389 THR
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  571 GLN
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  601 PHE
Chi-restraints excluded: chain A residue  629 TYR
Chi-restraints excluded: chain A residue  634 CYS
Chi-restraints excluded: chain A residue  657 MET
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  669 ILE
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  747 ASN
Chi-restraints excluded: chain A residue  777 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 136 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 122 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   chunk 137 optimal weight:    0.7980
   chunk 56 optimal weight:   20.0000
   chunk 48 optimal weight:    7.9990
   chunk 143 optimal weight:    0.8980
   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 747 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.143672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.118348 restraints weight = 21872.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.117753 restraints weight = 15993.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.118637 restraints weight = 15156.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11934  Z= 0.116
  Angle     :  0.545  14.290  16242  Z= 0.272
  Chirality :  0.041   0.148   1852
  Planarity :  0.004   0.058   2058
  Dihedral  :  4.147  20.377   1662
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 17.67 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.22), residues: 1522
  helix:  1.62 (0.20), residues: 660
  sheet: -1.23 (0.40), residues: 180
  loop : -1.05 (0.24), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 575 
 HIS   0.003   0.001   HIS B  30 
 PHE   0.026   0.001   PHE A 712 
 TYR   0.018   0.001   TYR A 629 
 ARG   0.007   0.000   ARG B 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03809 (  527)
  hydrogen bonds       : angle       3.66335 ( 1527)
  SS BOND              : bond        0.00207 (   16)
  SS BOND              : angle       0.76215 (   32)
  covalent geometry    : bond        0.00272 (11918)
  covalent geometry    : angle       0.54432 (16210)

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

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

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3044 Ramachandran restraints generated.
    1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 130
  time to evaluate  : 1.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7661 (tt)
REVERT: B  474 MET cc_start: 0.8099 (mmp) cc_final: 0.7875 (mmp)
REVERT: B  601 PHE cc_start: 0.7513 (OUTLIER) cc_final: 0.6595 (t80)
REVERT: B  625 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.7886 (mt)
REVERT: B  688 MET cc_start: 0.6725 (mmt) cc_final: 0.6385 (mmt)
REVERT: A   79 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7820 (tt)
REVERT: A  601 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.6545 (t80)
  outliers start: 37
  outliers final: 31
  residues processed: 160
  average time/residue: 0.2007
  time to fit residues: 49.4527
Evaluate side-chains
  163 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 127
  time to evaluate  : 1.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   79 ILE
Chi-restraints excluded: chain B residue  389 THR
Chi-restraints excluded: chain B residue  547 TYR
Chi-restraints excluded: chain B residue  548 THR
Chi-restraints excluded: chain B residue  554 LEU
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  591 LEU
Chi-restraints excluded: chain B residue  601 PHE
Chi-restraints excluded: chain B residue  625 ILE
Chi-restraints excluded: chain B residue  629 TYR
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  653 LEU
Chi-restraints excluded: chain B residue  663 VAL
Chi-restraints excluded: chain B residue  664 THR
Chi-restraints excluded: chain B residue  669 ILE
Chi-restraints excluded: chain B residue  672 ILE
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  326 THR
Chi-restraints excluded: chain A residue  389 THR
Chi-restraints excluded: chain A residue  547 TYR
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  571 GLN
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  601 PHE
Chi-restraints excluded: chain A residue  629 TYR
Chi-restraints excluded: chain A residue  634 CYS
Chi-restraints excluded: chain A residue  657 MET
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  669 ILE
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  777 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 150 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 84 optimal weight:    1.9990
   chunk 124 optimal weight:    8.9990
   chunk 5 optimal weight:    6.9990
   chunk 137 optimal weight:    0.9990
   chunk 88 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 571 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.142774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.117501 restraints weight = 21912.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.116481 restraints weight = 16791.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.117234 restraints weight = 18472.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11934  Z= 0.136
  Angle     :  0.558  13.630  16242  Z= 0.280
  Chirality :  0.042   0.148   1852
  Planarity :  0.004   0.044   2058
  Dihedral  :  4.180  19.987   1662
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 17.84 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.22), residues: 1522
  helix:  1.56 (0.20), residues: 666
  sheet: -1.39 (0.39), residues: 184
  loop : -1.05 (0.24), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 575 
 HIS   0.004   0.001   HIS B 218 
 PHE   0.026   0.001   PHE A 712 
 TYR   0.018   0.001   TYR A 629 
 ARG   0.008   0.000   ARG B 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04116 (  527)
  hydrogen bonds       : angle       3.69444 ( 1527)
  SS BOND              : bond        0.00220 (   16)
  SS BOND              : angle       0.78717 (   32)
  covalent geometry    : bond        0.00325 (11918)
  covalent geometry    : angle       0.55708 (16210)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3458.83 seconds
wall clock time: 60 minutes 34.33 seconds (3634.33 seconds total)