Starting phenix.real_space_refine
on Sun Aug 24 15:54:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9flv_50540/08_2025/9flv_50540.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9flv_50540/08_2025/9flv_50540.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9flv_50540/08_2025/9flv_50540.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9flv_50540/08_2025/9flv_50540.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9flv_50540/08_2025/9flv_50540.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9flv_50540/08_2025/9flv_50540.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.126
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      98      5.16       5
     C   12852      2.51       5
     N    3416      2.21       5
     O    4452      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 20818
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2974
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 2974
          Classifications: {'peptide': 415}
          Link IDs: {'PTRANS': 30, 'TRANS': 384}
    Chain: "B"
      Number of atoms: 2974
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 2974
          Classifications: {'peptide': 415}
          Link IDs: {'PTRANS': 30, 'TRANS': 384}
    Chain: "C"
      Number of atoms: 2974
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 2974
          Classifications: {'peptide': 415}
          Link IDs: {'PTRANS': 30, 'TRANS': 384}
    Chain: "D"
      Number of atoms: 2974
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 2974
          Classifications: {'peptide': 415}
          Link IDs: {'PTRANS': 30, 'TRANS': 384}
    Chain: "E"
      Number of atoms: 2974
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 2974
          Classifications: {'peptide': 415}
          Link IDs: {'PTRANS': 30, 'TRANS': 384}
    Chain: "F"
      Number of atoms: 2974
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 2974
          Classifications: {'peptide': 415}
          Link IDs: {'PTRANS': 30, 'TRANS': 384}
    Chain: "G"
      Number of atoms: 2974
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 2974
          Classifications: {'peptide': 415}
          Link IDs: {'PTRANS': 30, 'TRANS': 384}
  Time building chain proxies: 4.35, per 1000 atoms: 0.21
  Number of scatterers: 20818
  At special positions: 0
  Unit cell: (94.785, 95.85, 222.585, 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      98     16.00
     O    4452      8.00
     N    3416      7.00
     C   12852      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A2490 " - pdb=" SG  CYS A2629 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A2656 " - pdb=" SG  CYS A2796 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B2490 " - pdb=" SG  CYS B2629 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B2656 " - pdb=" SG  CYS B2796 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C2490 " - pdb=" SG  CYS C2629 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C2656 " - pdb=" SG  CYS C2796 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D2490 " - pdb=" SG  CYS D2629 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D2656 " - pdb=" SG  CYS D2796 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E2490 " - pdb=" SG  CYS E2629 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E2656 " - pdb=" SG  CYS E2796 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F2490 " - pdb=" SG  CYS F2629 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F2656 " - pdb=" SG  CYS F2796 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G2490 " - pdb=" SG  CYS G2629 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G2656 " - pdb=" SG  CYS G2796 " 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: 1.26
  Conformation dependent library (CDL) restraints added in 711.4 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  5782 Ramachandran restraints generated.
    2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5432

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 70 sheets defined
      3.1% alpha, 32.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2446 through 2450
    Processing helix  chain 'A' and resid 2677 through 2679
      No H-bonds generated for 'chain 'A' and resid 2677 through 2679'
    Processing helix  chain 'A' and resid 2694 through 2698
    Processing helix  chain 'B' and resid 2446 through 2450
    Processing helix  chain 'B' and resid 2677 through 2679
      No H-bonds generated for 'chain 'B' and resid 2677 through 2679'
    Processing helix  chain 'B' and resid 2694 through 2698
    Processing helix  chain 'C' and resid 2446 through 2450
    Processing helix  chain 'C' and resid 2677 through 2679
      No H-bonds generated for 'chain 'C' and resid 2677 through 2679'
    Processing helix  chain 'C' and resid 2694 through 2698
    Processing helix  chain 'D' and resid 2446 through 2450
    Processing helix  chain 'D' and resid 2677 through 2679
      No H-bonds generated for 'chain 'D' and resid 2677 through 2679'
    Processing helix  chain 'D' and resid 2694 through 2698
    Processing helix  chain 'E' and resid 2446 through 2450
    Processing helix  chain 'E' and resid 2677 through 2679
      No H-bonds generated for 'chain 'E' and resid 2677 through 2679'
    Processing helix  chain 'E' and resid 2694 through 2698
    Processing helix  chain 'F' and resid 2446 through 2450
    Processing helix  chain 'F' and resid 2677 through 2679
      No H-bonds generated for 'chain 'F' and resid 2677 through 2679'
    Processing helix  chain 'F' and resid 2694 through 2698
    Processing helix  chain 'G' and resid 2446 through 2450
    Processing helix  chain 'G' and resid 2677 through 2679
      No H-bonds generated for 'chain 'G' and resid 2677 through 2679'
    Processing helix  chain 'G' and resid 2694 through 2698
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2405 through 2408
      removed outlier: 6.677A  pdb=" N   PHE A2405 " --> pdb=" O   THR A2473 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   ASN A2475 " --> pdb=" O   PHE A2405 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL A2407 " --> pdb=" O   ASN A2475 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 2483 through 2485
    Processing sheet with id=AA3, first strand: chain 'A' and resid 2488 through 2490
      removed outlier: 6.855A  pdb=" N   ILE A2489 " --> pdb=" O   ASN A2560 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 2567 through 2568
    Processing sheet with id=AA5, first strand: chain 'A' and resid 2579 through 2580
    Processing sheet with id=AA6, first strand: chain 'A' and resid 2602 through 2604
      removed outlier: 6.808A  pdb=" N   TRP A2593 " --> pdb=" O   ILE A2603 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 2602 through 2604
      removed outlier: 6.808A  pdb=" N   TRP A2593 " --> pdb=" O   ILE A2603 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 2653 through 2656
      removed outlier: 6.799A  pdb=" N   PHE A2653 " --> pdb=" O   GLY A2721 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   ASN A2723 " --> pdb=" O   PHE A2653 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   VAL A2655 " --> pdb=" O   ASN A2723 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 2731 through 2732
    Processing sheet with id=AB1, first strand: chain 'A' and resid 2763 through 2766
      removed outlier: 4.856A  pdb=" N   THR A2753 " --> pdb=" O   GLN A2791 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   GLN A2791 " --> pdb=" O   THR A2753 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 2405 through 2408
      removed outlier: 6.677A  pdb=" N   PHE B2405 " --> pdb=" O   THR B2473 " (cutoff:3.500A)
      removed outlier: 7.778A  pdb=" N   ASN B2475 " --> pdb=" O   PHE B2405 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   VAL B2407 " --> pdb=" O   ASN B2475 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 2483 through 2485
    Processing sheet with id=AB4, first strand: chain 'B' and resid 2488 through 2490
      removed outlier: 6.855A  pdb=" N   ILE B2489 " --> pdb=" O   ASN B2560 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 2567 through 2568
    Processing sheet with id=AB6, first strand: chain 'B' and resid 2579 through 2580
    Processing sheet with id=AB7, first strand: chain 'B' and resid 2602 through 2604
      removed outlier: 6.809A  pdb=" N   TRP B2593 " --> pdb=" O   ILE B2603 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 2602 through 2604
      removed outlier: 6.809A  pdb=" N   TRP B2593 " --> pdb=" O   ILE B2603 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 2653 through 2656
      removed outlier: 6.800A  pdb=" N   PHE B2653 " --> pdb=" O   GLY B2721 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   ASN B2723 " --> pdb=" O   PHE B2653 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   VAL B2655 " --> pdb=" O   ASN B2723 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 2731 through 2732
    Processing sheet with id=AC2, first strand: chain 'B' and resid 2763 through 2766
      removed outlier: 4.856A  pdb=" N   THR B2753 " --> pdb=" O   GLN B2791 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   GLN B2791 " --> pdb=" O   THR B2753 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 2405 through 2408
      removed outlier: 6.676A  pdb=" N   PHE C2405 " --> pdb=" O   THR C2473 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   ASN C2475 " --> pdb=" O   PHE C2405 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL C2407 " --> pdb=" O   ASN C2475 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 2483 through 2485
    Processing sheet with id=AC5, first strand: chain 'C' and resid 2488 through 2490
      removed outlier: 6.855A  pdb=" N   ILE C2489 " --> pdb=" O   ASN C2560 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 2567 through 2568
    Processing sheet with id=AC7, first strand: chain 'C' and resid 2579 through 2580
    Processing sheet with id=AC8, first strand: chain 'C' and resid 2602 through 2604
      removed outlier: 6.808A  pdb=" N   TRP C2593 " --> pdb=" O   ILE C2603 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'C' and resid 2602 through 2604
      removed outlier: 6.808A  pdb=" N   TRP C2593 " --> pdb=" O   ILE C2603 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'C' and resid 2653 through 2656
      removed outlier: 6.799A  pdb=" N   PHE C2653 " --> pdb=" O   GLY C2721 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   ASN C2723 " --> pdb=" O   PHE C2653 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   VAL C2655 " --> pdb=" O   ASN C2723 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'C' and resid 2731 through 2732
    Processing sheet with id=AD3, first strand: chain 'C' and resid 2763 through 2766
      removed outlier: 4.856A  pdb=" N   THR C2753 " --> pdb=" O   GLN C2791 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   GLN C2791 " --> pdb=" O   THR C2753 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'D' and resid 2405 through 2408
      removed outlier: 6.677A  pdb=" N   PHE D2405 " --> pdb=" O   THR D2473 " (cutoff:3.500A)
      removed outlier: 7.776A  pdb=" N   ASN D2475 " --> pdb=" O   PHE D2405 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL D2407 " --> pdb=" O   ASN D2475 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'D' and resid 2483 through 2485
    Processing sheet with id=AD6, first strand: chain 'D' and resid 2488 through 2490
      removed outlier: 6.855A  pdb=" N   ILE D2489 " --> pdb=" O   ASN D2560 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'D' and resid 2567 through 2568
    Processing sheet with id=AD8, first strand: chain 'D' and resid 2579 through 2580
    Processing sheet with id=AD9, first strand: chain 'D' and resid 2602 through 2604
      removed outlier: 6.808A  pdb=" N   TRP D2593 " --> pdb=" O   ILE D2603 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'D' and resid 2602 through 2604
      removed outlier: 6.808A  pdb=" N   TRP D2593 " --> pdb=" O   ILE D2603 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'D' and resid 2653 through 2656
      removed outlier: 6.800A  pdb=" N   PHE D2653 " --> pdb=" O   GLY D2721 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   ASN D2723 " --> pdb=" O   PHE D2653 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   VAL D2655 " --> pdb=" O   ASN D2723 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'D' and resid 2731 through 2732
    Processing sheet with id=AE4, first strand: chain 'D' and resid 2763 through 2766
      removed outlier: 4.856A  pdb=" N   THR D2753 " --> pdb=" O   GLN D2791 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   GLN D2791 " --> pdb=" O   THR D2753 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'E' and resid 2405 through 2408
      removed outlier: 6.677A  pdb=" N   PHE E2405 " --> pdb=" O   THR E2473 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   ASN E2475 " --> pdb=" O   PHE E2405 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL E2407 " --> pdb=" O   ASN E2475 " (cutoff:3.500A)
    Processing sheet with id=AE6, first strand: chain 'E' and resid 2483 through 2485
    Processing sheet with id=AE7, first strand: chain 'E' and resid 2488 through 2490
      removed outlier: 6.855A  pdb=" N   ILE E2489 " --> pdb=" O   ASN E2560 " (cutoff:3.500A)
    Processing sheet with id=AE8, first strand: chain 'E' and resid 2567 through 2568
    Processing sheet with id=AE9, first strand: chain 'E' and resid 2579 through 2580
    Processing sheet with id=AF1, first strand: chain 'E' and resid 2602 through 2604
      removed outlier: 6.808A  pdb=" N   TRP E2593 " --> pdb=" O   ILE E2603 " (cutoff:3.500A)
    Processing sheet with id=AF2, first strand: chain 'E' and resid 2602 through 2604
      removed outlier: 6.808A  pdb=" N   TRP E2593 " --> pdb=" O   ILE E2603 " (cutoff:3.500A)
    Processing sheet with id=AF3, first strand: chain 'E' and resid 2653 through 2656
      removed outlier: 6.799A  pdb=" N   PHE E2653 " --> pdb=" O   GLY E2721 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   ASN E2723 " --> pdb=" O   PHE E2653 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   VAL E2655 " --> pdb=" O   ASN E2723 " (cutoff:3.500A)
    Processing sheet with id=AF4, first strand: chain 'E' and resid 2731 through 2732
    Processing sheet with id=AF5, first strand: chain 'E' and resid 2763 through 2766
      removed outlier: 4.855A  pdb=" N   THR E2753 " --> pdb=" O   GLN E2791 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   GLN E2791 " --> pdb=" O   THR E2753 " (cutoff:3.500A)
    Processing sheet with id=AF6, first strand: chain 'F' and resid 2405 through 2408
      removed outlier: 6.677A  pdb=" N   PHE F2405 " --> pdb=" O   THR F2473 " (cutoff:3.500A)
      removed outlier: 7.778A  pdb=" N   ASN F2475 " --> pdb=" O   PHE F2405 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   VAL F2407 " --> pdb=" O   ASN F2475 " (cutoff:3.500A)
    Processing sheet with id=AF7, first strand: chain 'F' and resid 2483 through 2485
    Processing sheet with id=AF8, first strand: chain 'F' and resid 2488 through 2490
      removed outlier: 6.855A  pdb=" N   ILE F2489 " --> pdb=" O   ASN F2560 " (cutoff:3.500A)
    Processing sheet with id=AF9, first strand: chain 'F' and resid 2567 through 2568
    Processing sheet with id=AG1, first strand: chain 'F' and resid 2579 through 2580
    Processing sheet with id=AG2, first strand: chain 'F' and resid 2602 through 2604
      removed outlier: 6.808A  pdb=" N   TRP F2593 " --> pdb=" O   ILE F2603 " (cutoff:3.500A)
    Processing sheet with id=AG3, first strand: chain 'F' and resid 2602 through 2604
      removed outlier: 6.808A  pdb=" N   TRP F2593 " --> pdb=" O   ILE F2603 " (cutoff:3.500A)
    Processing sheet with id=AG4, first strand: chain 'F' and resid 2653 through 2656
      removed outlier: 6.800A  pdb=" N   PHE F2653 " --> pdb=" O   GLY F2721 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   ASN F2723 " --> pdb=" O   PHE F2653 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   VAL F2655 " --> pdb=" O   ASN F2723 " (cutoff:3.500A)
    Processing sheet with id=AG5, first strand: chain 'F' and resid 2731 through 2732
    Processing sheet with id=AG6, first strand: chain 'F' and resid 2763 through 2766
      removed outlier: 4.857A  pdb=" N   THR F2753 " --> pdb=" O   GLN F2791 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   GLN F2791 " --> pdb=" O   THR F2753 " (cutoff:3.500A)
    Processing sheet with id=AG7, first strand: chain 'G' and resid 2405 through 2408
      removed outlier: 6.677A  pdb=" N   PHE G2405 " --> pdb=" O   THR G2473 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   ASN G2475 " --> pdb=" O   PHE G2405 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL G2407 " --> pdb=" O   ASN G2475 " (cutoff:3.500A)
    Processing sheet with id=AG8, first strand: chain 'G' and resid 2483 through 2485
    Processing sheet with id=AG9, first strand: chain 'G' and resid 2488 through 2490
      removed outlier: 6.854A  pdb=" N   ILE G2489 " --> pdb=" O   ASN G2560 " (cutoff:3.500A)
    Processing sheet with id=AH1, first strand: chain 'G' and resid 2567 through 2568
    Processing sheet with id=AH2, first strand: chain 'G' and resid 2579 through 2580
    Processing sheet with id=AH3, first strand: chain 'G' and resid 2602 through 2604
      removed outlier: 6.808A  pdb=" N   TRP G2593 " --> pdb=" O   ILE G2603 " (cutoff:3.500A)
    Processing sheet with id=AH4, first strand: chain 'G' and resid 2602 through 2604
      removed outlier: 6.808A  pdb=" N   TRP G2593 " --> pdb=" O   ILE G2603 " (cutoff:3.500A)
    Processing sheet with id=AH5, first strand: chain 'G' and resid 2653 through 2656
      removed outlier: 6.799A  pdb=" N   PHE G2653 " --> pdb=" O   GLY G2721 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   ASN G2723 " --> pdb=" O   PHE G2653 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   VAL G2655 " --> pdb=" O   ASN G2723 " (cutoff:3.500A)
    Processing sheet with id=AH6, first strand: chain 'G' and resid 2731 through 2732
    Processing sheet with id=AH7, first strand: chain 'G' and resid 2763 through 2766
      removed outlier: 4.856A  pdb=" N   THR G2753 " --> pdb=" O   GLN G2791 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   GLN G2791 " --> pdb=" O   THR G2753 " (cutoff:3.500A)

    672 hydrogen bonds defined for protein.
    1512 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: 3.81

  Time building geometry restraints manager: 1.63 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 3749
        1.30 -     1.43: 5301
        1.43 -     1.56: 12017
        1.56 -     1.69: 73
        1.69 -     1.82: 126
  Bond restraints: 21266
  Sorted by residual:
  bond pdb=" CA  SER C2434 "
       pdb=" CB  SER C2434 "
    ideal  model  delta    sigma   weight residual
    1.532  1.441  0.092 1.68e-02 3.54e+03 2.98e+01
  bond pdb=" CA  SER D2434 "
       pdb=" CB  SER D2434 "
    ideal  model  delta    sigma   weight residual
    1.532  1.441  0.092 1.68e-02 3.54e+03 2.97e+01
  bond pdb=" CA  SER A2434 "
       pdb=" CB  SER A2434 "
    ideal  model  delta    sigma   weight residual
    1.532  1.441  0.092 1.68e-02 3.54e+03 2.97e+01
  bond pdb=" CA  SER F2434 "
       pdb=" CB  SER F2434 "
    ideal  model  delta    sigma   weight residual
    1.532  1.441  0.092 1.68e-02 3.54e+03 2.97e+01
  bond pdb=" CA  SER G2434 "
       pdb=" CB  SER G2434 "
    ideal  model  delta    sigma   weight residual
    1.532  1.441  0.091 1.68e-02 3.54e+03 2.96e+01
  ... (remaining 21261 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.44: 25216
        2.44 -     4.89: 3284
        4.89 -     7.33: 802
        7.33 -     9.78: 126
        9.78 -    12.22: 35
  Bond angle restraints: 29463
  Sorted by residual:
  angle pdb=" CA  PHE B2405 "
        pdb=" CB  PHE B2405 "
        pdb=" CG  PHE B2405 "
      ideal   model   delta    sigma   weight residual
     113.80  122.73   -8.93 1.00e+00 1.00e+00 7.98e+01
  angle pdb=" CA  PHE D2405 "
        pdb=" CB  PHE D2405 "
        pdb=" CG  PHE D2405 "
      ideal   model   delta    sigma   weight residual
     113.80  122.72   -8.92 1.00e+00 1.00e+00 7.96e+01
  angle pdb=" CA  PHE G2405 "
        pdb=" CB  PHE G2405 "
        pdb=" CG  PHE G2405 "
      ideal   model   delta    sigma   weight residual
     113.80  122.72   -8.92 1.00e+00 1.00e+00 7.96e+01
  angle pdb=" CA  PHE A2405 "
        pdb=" CB  PHE A2405 "
        pdb=" CG  PHE A2405 "
      ideal   model   delta    sigma   weight residual
     113.80  122.71   -8.91 1.00e+00 1.00e+00 7.94e+01
  angle pdb=" CA  PHE E2405 "
        pdb=" CB  PHE E2405 "
        pdb=" CG  PHE E2405 "
      ideal   model   delta    sigma   weight residual
     113.80  122.70   -8.90 1.00e+00 1.00e+00 7.92e+01
  ... (remaining 29458 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 12278
       17.85 -    35.70: 224
       35.70 -    53.55: 77
       53.55 -    71.40: 0
       71.40 -    89.25: 14
  Dihedral angle restraints: 12593
    sinusoidal: 4179
      harmonic: 8414
  Sorted by residual:
  dihedral pdb=" CB  CYS F2656 "
           pdb=" SG  CYS F2656 "
           pdb=" SG  CYS F2796 "
           pdb=" CB  CYS F2796 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.51  -52.51     1      1.00e+01 1.00e-02 3.76e+01
  dihedral pdb=" CB  CYS C2656 "
           pdb=" SG  CYS C2656 "
           pdb=" SG  CYS C2796 "
           pdb=" CB  CYS C2796 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.49  -52.49     1      1.00e+01 1.00e-02 3.75e+01
  dihedral pdb=" CB  CYS B2656 "
           pdb=" SG  CYS B2656 "
           pdb=" SG  CYS B2796 "
           pdb=" CB  CYS B2796 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.49  -52.49     1      1.00e+01 1.00e-02 3.75e+01
  ... (remaining 12590 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 2631
       0.084 -    0.168: 785
       0.168 -    0.253: 203
       0.253 -    0.337: 63
       0.337 -    0.421: 21
  Chirality restraints: 3703
  Sorted by residual:
  chirality pdb=" CB  VAL E2807 "
            pdb=" CA  VAL E2807 "
            pdb=" CG1 VAL E2807 "
            pdb=" CG2 VAL E2807 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -3.05    0.42 2.00e-01 2.50e+01 4.43e+00
  chirality pdb=" CB  VAL A2807 "
            pdb=" CA  VAL A2807 "
            pdb=" CG1 VAL A2807 "
            pdb=" CG2 VAL A2807 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -3.05    0.42 2.00e-01 2.50e+01 4.39e+00
  chirality pdb=" CB  VAL B2807 "
            pdb=" CA  VAL B2807 "
            pdb=" CG1 VAL B2807 "
            pdb=" CG2 VAL B2807 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -3.05    0.42 2.00e-01 2.50e+01 4.38e+00
  ... (remaining 3700 not shown)

  Planarity restraints: 3864
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C2753 "   -0.028 2.00e-02 2.50e+03   5.57e-02 3.10e+01
        pdb=" C   THR C2753 "    0.096 2.00e-02 2.50e+03
        pdb=" O   THR C2753 "   -0.036 2.00e-02 2.50e+03
        pdb=" N   PHE C2754 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B2753 "   -0.028 2.00e-02 2.50e+03   5.56e-02 3.10e+01
        pdb=" C   THR B2753 "    0.096 2.00e-02 2.50e+03
        pdb=" O   THR B2753 "   -0.036 2.00e-02 2.50e+03
        pdb=" N   PHE B2754 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR F2753 "    0.028 2.00e-02 2.50e+03   5.56e-02 3.09e+01
        pdb=" C   THR F2753 "   -0.096 2.00e-02 2.50e+03
        pdb=" O   THR F2753 "    0.036 2.00e-02 2.50e+03
        pdb=" N   PHE F2754 "    0.032 2.00e-02 2.50e+03
  ... (remaining 3861 not shown)

  Histogram of nonbonded interaction distances:
        1.20 -     1.94: 14
        1.94 -     2.68: 1057
        2.68 -     3.42: 27815
        3.42 -     4.16: 51739
        4.16 -     4.90: 84631
  Nonbonded interactions: 165256
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG B2755 "
            pdb=" OD2 ASP B2763 "
     model   vdw
     1.202 3.120
  nonbonded pdb=" NH2 ARG F2755 "
            pdb=" OD2 ASP F2763 "
     model   vdw
     1.202 3.120
  nonbonded pdb=" NH2 ARG A2755 "
            pdb=" OD2 ASP A2763 "
     model   vdw
     1.203 3.120
  nonbonded pdb=" NH2 ARG D2755 "
            pdb=" OD2 ASP D2763 "
     model   vdw
     1.203 3.120
  nonbonded pdb=" NH2 ARG E2755 "
            pdb=" OD2 ASP E2763 "
     model   vdw
     1.203 3.120
  ... (remaining 165251 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.130
  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:             0.020
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.260
  Find NCS groups from input model:        0.150
  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:             0.010
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
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      :  0.018   0.120  21280  Z= 0.996
  Angle     :  1.887  12.220  29491  Z= 1.303
  Chirality :  0.095   0.421   3703
  Planarity :  0.013   0.221   3864
  Dihedral  :  8.987  89.246   7119
  Min Nonbonded Distance : 1.202

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.52 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.14), residues: 2891
  helix:  None (None), residues: 0
  sheet:  1.67 (0.15), residues: 980
  loop :  0.50 (0.13), residues: 1911

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG F2755 
 TYR   0.082   0.010   TYR B2393 
 PHE   0.039   0.010   PHE F2405 
 TRP   0.052   0.010   TRP B2674 
 HIS   0.006   0.004   HIS F2641 

Details of bonding type rmsd
  covalent geometry    : bond        0.01814 (21266)
  covalent geometry    : angle       1.88740 (29463)
  SS BOND              : bond        0.00547 (   14)
  SS BOND              : angle       0.90276 (   28)
  hydrogen bonds       : bond        0.17888 (  623)
  hydrogen bonds       : angle       8.00491 ( 1512)

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

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

  5782 Ramachandran restraints generated.
    2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5782 Ramachandran restraints generated.
    2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  422 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 422
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2412 ASP cc_start: 0.7969 (m-30) cc_final: 0.7714 (m-30)
REVERT: A 2608 ASN cc_start: 0.8887 (m110) cc_final: 0.8290 (m-40)
REVERT: A 2610 THR cc_start: 0.8817 (m) cc_final: 0.8589 (p)
REVERT: A 2634 VAL cc_start: 0.8399 (t) cc_final: 0.8083 (m)
REVERT: A 2772 MET cc_start: 0.6756 (ttm) cc_final: 0.6128 (pmm)
REVERT: B 2420 VAL cc_start: 0.8892 (t) cc_final: 0.8677 (m)
REVERT: B 2483 MET cc_start: 0.8360 (ttm) cc_final: 0.8128 (ttt)
REVERT: B 2772 MET cc_start: 0.6887 (ttm) cc_final: 0.6362 (pmm)
REVERT: C 2420 VAL cc_start: 0.8962 (t) cc_final: 0.8693 (m)
REVERT: C 2444 ASN cc_start: 0.8339 (t0) cc_final: 0.8131 (t0)
REVERT: C 2483 MET cc_start: 0.8281 (ttm) cc_final: 0.8051 (ttt)
REVERT: C 2625 THR cc_start: 0.8729 (m) cc_final: 0.8480 (p)
REVERT: C 2772 MET cc_start: 0.6803 (ttm) cc_final: 0.6359 (pmm)
REVERT: D 2420 VAL cc_start: 0.8899 (t) cc_final: 0.8668 (m)
REVERT: D 2496 VAL cc_start: 0.8708 (t) cc_final: 0.8491 (p)
REVERT: D 2772 MET cc_start: 0.6899 (ttm) cc_final: 0.6470 (pmm)
REVERT: E 2420 VAL cc_start: 0.8862 (t) cc_final: 0.8660 (m)
REVERT: E 2483 MET cc_start: 0.8399 (ttm) cc_final: 0.8117 (ttt)
REVERT: E 2608 ASN cc_start: 0.8865 (m110) cc_final: 0.8590 (m-40)
REVERT: E 2610 THR cc_start: 0.8742 (m) cc_final: 0.8428 (p)
REVERT: E 2625 THR cc_start: 0.8688 (m) cc_final: 0.8404 (p)
REVERT: E 2772 MET cc_start: 0.6741 (ttm) cc_final: 0.6303 (pmm)
REVERT: F 2772 MET cc_start: 0.6459 (ttm) cc_final: 0.6167 (pmm)
REVERT: G 2420 VAL cc_start: 0.8996 (t) cc_final: 0.8747 (m)
REVERT: G 2608 ASN cc_start: 0.8851 (m110) cc_final: 0.8542 (m-40)
REVERT: G 2678 ASN cc_start: 0.8318 (m-40) cc_final: 0.7878 (t0)
REVERT: G 2772 MET cc_start: 0.6679 (ttm) cc_final: 0.6122 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 422
  average time/residue: 0.0844
  time to fit residues: 61.5070
Evaluate side-chains
  194 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 197 optimal weight:    6.9990
   chunk 215 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 132 optimal weight:    2.9990
   chunk 261 optimal weight:    0.8980
   chunk 248 optimal weight:    6.9990
   chunk 207 optimal weight:    6.9990
   chunk 155 optimal weight:    0.9990
   chunk 244 optimal weight:    5.9990
   chunk 183 optimal weight:    0.9980
   chunk 111 optimal weight:    1.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A2760 ASN
B2582 ASN
B2608 ASN
B2760 ASN
C2438 ASN
C2461 ASN
C2608 ASN
C2760 ASN
D2582 ASN
D2608 ASN
D2760 ASN
E2760 ASN
F2444 ASN
F2760 ASN
G2760 ASN
G2795 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.138040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.104098 restraints weight = 25770.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.102058 restraints weight = 41186.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.103366 restraints weight = 41316.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.103736 restraints weight = 26309.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.103984 restraints weight = 23399.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  21280  Z= 0.145
  Angle     :  0.577   6.295  29491  Z= 0.317
  Chirality :  0.048   0.183   3703
  Planarity :  0.005   0.031   3864
  Dihedral  :  4.654  18.151   3010
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  :  6.16 %
    Favored  : 91.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.15), residues: 2891
  helix:  None (None), residues: 0
  sheet:  1.30 (0.15), residues: 1085
  loop :  0.31 (0.14), residues: 1806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D2755 
 TYR   0.014   0.001   TYR C2672 
 PHE   0.019   0.003   PHE B2704 
 TRP   0.018   0.002   TRP F2674 
 HIS   0.002   0.001   HIS G2641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (21266)
  covalent geometry    : angle       0.57535 (29463)
  SS BOND              : bond        0.00302 (   14)
  SS BOND              : angle       1.49708 (   28)
  hydrogen bonds       : bond        0.04405 (  623)
  hydrogen bonds       : angle       5.95959 ( 1512)

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

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

  5782 Ramachandran restraints generated.
    2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5782 Ramachandran restraints generated.
    2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 243
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2393 TYR cc_start: 0.6978 (OUTLIER) cc_final: 0.6224 (t80)
REVERT: A 2520 SER cc_start: 0.8531 (t) cc_final: 0.8166 (p)
REVERT: A 2678 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8311 (t0)
REVERT: A 2772 MET cc_start: 0.6513 (ttm) cc_final: 0.6253 (pmm)
REVERT: B 2393 TYR cc_start: 0.6897 (OUTLIER) cc_final: 0.5994 (t80)
REVERT: B 2461 ASN cc_start: 0.7992 (m-40) cc_final: 0.7293 (m-40)
REVERT: B 2504 ASN cc_start: 0.7838 (m-40) cc_final: 0.7598 (t0)
REVERT: B 2520 SER cc_start: 0.8668 (t) cc_final: 0.8342 (p)
REVERT: C 2393 TYR cc_start: 0.7227 (OUTLIER) cc_final: 0.5916 (t80)
REVERT: C 2497 MET cc_start: 0.8690 (mtm) cc_final: 0.8320 (mtm)
REVERT: C 2634 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8403 (m)
REVERT: D 2393 TYR cc_start: 0.6881 (OUTLIER) cc_final: 0.5993 (t80)
REVERT: D 2461 ASN cc_start: 0.7962 (m-40) cc_final: 0.7335 (m-40)
REVERT: D 2520 SER cc_start: 0.8545 (t) cc_final: 0.8252 (p)
REVERT: D 2772 MET cc_start: 0.6879 (ttm) cc_final: 0.6498 (pmm)
REVERT: E 2393 TYR cc_start: 0.6638 (OUTLIER) cc_final: 0.5748 (t80)
REVERT: E 2461 ASN cc_start: 0.7915 (m-40) cc_final: 0.7333 (m-40)
REVERT: F 2393 TYR cc_start: 0.6697 (OUTLIER) cc_final: 0.5776 (t80)
REVERT: F 2405 PHE cc_start: 0.7672 (m-80) cc_final: 0.7468 (m-10)
REVERT: F 2461 ASN cc_start: 0.7792 (m-40) cc_final: 0.7354 (m-40)
REVERT: F 2520 SER cc_start: 0.8522 (t) cc_final: 0.8279 (p)
REVERT: F 2582 ASN cc_start: 0.8030 (t0) cc_final: 0.7742 (m-40)
REVERT: G 2393 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6465 (t80)
REVERT: G 2461 ASN cc_start: 0.7901 (m-40) cc_final: 0.7251 (m-40)
REVERT: G 2483 MET cc_start: 0.8099 (ttt) cc_final: 0.7690 (ttt)
REVERT: G 2504 ASN cc_start: 0.7713 (m-40) cc_final: 0.7460 (t0)
REVERT: G 2520 SER cc_start: 0.8424 (t) cc_final: 0.8196 (p)
REVERT: G 2765 ILE cc_start: 0.9286 (mp) cc_final: 0.9015 (mt)
REVERT: G 2795 ASN cc_start: 0.8313 (t160) cc_final: 0.8110 (t0)
  outliers start: 50
  outliers final: 20
  residues processed: 279
  average time/residue: 0.0805
  time to fit residues: 39.8981
Evaluate side-chains
  173 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 144
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2393 TYR
Chi-restraints excluded: chain A residue 2408 CYS
Chi-restraints excluded: chain A residue 2678 ASN
Chi-restraints excluded: chain A residue 2787 THR
Chi-restraints excluded: chain B residue 2393 TYR
Chi-restraints excluded: chain B residue 2408 CYS
Chi-restraints excluded: chain B residue 2552 SER
Chi-restraints excluded: chain B residue 2641 HIS
Chi-restraints excluded: chain C residue 2393 TYR
Chi-restraints excluded: chain C residue 2408 CYS
Chi-restraints excluded: chain C residue 2490 CYS
Chi-restraints excluded: chain C residue 2634 VAL
Chi-restraints excluded: chain C residue 2641 HIS
Chi-restraints excluded: chain D residue 2393 TYR
Chi-restraints excluded: chain D residue 2408 CYS
Chi-restraints excluded: chain D residue 2415 LEU
Chi-restraints excluded: chain D residue 2700 SER
Chi-restraints excluded: chain E residue 2393 TYR
Chi-restraints excluded: chain E residue 2408 CYS
Chi-restraints excluded: chain E residue 2552 SER
Chi-restraints excluded: chain E residue 2641 HIS
Chi-restraints excluded: chain E residue 2659 GLU
Chi-restraints excluded: chain E residue 2787 THR
Chi-restraints excluded: chain F residue 2393 TYR
Chi-restraints excluded: chain F residue 2408 CYS
Chi-restraints excluded: chain G residue 2393 TYR
Chi-restraints excluded: chain G residue 2408 CYS
Chi-restraints excluded: chain G residue 2490 CYS
Chi-restraints excluded: chain G residue 2787 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 117 optimal weight:   20.0000
   chunk 136 optimal weight:    0.0060
   chunk 282 optimal weight:    2.9990
   chunk 95 optimal weight:    0.4980
   chunk 141 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 197 optimal weight:    3.9990
   chunk 85 optimal weight:    6.9990
   chunk 79 optimal weight:    1.9990
   chunk 209 optimal weight:    0.7980
   chunk 186 optimal weight:    3.9990
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
A2712 GLN
A2795 ASN
B2607 GLN
B2712 GLN
B2795 ASN
C2795 ASN
D2795 ASN
E2582 ASN
E2607 GLN
E2712 GLN
E2795 ASN
F2712 GLN
F2795 ASN
G2582 ASN
G2607 GLN
G2795 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.138646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.104991 restraints weight = 25329.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.103461 restraints weight = 42153.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.104815 restraints weight = 41346.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.105275 restraints weight = 23782.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.105714 restraints weight = 21099.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.3256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  21280  Z= 0.105
  Angle     :  0.514   5.904  29491  Z= 0.276
  Chirality :  0.045   0.139   3703
  Planarity :  0.005   0.035   3864
  Dihedral  :  4.137  16.738   3010
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  :  8.58 %
    Favored  : 89.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.15), residues: 2891
  helix:  None (None), residues: 0
  sheet:  1.34 (0.15), residues: 1106
  loop :  0.46 (0.14), residues: 1785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D2755 
 TYR   0.009   0.001   TYR C2672 
 PHE   0.021   0.002   PHE B2704 
 TRP   0.015   0.001   TRP B2674 
 HIS   0.002   0.001   HIS E2641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 (21266)
  covalent geometry    : angle       0.51331 (29463)
  SS BOND              : bond        0.00092 (   14)
  SS BOND              : angle       0.94224 (   28)
  hydrogen bonds       : bond        0.03581 (  623)
  hydrogen bonds       : angle       5.34483 ( 1512)

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

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

  5782 Ramachandran restraints generated.
    2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5782 Ramachandran restraints generated.
    2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 167
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
REVERT: A 2393 TYR cc_start: 0.6738 (OUTLIER) cc_final: 0.6165 (t80)
REVERT: A 2461 ASN cc_start: 0.7834 (m-40) cc_final: 0.7359 (m-40)
REVERT: A 2520 SER cc_start: 0.8392 (t) cc_final: 0.8055 (p)
REVERT: A 2745 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8187 (mm)
REVERT: B 2393 TYR cc_start: 0.6705 (OUTLIER) cc_final: 0.5819 (t80)
REVERT: B 2461 ASN cc_start: 0.8001 (m-40) cc_final: 0.7372 (m-40)
REVERT: B 2520 SER cc_start: 0.8602 (t) cc_final: 0.8299 (p)
REVERT: C 2393 TYR cc_start: 0.7035 (OUTLIER) cc_final: 0.5713 (t80)
REVERT: C 2497 MET cc_start: 0.8668 (mtm) cc_final: 0.8271 (mtm)
REVERT: C 2634 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8335 (m)
REVERT: E 2393 TYR cc_start: 0.6676 (OUTLIER) cc_final: 0.5793 (t80)
REVERT: E 2461 ASN cc_start: 0.7885 (m-40) cc_final: 0.7458 (m-40)
REVERT: E 2796 CYS cc_start: 0.6024 (m) cc_final: 0.5705 (m)
REVERT: F 2393 TYR cc_start: 0.6608 (OUTLIER) cc_final: 0.5805 (t80)
REVERT: F 2461 ASN cc_start: 0.7989 (m-40) cc_final: 0.7596 (m-40)
REVERT: G 2393 TYR cc_start: 0.6913 (OUTLIER) cc_final: 0.6065 (t80)
REVERT: G 2461 ASN cc_start: 0.7749 (m-40) cc_final: 0.7398 (m-40)
REVERT: G 2483 MET cc_start: 0.8152 (ttt) cc_final: 0.7724 (ttt)
REVERT: G 2504 ASN cc_start: 0.7813 (m-40) cc_final: 0.7572 (m-40)
REVERT: G 2796 CYS cc_start: 0.6156 (m) cc_final: 0.5757 (m)
  outliers start: 50
  outliers final: 27
  residues processed: 204
  average time/residue: 0.0815
  time to fit residues: 29.7352
Evaluate side-chains
  166 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 131
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2393 TYR
Chi-restraints excluded: chain A residue 2408 CYS
Chi-restraints excluded: chain A residue 2641 HIS
Chi-restraints excluded: chain A residue 2745 LEU
Chi-restraints excluded: chain A residue 2787 THR
Chi-restraints excluded: chain B residue 2393 TYR
Chi-restraints excluded: chain B residue 2408 CYS
Chi-restraints excluded: chain B residue 2552 SER
Chi-restraints excluded: chain B residue 2641 HIS
Chi-restraints excluded: chain C residue 2393 TYR
Chi-restraints excluded: chain C residue 2408 CYS
Chi-restraints excluded: chain C residue 2490 CYS
Chi-restraints excluded: chain C residue 2634 VAL
Chi-restraints excluded: chain C residue 2641 HIS
Chi-restraints excluded: chain C residue 2795 ASN
Chi-restraints excluded: chain D residue 2393 TYR
Chi-restraints excluded: chain D residue 2408 CYS
Chi-restraints excluded: chain D residue 2443 THR
Chi-restraints excluded: chain D residue 2700 SER
Chi-restraints excluded: chain D residue 2705 ILE
Chi-restraints excluded: chain D residue 2795 ASN
Chi-restraints excluded: chain E residue 2393 TYR
Chi-restraints excluded: chain E residue 2408 CYS
Chi-restraints excluded: chain E residue 2490 CYS
Chi-restraints excluded: chain E residue 2552 SER
Chi-restraints excluded: chain E residue 2641 HIS
Chi-restraints excluded: chain E residue 2795 ASN
Chi-restraints excluded: chain F residue 2393 TYR
Chi-restraints excluded: chain F residue 2408 CYS
Chi-restraints excluded: chain F residue 2479 THR
Chi-restraints excluded: chain F residue 2703 LEU
Chi-restraints excluded: chain G residue 2393 TYR
Chi-restraints excluded: chain G residue 2408 CYS
Chi-restraints excluded: chain G residue 2617 ASP
Chi-restraints excluded: chain G residue 2637 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 281 optimal weight:   20.0000
   chunk 28 optimal weight:    2.9990
   chunk 108 optimal weight:    0.9980
   chunk 268 optimal weight:    4.9990
   chunk 171 optimal weight:    0.9990
   chunk 177 optimal weight:    5.9990
   chunk 161 optimal weight:    8.9990
   chunk 14 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   chunk 283 optimal weight:    5.9990
   chunk 276 optimal weight:    7.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A2795 ASN
B2795 ASN
D2461 ASN
F2795 ASN
G2582 ASN
G2678 ASN
G2795 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.131573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.094267 restraints weight = 25847.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.095482 restraints weight = 52973.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.096582 restraints weight = 45053.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.096734 restraints weight = 25501.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.097401 restraints weight = 22642.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.3639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055  21280  Z= 0.249
  Angle     :  0.607   6.689  29491  Z= 0.325
  Chirality :  0.049   0.153   3703
  Planarity :  0.005   0.040   3864
  Dihedral  :  4.710  22.532   3010
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  :  9.58 %
    Favored  : 87.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.14), residues: 2891
  helix:  None (None), residues: 0
  sheet:  1.09 (0.14), residues: 1057
  loop :  0.16 (0.14), residues: 1834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G2755 
 TYR   0.013   0.001   TYR A2532 
 PHE   0.023   0.003   PHE D2704 
 TRP   0.016   0.002   TRP F2674 
 HIS   0.003   0.001   HIS B2641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00603 (21266)
  covalent geometry    : angle       0.60323 (29463)
  SS BOND              : bond        0.00495 (   14)
  SS BOND              : angle       2.13472 (   28)
  hydrogen bonds       : bond        0.04495 (  623)
  hydrogen bonds       : angle       5.36869 ( 1512)

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

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

  5782 Ramachandran restraints generated.
    2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5782 Ramachandran restraints generated.
    2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 140
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
REVERT: A 2393 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.6461 (t80)
REVERT: A 2400 SER cc_start: 0.9096 (t) cc_final: 0.8888 (p)
REVERT: A 2420 VAL cc_start: 0.9251 (t) cc_final: 0.9009 (p)
REVERT: A 2520 SER cc_start: 0.8508 (t) cc_final: 0.8175 (p)
REVERT: A 2556 MET cc_start: 0.7887 (tpp) cc_final: 0.7463 (ttt)
REVERT: A 2678 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8372 (t0)
REVERT: A 2745 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8166 (mm)
REVERT: A 2795 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.8120 (t0)
REVERT: B 2393 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.6093 (t80)
REVERT: B 2420 VAL cc_start: 0.9278 (t) cc_final: 0.8994 (p)
REVERT: B 2461 ASN cc_start: 0.8281 (m-40) cc_final: 0.7623 (m-40)
REVERT: B 2772 MET cc_start: 0.7434 (tpp) cc_final: 0.6039 (pmm)
REVERT: B 2795 ASN cc_start: 0.8244 (OUTLIER) cc_final: 0.8035 (t0)
REVERT: C 2393 TYR cc_start: 0.7143 (OUTLIER) cc_final: 0.5968 (t80)
REVERT: C 2497 MET cc_start: 0.8708 (mtm) cc_final: 0.8358 (mtm)
REVERT: C 2745 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8331 (mm)
REVERT: C 2772 MET cc_start: 0.7325 (tpp) cc_final: 0.5924 (pmm)
REVERT: D 2772 MET cc_start: 0.7699 (tpp) cc_final: 0.6287 (pmm)
REVERT: E 2393 TYR cc_start: 0.6675 (OUTLIER) cc_final: 0.6034 (t80)
REVERT: E 2461 ASN cc_start: 0.8127 (m-40) cc_final: 0.7727 (m-40)
REVERT: E 2772 MET cc_start: 0.7429 (tpp) cc_final: 0.6022 (pmm)
REVERT: F 2393 TYR cc_start: 0.6557 (OUTLIER) cc_final: 0.6054 (t80)
REVERT: F 2461 ASN cc_start: 0.8324 (m-40) cc_final: 0.7953 (m-40)
REVERT: F 2772 MET cc_start: 0.7275 (tpp) cc_final: 0.5903 (pmm)
REVERT: G 2393 TYR cc_start: 0.7002 (OUTLIER) cc_final: 0.6167 (t80)
REVERT: G 2461 ASN cc_start: 0.8187 (m-40) cc_final: 0.7845 (m-40)
REVERT: G 2772 MET cc_start: 0.7586 (tpp) cc_final: 0.6236 (pmm)
REVERT: G 2795 ASN cc_start: 0.8177 (t160) cc_final: 0.7976 (t0)
REVERT: G 2796 CYS cc_start: 0.6462 (m) cc_final: 0.6062 (m)
  outliers start: 65
  outliers final: 34
  residues processed: 189
  average time/residue: 0.0832
  time to fit residues: 28.1647
Evaluate side-chains
  157 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 112
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2393 TYR
Chi-restraints excluded: chain A residue 2408 CYS
Chi-restraints excluded: chain A residue 2678 ASN
Chi-restraints excluded: chain A residue 2745 LEU
Chi-restraints excluded: chain A residue 2795 ASN
Chi-restraints excluded: chain B residue 2393 TYR
Chi-restraints excluded: chain B residue 2408 CYS
Chi-restraints excluded: chain B residue 2549 SER
Chi-restraints excluded: chain B residue 2552 SER
Chi-restraints excluded: chain B residue 2641 HIS
Chi-restraints excluded: chain B residue 2671 SER
Chi-restraints excluded: chain B residue 2795 ASN
Chi-restraints excluded: chain C residue 2393 TYR
Chi-restraints excluded: chain C residue 2408 CYS
Chi-restraints excluded: chain C residue 2490 CYS
Chi-restraints excluded: chain C residue 2496 VAL
Chi-restraints excluded: chain C residue 2549 SER
Chi-restraints excluded: chain C residue 2626 VAL
Chi-restraints excluded: chain C residue 2634 VAL
Chi-restraints excluded: chain C residue 2641 HIS
Chi-restraints excluded: chain C residue 2745 LEU
Chi-restraints excluded: chain D residue 2393 TYR
Chi-restraints excluded: chain D residue 2395 LEU
Chi-restraints excluded: chain D residue 2408 CYS
Chi-restraints excluded: chain D residue 2443 THR
Chi-restraints excluded: chain D residue 2461 ASN
Chi-restraints excluded: chain D residue 2549 SER
Chi-restraints excluded: chain D residue 2603 ILE
Chi-restraints excluded: chain D residue 2700 SER
Chi-restraints excluded: chain D residue 2705 ILE
Chi-restraints excluded: chain E residue 2393 TYR
Chi-restraints excluded: chain E residue 2408 CYS
Chi-restraints excluded: chain E residue 2490 CYS
Chi-restraints excluded: chain E residue 2549 SER
Chi-restraints excluded: chain E residue 2552 SER
Chi-restraints excluded: chain E residue 2659 GLU
Chi-restraints excluded: chain F residue 2393 TYR
Chi-restraints excluded: chain F residue 2408 CYS
Chi-restraints excluded: chain F residue 2479 THR
Chi-restraints excluded: chain F residue 2549 SER
Chi-restraints excluded: chain G residue 2393 TYR
Chi-restraints excluded: chain G residue 2408 CYS
Chi-restraints excluded: chain G residue 2549 SER
Chi-restraints excluded: chain G residue 2617 ASP
Chi-restraints excluded: chain G residue 2637 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 182 optimal weight:    0.6980
   chunk 144 optimal weight:    0.5980
   chunk 221 optimal weight:    4.9990
   chunk 261 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9980
   chunk 81 optimal weight:   20.0000
   chunk 260 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 107 optimal weight:    0.5980
   chunk 205 optimal weight:    8.9990
   chunk 225 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B2607 GLN
C2795 ASN
D2795 ASN
E2795 ASN
F2795 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.135384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.100688 restraints weight = 25430.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.101126 restraints weight = 59501.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.102487 restraints weight = 50819.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.102239 restraints weight = 31710.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.103755 restraints weight = 25936.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.3876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  21280  Z= 0.106
  Angle     :  0.490   6.061  29491  Z= 0.259
  Chirality :  0.045   0.144   3703
  Planarity :  0.005   0.039   3864
  Dihedral  :  4.089  18.361   3010
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 11.33 %
    Favored  : 86.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.14), residues: 2891
  helix:  None (None), residues: 0
  sheet:  1.21 (0.14), residues: 1057
  loop :  0.28 (0.14), residues: 1834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F2755 
 TYR   0.008   0.001   TYR B2672 
 PHE   0.019   0.002   PHE G2704 
 TRP   0.014   0.001   TRP F2674 
 HIS   0.001   0.001   HIS D2641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (21266)
  covalent geometry    : angle       0.48954 (29463)
  SS BOND              : bond        0.00204 (   14)
  SS BOND              : angle       0.95500 (   28)
  hydrogen bonds       : bond        0.03408 (  623)
  hydrogen bonds       : angle       5.02871 ( 1512)

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

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

  5782 Ramachandran restraints generated.
    2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5782 Ramachandran restraints generated.
    2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 155
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
REVERT: A 2393 TYR cc_start: 0.6706 (OUTLIER) cc_final: 0.6099 (t80)
REVERT: A 2420 VAL cc_start: 0.9195 (t) cc_final: 0.8962 (p)
REVERT: A 2461 ASN cc_start: 0.7924 (m-40) cc_final: 0.7521 (m-40)
REVERT: A 2745 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8225 (mm)
REVERT: A 2772 MET cc_start: 0.7340 (tpp) cc_final: 0.5844 (pmm)
REVERT: B 2393 TYR cc_start: 0.6715 (OUTLIER) cc_final: 0.5872 (t80)
REVERT: B 2420 VAL cc_start: 0.9274 (t) cc_final: 0.9013 (p)
REVERT: B 2461 ASN cc_start: 0.8103 (m-40) cc_final: 0.7389 (m-40)
REVERT: B 2772 MET cc_start: 0.7384 (tpp) cc_final: 0.6145 (pmm)
REVERT: C 2497 MET cc_start: 0.8698 (mtm) cc_final: 0.8283 (mtm)
REVERT: C 2745 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8325 (mm)
REVERT: C 2772 MET cc_start: 0.7234 (tpp) cc_final: 0.5947 (pmm)
REVERT: D 2393 TYR cc_start: 0.6212 (OUTLIER) cc_final: 0.4403 (t80)
REVERT: D 2772 MET cc_start: 0.7614 (tpp) cc_final: 0.6322 (pmm)
REVERT: E 2393 TYR cc_start: 0.6748 (OUTLIER) cc_final: 0.5956 (t80)
REVERT: E 2461 ASN cc_start: 0.7955 (m-40) cc_final: 0.7560 (m-40)
REVERT: E 2772 MET cc_start: 0.7276 (tpp) cc_final: 0.5923 (pmm)
REVERT: E 2796 CYS cc_start: 0.6130 (m) cc_final: 0.5826 (m)
REVERT: F 2393 TYR cc_start: 0.6413 (OUTLIER) cc_final: 0.5729 (t80)
REVERT: F 2461 ASN cc_start: 0.8192 (m-40) cc_final: 0.7730 (m-40)
REVERT: F 2772 MET cc_start: 0.7354 (tpp) cc_final: 0.6039 (pmm)
REVERT: G 2393 TYR cc_start: 0.6645 (OUTLIER) cc_final: 0.5690 (t80)
REVERT: G 2461 ASN cc_start: 0.8096 (m-40) cc_final: 0.7600 (m-40)
REVERT: G 2772 MET cc_start: 0.7415 (tpp) cc_final: 0.6252 (pmm)
REVERT: G 2795 ASN cc_start: 0.8292 (t160) cc_final: 0.7955 (t0)
REVERT: G 2796 CYS cc_start: 0.6205 (m) cc_final: 0.5866 (m)
  outliers start: 50
  outliers final: 22
  residues processed: 191
  average time/residue: 0.0842
  time to fit residues: 29.1037
Evaluate side-chains
  156 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 126
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2393 TYR
Chi-restraints excluded: chain A residue 2549 SER
Chi-restraints excluded: chain A residue 2745 LEU
Chi-restraints excluded: chain B residue 2393 TYR
Chi-restraints excluded: chain B residue 2552 SER
Chi-restraints excluded: chain B residue 2641 HIS
Chi-restraints excluded: chain B residue 2671 SER
Chi-restraints excluded: chain C residue 2393 TYR
Chi-restraints excluded: chain C residue 2395 LEU
Chi-restraints excluded: chain C residue 2479 THR
Chi-restraints excluded: chain C residue 2490 CYS
Chi-restraints excluded: chain C residue 2634 VAL
Chi-restraints excluded: chain C residue 2641 HIS
Chi-restraints excluded: chain C residue 2745 LEU
Chi-restraints excluded: chain D residue 2393 TYR
Chi-restraints excluded: chain D residue 2420 VAL
Chi-restraints excluded: chain E residue 2393 TYR
Chi-restraints excluded: chain E residue 2490 CYS
Chi-restraints excluded: chain E residue 2552 SER
Chi-restraints excluded: chain E residue 2641 HIS
Chi-restraints excluded: chain E residue 2659 GLU
Chi-restraints excluded: chain E residue 2705 ILE
Chi-restraints excluded: chain F residue 2393 TYR
Chi-restraints excluded: chain F residue 2549 SER
Chi-restraints excluded: chain F residue 2705 ILE
Chi-restraints excluded: chain F residue 2795 ASN
Chi-restraints excluded: chain G residue 2393 TYR
Chi-restraints excluded: chain G residue 2617 ASP
Chi-restraints excluded: chain G residue 2626 VAL
Chi-restraints excluded: chain G residue 2637 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   chunk 191 optimal weight:    7.9990
   chunk 248 optimal weight:    5.9990
   chunk 68 optimal weight:    7.9990
   chunk 207 optimal weight:    6.9990
   chunk 188 optimal weight:    6.9990
   chunk 220 optimal weight:    5.9990
   chunk 149 optimal weight:    5.9990
   chunk 254 optimal weight:    4.9990
   chunk 128 optimal weight:    7.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
A2533 GLN
A2795 ASN
C2795 ASN
E2607 GLN
E2795 ASN
G2607 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.126196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.089041 restraints weight = 26352.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.089323 restraints weight = 58501.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.090940 restraints weight = 48006.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.090637 restraints weight = 29501.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.092523 restraints weight = 24224.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.4210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.097  21280  Z= 0.499
  Angle     :  0.809   9.652  29491  Z= 0.435
  Chirality :  0.056   0.267   3703
  Planarity :  0.007   0.063   3864
  Dihedral  :  5.663  28.033   3010
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 10.75 %
    Favored  : 85.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.14), residues: 2891
  helix:  None (None), residues: 0
  sheet:  0.06 (0.14), residues: 1064
  loop : -0.44 (0.13), residues: 1827

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C2755 
 TYR   0.023   0.003   TYR D2506 
 PHE   0.027   0.004   PHE C2704 
 TRP   0.017   0.003   TRP F2674 
 HIS   0.004   0.002   HIS B2641 

Details of bonding type rmsd
  covalent geometry    : bond        0.01214 (21266)
  covalent geometry    : angle       0.80177 (29463)
  SS BOND              : bond        0.00980 (   14)
  SS BOND              : angle       3.68344 (   28)
  hydrogen bonds       : bond        0.05661 (  623)
  hydrogen bonds       : angle       5.96273 ( 1512)

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

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

  5782 Ramachandran restraints generated.
    2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5782 Ramachandran restraints generated.
    2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 96
    poor density    : 126
  time to evaluate  : 0.499 
Fit side-chains
REVERT: A 2556 MET cc_start: 0.8037 (tpp) cc_final: 0.7293 (ttt)
REVERT: A 2678 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8534 (t0)
REVERT: A 2745 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8184 (mm)
REVERT: A 2772 MET cc_start: 0.7596 (tpp) cc_final: 0.6080 (pmm)
REVERT: B 2393 TYR cc_start: 0.6928 (OUTLIER) cc_final: 0.6369 (t80)
REVERT: B 2461 ASN cc_start: 0.8470 (m-40) cc_final: 0.7963 (m-40)
REVERT: C 2393 TYR cc_start: 0.6554 (OUTLIER) cc_final: 0.5993 (t80)
REVERT: D 2393 TYR cc_start: 0.6649 (OUTLIER) cc_final: 0.5735 (t80)
REVERT: D 2420 VAL cc_start: 0.9258 (OUTLIER) cc_final: 0.9025 (p)
REVERT: D 2795 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8170 (t0)
REVERT: E 2393 TYR cc_start: 0.6526 (OUTLIER) cc_final: 0.6228 (t80)
REVERT: E 2795 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.8052 (t0)
REVERT: E 2796 CYS cc_start: 0.6351 (m) cc_final: 0.6045 (m)
REVERT: F 2393 TYR cc_start: 0.6781 (OUTLIER) cc_final: 0.6554 (t80)
REVERT: G 2393 TYR cc_start: 0.6660 (OUTLIER) cc_final: 0.5998 (t80)
REVERT: G 2461 ASN cc_start: 0.8498 (m-40) cc_final: 0.8145 (m-40)
REVERT: G 2796 CYS cc_start: 0.6244 (m) cc_final: 0.5944 (m)
  outliers start: 96
  outliers final: 58
  residues processed: 202
  average time/residue: 0.0807
  time to fit residues: 29.2438
Evaluate side-chains
  169 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 100
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2400 SER
Chi-restraints excluded: chain A residue 2408 CYS
Chi-restraints excluded: chain A residue 2515 ASP
Chi-restraints excluded: chain A residue 2549 SER
Chi-restraints excluded: chain A residue 2678 ASN
Chi-restraints excluded: chain A residue 2745 LEU
Chi-restraints excluded: chain B residue 2393 TYR
Chi-restraints excluded: chain B residue 2549 SER
Chi-restraints excluded: chain B residue 2552 SER
Chi-restraints excluded: chain B residue 2603 ILE
Chi-restraints excluded: chain B residue 2671 SER
Chi-restraints excluded: chain B residue 2731 LEU
Chi-restraints excluded: chain B residue 2745 LEU
Chi-restraints excluded: chain C residue 2393 TYR
Chi-restraints excluded: chain C residue 2408 CYS
Chi-restraints excluded: chain C residue 2411 ASP
Chi-restraints excluded: chain C residue 2420 VAL
Chi-restraints excluded: chain C residue 2479 THR
Chi-restraints excluded: chain C residue 2490 CYS
Chi-restraints excluded: chain C residue 2515 ASP
Chi-restraints excluded: chain C residue 2549 SER
Chi-restraints excluded: chain C residue 2615 THR
Chi-restraints excluded: chain C residue 2634 VAL
Chi-restraints excluded: chain C residue 2745 LEU
Chi-restraints excluded: chain C residue 2795 ASN
Chi-restraints excluded: chain D residue 2393 TYR
Chi-restraints excluded: chain D residue 2395 LEU
Chi-restraints excluded: chain D residue 2408 CYS
Chi-restraints excluded: chain D residue 2420 VAL
Chi-restraints excluded: chain D residue 2490 CYS
Chi-restraints excluded: chain D residue 2549 SER
Chi-restraints excluded: chain D residue 2552 SER
Chi-restraints excluded: chain D residue 2603 ILE
Chi-restraints excluded: chain D residue 2615 THR
Chi-restraints excluded: chain D residue 2637 THR
Chi-restraints excluded: chain D residue 2649 ILE
Chi-restraints excluded: chain D residue 2700 SER
Chi-restraints excluded: chain D residue 2795 ASN
Chi-restraints excluded: chain E residue 2393 TYR
Chi-restraints excluded: chain E residue 2411 ASP
Chi-restraints excluded: chain E residue 2490 CYS
Chi-restraints excluded: chain E residue 2549 SER
Chi-restraints excluded: chain E residue 2552 SER
Chi-restraints excluded: chain E residue 2654 VAL
Chi-restraints excluded: chain E residue 2659 GLU
Chi-restraints excluded: chain E residue 2694 THR
Chi-restraints excluded: chain E residue 2705 ILE
Chi-restraints excluded: chain E residue 2731 LEU
Chi-restraints excluded: chain E residue 2795 ASN
Chi-restraints excluded: chain F residue 2393 TYR
Chi-restraints excluded: chain F residue 2408 CYS
Chi-restraints excluded: chain F residue 2411 ASP
Chi-restraints excluded: chain F residue 2420 VAL
Chi-restraints excluded: chain F residue 2479 THR
Chi-restraints excluded: chain F residue 2549 SER
Chi-restraints excluded: chain F residue 2636 THR
Chi-restraints excluded: chain F residue 2705 ILE
Chi-restraints excluded: chain G residue 2393 TYR
Chi-restraints excluded: chain G residue 2408 CYS
Chi-restraints excluded: chain G residue 2422 SER
Chi-restraints excluded: chain G residue 2470 VAL
Chi-restraints excluded: chain G residue 2504 ASN
Chi-restraints excluded: chain G residue 2538 THR
Chi-restraints excluded: chain G residue 2549 SER
Chi-restraints excluded: chain G residue 2617 ASP
Chi-restraints excluded: chain G residue 2626 VAL
Chi-restraints excluded: chain G residue 2637 THR
Chi-restraints excluded: chain G residue 2713 SER
Chi-restraints excluded: chain G residue 2745 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 113 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 149 optimal weight:    0.9980
   chunk 259 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 25 optimal weight:    0.1980
   chunk 120 optimal weight:    6.9990
   chunk 116 optimal weight:    0.9980
   chunk 164 optimal weight:    4.9990
   chunk 249 optimal weight:    0.4980
   chunk 220 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A2533 GLN
A2795 ASN
C2712 GLN
C2795 ASN
D2712 GLN
E2733 ASN
G2712 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.133477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.099226 restraints weight = 25640.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.099660 restraints weight = 54755.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.100669 restraints weight = 50165.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.100678 restraints weight = 28864.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.101283 restraints weight = 26843.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.4325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  21280  Z= 0.107
  Angle     :  0.509   6.207  29491  Z= 0.269
  Chirality :  0.045   0.138   3703
  Planarity :  0.005   0.039   3864
  Dihedral  :  4.385  19.819   3010
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 12.20 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.14), residues: 2891
  helix:  None (None), residues: 0
  sheet:  0.58 (0.15), residues: 1022
  loop : -0.09 (0.14), residues: 1869

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A2755 
 TYR   0.005   0.001   TYR D2532 
 PHE   0.015   0.002   PHE E2704 
 TRP   0.017   0.001   TRP G2674 
 HIS   0.001   0.000   HIS C2641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (21266)
  covalent geometry    : angle       0.50794 (29463)
  SS BOND              : bond        0.00203 (   14)
  SS BOND              : angle       1.06724 (   28)
  hydrogen bonds       : bond        0.03430 (  623)
  hydrogen bonds       : angle       5.19252 ( 1512)

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

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

  5782 Ramachandran restraints generated.
    2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5782 Ramachandran restraints generated.
    2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 145
  time to evaluate  : 0.489 
Fit side-chains
REVERT: A 2745 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8234 (mm)
REVERT: B 2393 TYR cc_start: 0.6530 (OUTLIER) cc_final: 0.5788 (t80)
REVERT: B 2461 ASN cc_start: 0.8117 (m-40) cc_final: 0.7601 (m110)
REVERT: C 2393 TYR cc_start: 0.6600 (OUTLIER) cc_final: 0.5605 (t80)
REVERT: C 2772 MET cc_start: 0.7497 (tpp) cc_final: 0.5755 (pmm)
REVERT: D 2393 TYR cc_start: 0.6279 (OUTLIER) cc_final: 0.5096 (t80)
REVERT: D 2420 VAL cc_start: 0.9228 (OUTLIER) cc_final: 0.8969 (p)
REVERT: D 2795 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.8117 (t0)
REVERT: E 2393 TYR cc_start: 0.6163 (OUTLIER) cc_final: 0.5744 (t80)
REVERT: E 2461 ASN cc_start: 0.7996 (m-40) cc_final: 0.7778 (m110)
REVERT: F 2393 TYR cc_start: 0.6350 (OUTLIER) cc_final: 0.5814 (t80)
REVERT: G 2393 TYR cc_start: 0.6479 (OUTLIER) cc_final: 0.5736 (t80)
REVERT: G 2461 ASN cc_start: 0.8141 (m-40) cc_final: 0.7894 (m-40)
REVERT: G 2772 MET cc_start: 0.7543 (tpp) cc_final: 0.5944 (pmm)
REVERT: G 2795 ASN cc_start: 0.8130 (t160) cc_final: 0.7760 (t0)
REVERT: G 2796 CYS cc_start: 0.6295 (m) cc_final: 0.5967 (m)
  outliers start: 65
  outliers final: 34
  residues processed: 193
  average time/residue: 0.0857
  time to fit residues: 29.8646
Evaluate side-chains
  169 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 126
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2422 SER
Chi-restraints excluded: chain A residue 2549 SER
Chi-restraints excluded: chain A residue 2649 ILE
Chi-restraints excluded: chain A residue 2745 LEU
Chi-restraints excluded: chain A residue 2795 ASN
Chi-restraints excluded: chain B residue 2393 TYR
Chi-restraints excluded: chain B residue 2395 LEU
Chi-restraints excluded: chain B residue 2479 THR
Chi-restraints excluded: chain B residue 2552 SER
Chi-restraints excluded: chain B residue 2649 ILE
Chi-restraints excluded: chain B residue 2671 SER
Chi-restraints excluded: chain C residue 2393 TYR
Chi-restraints excluded: chain C residue 2395 LEU
Chi-restraints excluded: chain C residue 2420 VAL
Chi-restraints excluded: chain C residue 2479 THR
Chi-restraints excluded: chain C residue 2490 CYS
Chi-restraints excluded: chain C residue 2549 SER
Chi-restraints excluded: chain C residue 2610 THR
Chi-restraints excluded: chain C residue 2795 ASN
Chi-restraints excluded: chain D residue 2393 TYR
Chi-restraints excluded: chain D residue 2420 VAL
Chi-restraints excluded: chain D residue 2470 VAL
Chi-restraints excluded: chain D residue 2649 ILE
Chi-restraints excluded: chain D residue 2695 THR
Chi-restraints excluded: chain D residue 2703 LEU
Chi-restraints excluded: chain D residue 2795 ASN
Chi-restraints excluded: chain E residue 2393 TYR
Chi-restraints excluded: chain E residue 2490 CYS
Chi-restraints excluded: chain E residue 2552 SER
Chi-restraints excluded: chain E residue 2659 GLU
Chi-restraints excluded: chain E residue 2705 ILE
Chi-restraints excluded: chain F residue 2393 TYR
Chi-restraints excluded: chain F residue 2420 VAL
Chi-restraints excluded: chain F residue 2479 THR
Chi-restraints excluded: chain F residue 2549 SER
Chi-restraints excluded: chain F residue 2649 ILE
Chi-restraints excluded: chain G residue 2393 TYR
Chi-restraints excluded: chain G residue 2422 SER
Chi-restraints excluded: chain G residue 2479 THR
Chi-restraints excluded: chain G residue 2538 THR
Chi-restraints excluded: chain G residue 2617 ASP
Chi-restraints excluded: chain G residue 2626 VAL
Chi-restraints excluded: chain G residue 2637 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 217 optimal weight:    5.9990
   chunk 159 optimal weight:    9.9990
   chunk 265 optimal weight:    5.9990
   chunk 192 optimal weight:    0.5980
   chunk 88 optimal weight:    2.9990
   chunk 91 optimal weight:    9.9990
   chunk 186 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 154 optimal weight:    0.8980
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
A2533 GLN
** A2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2795 ASN
** F2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.129727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.095505 restraints weight = 25779.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.095722 restraints weight = 62269.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.096756 restraints weight = 50851.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.096933 restraints weight = 28715.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.097442 restraints weight = 27154.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.4414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  21280  Z= 0.251
  Angle     :  0.598   6.447  29491  Z= 0.316
  Chirality :  0.049   0.257   3703
  Planarity :  0.005   0.045   3864
  Dihedral  :  4.738  23.090   3010
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 11.50 %
    Favored  : 85.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.15), residues: 2891
  helix:  None (None), residues: 0
  sheet:  0.33 (0.15), residues: 1050
  loop : -0.19 (0.14), residues: 1841

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D2755 
 TYR   0.010   0.001   TYR A2506 
 PHE   0.022   0.003   PHE E2704 
 TRP   0.020   0.002   TRP A2674 
 HIS   0.002   0.001   HIS B2641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00609 (21266)
  covalent geometry    : angle       0.59408 (29463)
  SS BOND              : bond        0.00565 (   14)
  SS BOND              : angle       2.37308 (   28)
  hydrogen bonds       : bond        0.04193 (  623)
  hydrogen bonds       : angle       5.24544 ( 1512)

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

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

  5782 Ramachandran restraints generated.
    2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5782 Ramachandran restraints generated.
    2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 120
  time to evaluate  : 0.721 
Fit side-chains
REVERT: A 2745 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8184 (mm)
REVERT: B 2393 TYR cc_start: 0.6700 (OUTLIER) cc_final: 0.6129 (t80)
REVERT: C 2393 TYR cc_start: 0.6482 (OUTLIER) cc_final: 0.5768 (t80)
REVERT: C 2400 SER cc_start: 0.9009 (t) cc_final: 0.8702 (p)
REVERT: D 2393 TYR cc_start: 0.6627 (OUTLIER) cc_final: 0.5680 (t80)
REVERT: D 2420 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8981 (p)
REVERT: D 2795 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.8082 (t0)
REVERT: E 2393 TYR cc_start: 0.6353 (OUTLIER) cc_final: 0.5897 (t80)
REVERT: E 2461 ASN cc_start: 0.8247 (m-40) cc_final: 0.7836 (m-40)
REVERT: E 2795 ASN cc_start: 0.8083 (t0) cc_final: 0.7832 (t0)
REVERT: G 2393 TYR cc_start: 0.6330 (OUTLIER) cc_final: 0.5757 (t80)
REVERT: G 2461 ASN cc_start: 0.8257 (m-40) cc_final: 0.7945 (m-40)
REVERT: G 2795 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7792 (t0)
  outliers start: 79
  outliers final: 56
  residues processed: 181
  average time/residue: 0.0912
  time to fit residues: 29.6444
Evaluate side-chains
  180 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 115
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2400 SER
Chi-restraints excluded: chain A residue 2408 CYS
Chi-restraints excluded: chain A residue 2422 SER
Chi-restraints excluded: chain A residue 2470 VAL
Chi-restraints excluded: chain A residue 2549 SER
Chi-restraints excluded: chain A residue 2603 ILE
Chi-restraints excluded: chain A residue 2703 LEU
Chi-restraints excluded: chain A residue 2745 LEU
Chi-restraints excluded: chain B residue 2393 TYR
Chi-restraints excluded: chain B residue 2470 VAL
Chi-restraints excluded: chain B residue 2479 THR
Chi-restraints excluded: chain B residue 2497 MET
Chi-restraints excluded: chain B residue 2552 SER
Chi-restraints excluded: chain B residue 2626 VAL
Chi-restraints excluded: chain B residue 2636 THR
Chi-restraints excluded: chain B residue 2671 SER
Chi-restraints excluded: chain B residue 2745 LEU
Chi-restraints excluded: chain C residue 2393 TYR
Chi-restraints excluded: chain C residue 2395 LEU
Chi-restraints excluded: chain C residue 2411 ASP
Chi-restraints excluded: chain C residue 2479 THR
Chi-restraints excluded: chain C residue 2490 CYS
Chi-restraints excluded: chain C residue 2549 SER
Chi-restraints excluded: chain C residue 2634 VAL
Chi-restraints excluded: chain C residue 2636 THR
Chi-restraints excluded: chain C residue 2640 LEU
Chi-restraints excluded: chain D residue 2393 TYR
Chi-restraints excluded: chain D residue 2408 CYS
Chi-restraints excluded: chain D residue 2420 VAL
Chi-restraints excluded: chain D residue 2470 VAL
Chi-restraints excluded: chain D residue 2636 THR
Chi-restraints excluded: chain D residue 2649 ILE
Chi-restraints excluded: chain D residue 2695 THR
Chi-restraints excluded: chain D residue 2703 LEU
Chi-restraints excluded: chain D residue 2745 LEU
Chi-restraints excluded: chain D residue 2795 ASN
Chi-restraints excluded: chain E residue 2393 TYR
Chi-restraints excluded: chain E residue 2470 VAL
Chi-restraints excluded: chain E residue 2490 CYS
Chi-restraints excluded: chain E residue 2538 THR
Chi-restraints excluded: chain E residue 2549 SER
Chi-restraints excluded: chain E residue 2552 SER
Chi-restraints excluded: chain E residue 2603 ILE
Chi-restraints excluded: chain E residue 2659 GLU
Chi-restraints excluded: chain E residue 2694 THR
Chi-restraints excluded: chain E residue 2705 ILE
Chi-restraints excluded: chain F residue 2395 LEU
Chi-restraints excluded: chain F residue 2420 VAL
Chi-restraints excluded: chain F residue 2479 THR
Chi-restraints excluded: chain F residue 2497 MET
Chi-restraints excluded: chain F residue 2549 SER
Chi-restraints excluded: chain F residue 2646 THR
Chi-restraints excluded: chain F residue 2649 ILE
Chi-restraints excluded: chain F residue 2705 ILE
Chi-restraints excluded: chain G residue 2393 TYR
Chi-restraints excluded: chain G residue 2408 CYS
Chi-restraints excluded: chain G residue 2422 SER
Chi-restraints excluded: chain G residue 2479 THR
Chi-restraints excluded: chain G residue 2538 THR
Chi-restraints excluded: chain G residue 2617 ASP
Chi-restraints excluded: chain G residue 2626 VAL
Chi-restraints excluded: chain G residue 2637 THR
Chi-restraints excluded: chain G residue 2640 LEU
Chi-restraints excluded: chain G residue 2745 LEU
Chi-restraints excluded: chain G residue 2795 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 71 optimal weight:    6.9990
   chunk 91 optimal weight:    8.9990
   chunk 218 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 171 optimal weight:    0.8980
   chunk 268 optimal weight:    3.9990
   chunk 250 optimal weight:    4.9990
   chunk 283 optimal weight:    8.9990
   chunk 188 optimal weight:    1.9990
   chunk 169 optimal weight:    3.9990
   chunk 116 optimal weight:    6.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
** A2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.130769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.093829 restraints weight = 25733.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.094344 restraints weight = 54852.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.095915 restraints weight = 44806.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.095621 restraints weight = 28384.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.097540 restraints weight = 23102.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.4524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  21280  Z= 0.199
  Angle     :  0.559   6.176  29491  Z= 0.295
  Chirality :  0.047   0.215   3703
  Planarity :  0.005   0.037   3864
  Dihedral  :  4.610  21.875   3010
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 11.41 %
    Favored  : 85.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.06 (0.15), residues: 2891
  helix:  None (None), residues: 0
  sheet:  0.29 (0.15), residues: 1050
  loop : -0.19 (0.14), residues: 1841

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2755 
 TYR   0.007   0.001   TYR A2506 
 PHE   0.020   0.002   PHE E2704 
 TRP   0.020   0.002   TRP F2674 
 HIS   0.001   0.001   HIS F2641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 (21266)
  covalent geometry    : angle       0.55617 (29463)
  SS BOND              : bond        0.00407 (   14)
  SS BOND              : angle       1.88395 (   28)
  hydrogen bonds       : bond        0.03845 (  623)
  hydrogen bonds       : angle       5.18087 ( 1512)

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

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

  5782 Ramachandran restraints generated.
    2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5782 Ramachandran restraints generated.
    2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 122
  time to evaluate  : 0.767 
Fit side-chains
REVERT: B 2393 TYR cc_start: 0.6563 (OUTLIER) cc_final: 0.5893 (t80)
REVERT: C 2393 TYR cc_start: 0.6511 (OUTLIER) cc_final: 0.5746 (t80)
REVERT: D 2393 TYR cc_start: 0.6440 (OUTLIER) cc_final: 0.5465 (t80)
REVERT: D 2420 VAL cc_start: 0.9250 (OUTLIER) cc_final: 0.9021 (p)
REVERT: D 2795 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.8169 (t0)
REVERT: E 2393 TYR cc_start: 0.6195 (OUTLIER) cc_final: 0.5654 (t80)
REVERT: E 2461 ASN cc_start: 0.8320 (m-40) cc_final: 0.7927 (m-40)
REVERT: E 2795 ASN cc_start: 0.8157 (t0) cc_final: 0.7889 (t0)
REVERT: F 2483 MET cc_start: 0.8287 (ttt) cc_final: 0.7862 (ttt)
REVERT: G 2393 TYR cc_start: 0.6270 (OUTLIER) cc_final: 0.5562 (t80)
REVERT: G 2461 ASN cc_start: 0.8389 (m-40) cc_final: 0.8014 (m-40)
REVERT: G 2483 MET cc_start: 0.8290 (ttt) cc_final: 0.8067 (ttt)
  outliers start: 74
  outliers final: 57
  residues processed: 180
  average time/residue: 0.1007
  time to fit residues: 32.7869
Evaluate side-chains
  178 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 114
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2408 CYS
Chi-restraints excluded: chain A residue 2470 VAL
Chi-restraints excluded: chain A residue 2549 SER
Chi-restraints excluded: chain A residue 2603 ILE
Chi-restraints excluded: chain A residue 2649 ILE
Chi-restraints excluded: chain A residue 2703 LEU
Chi-restraints excluded: chain A residue 2745 LEU
Chi-restraints excluded: chain B residue 2393 TYR
Chi-restraints excluded: chain B residue 2470 VAL
Chi-restraints excluded: chain B residue 2479 THR
Chi-restraints excluded: chain B residue 2552 SER
Chi-restraints excluded: chain B residue 2626 VAL
Chi-restraints excluded: chain B residue 2636 THR
Chi-restraints excluded: chain B residue 2671 SER
Chi-restraints excluded: chain B residue 2745 LEU
Chi-restraints excluded: chain C residue 2393 TYR
Chi-restraints excluded: chain C residue 2395 LEU
Chi-restraints excluded: chain C residue 2408 CYS
Chi-restraints excluded: chain C residue 2411 ASP
Chi-restraints excluded: chain C residue 2479 THR
Chi-restraints excluded: chain C residue 2490 CYS
Chi-restraints excluded: chain C residue 2549 SER
Chi-restraints excluded: chain C residue 2615 THR
Chi-restraints excluded: chain C residue 2626 VAL
Chi-restraints excluded: chain C residue 2634 VAL
Chi-restraints excluded: chain C residue 2636 THR
Chi-restraints excluded: chain C residue 2640 LEU
Chi-restraints excluded: chain D residue 2393 TYR
Chi-restraints excluded: chain D residue 2408 CYS
Chi-restraints excluded: chain D residue 2420 VAL
Chi-restraints excluded: chain D residue 2470 VAL
Chi-restraints excluded: chain D residue 2490 CYS
Chi-restraints excluded: chain D residue 2603 ILE
Chi-restraints excluded: chain D residue 2636 THR
Chi-restraints excluded: chain D residue 2649 ILE
Chi-restraints excluded: chain D residue 2695 THR
Chi-restraints excluded: chain D residue 2703 LEU
Chi-restraints excluded: chain D residue 2745 LEU
Chi-restraints excluded: chain D residue 2795 ASN
Chi-restraints excluded: chain E residue 2393 TYR
Chi-restraints excluded: chain E residue 2470 VAL
Chi-restraints excluded: chain E residue 2490 CYS
Chi-restraints excluded: chain E residue 2549 SER
Chi-restraints excluded: chain E residue 2552 SER
Chi-restraints excluded: chain E residue 2659 GLU
Chi-restraints excluded: chain E residue 2694 THR
Chi-restraints excluded: chain E residue 2705 ILE
Chi-restraints excluded: chain E residue 2731 LEU
Chi-restraints excluded: chain F residue 2395 LEU
Chi-restraints excluded: chain F residue 2420 VAL
Chi-restraints excluded: chain F residue 2479 THR
Chi-restraints excluded: chain F residue 2549 SER
Chi-restraints excluded: chain F residue 2646 THR
Chi-restraints excluded: chain F residue 2649 ILE
Chi-restraints excluded: chain F residue 2705 ILE
Chi-restraints excluded: chain G residue 2393 TYR
Chi-restraints excluded: chain G residue 2479 THR
Chi-restraints excluded: chain G residue 2538 THR
Chi-restraints excluded: chain G residue 2549 SER
Chi-restraints excluded: chain G residue 2617 ASP
Chi-restraints excluded: chain G residue 2626 VAL
Chi-restraints excluded: chain G residue 2636 THR
Chi-restraints excluded: chain G residue 2637 THR
Chi-restraints excluded: chain G residue 2745 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 187 optimal weight:    0.0980
   chunk 179 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 198 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 230 optimal weight:    2.9990
   chunk 231 optimal weight:    7.9990
   chunk 63 optimal weight:    0.0020
   chunk 99 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 37 optimal weight:    9.9990
   overall best weight:    1.2194

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

Flipped N/Q/H residues before XYZ refinement:
A2533 GLN
** A2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.132373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.096806 restraints weight = 25722.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.098204 restraints weight = 56904.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.099082 restraints weight = 42841.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.099226 restraints weight = 24582.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.099805 restraints weight = 23470.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.4598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  21280  Z= 0.140
  Angle     :  0.521   6.122  29491  Z= 0.272
  Chirality :  0.046   0.177   3703
  Planarity :  0.005   0.036   3864
  Dihedral  :  4.340  20.538   3010
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 11.87 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.05 (0.15), residues: 2891
  helix:  None (None), residues: 0
  sheet:  0.50 (0.15), residues: 1015
  loop : -0.18 (0.14), residues: 1876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A2755 
 TYR   0.005   0.001   TYR G2672 
 PHE   0.018   0.002   PHE E2704 
 TRP   0.018   0.002   TRP A2674 
 HIS   0.002   0.001   HIS G2641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (21266)
  covalent geometry    : angle       0.51876 (29463)
  SS BOND              : bond        0.00324 (   14)
  SS BOND              : angle       1.58072 (   28)
  hydrogen bonds       : bond        0.03449 (  623)
  hydrogen bonds       : angle       5.08064 ( 1512)

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

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

  5782 Ramachandran restraints generated.
    2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5782 Ramachandran restraints generated.
    2891 Oldfield, 0 Emsley, 2891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 142
  time to evaluate  : 0.680 
Fit side-chains
REVERT: B 2393 TYR cc_start: 0.6171 (OUTLIER) cc_final: 0.5482 (t80)
REVERT: C 2393 TYR cc_start: 0.6589 (OUTLIER) cc_final: 0.5757 (t80)
REVERT: D 2393 TYR cc_start: 0.6379 (OUTLIER) cc_final: 0.5398 (t80)
REVERT: D 2420 VAL cc_start: 0.9203 (OUTLIER) cc_final: 0.8969 (p)
REVERT: D 2795 ASN cc_start: 0.8313 (OUTLIER) cc_final: 0.8008 (t0)
REVERT: E 2393 TYR cc_start: 0.6214 (OUTLIER) cc_final: 0.5946 (t80)
REVERT: E 2795 ASN cc_start: 0.8044 (t0) cc_final: 0.7777 (t0)
REVERT: G 2393 TYR cc_start: 0.6248 (OUTLIER) cc_final: 0.5571 (t80)
REVERT: G 2483 MET cc_start: 0.8353 (ttt) cc_final: 0.8153 (ttt)
  outliers start: 65
  outliers final: 52
  residues processed: 189
  average time/residue: 0.0871
  time to fit residues: 29.8177
Evaluate side-chains
  188 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 129
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2400 SER
Chi-restraints excluded: chain A residue 2470 VAL
Chi-restraints excluded: chain A residue 2549 SER
Chi-restraints excluded: chain A residue 2649 ILE
Chi-restraints excluded: chain A residue 2703 LEU
Chi-restraints excluded: chain A residue 2745 LEU
Chi-restraints excluded: chain B residue 2393 TYR
Chi-restraints excluded: chain B residue 2470 VAL
Chi-restraints excluded: chain B residue 2479 THR
Chi-restraints excluded: chain B residue 2497 MET
Chi-restraints excluded: chain B residue 2552 SER
Chi-restraints excluded: chain B residue 2636 THR
Chi-restraints excluded: chain B residue 2671 SER
Chi-restraints excluded: chain B residue 2745 LEU
Chi-restraints excluded: chain C residue 2393 TYR
Chi-restraints excluded: chain C residue 2395 LEU
Chi-restraints excluded: chain C residue 2408 CYS
Chi-restraints excluded: chain C residue 2411 ASP
Chi-restraints excluded: chain C residue 2479 THR
Chi-restraints excluded: chain C residue 2490 CYS
Chi-restraints excluded: chain C residue 2549 SER
Chi-restraints excluded: chain C residue 2634 VAL
Chi-restraints excluded: chain C residue 2636 THR
Chi-restraints excluded: chain C residue 2640 LEU
Chi-restraints excluded: chain D residue 2393 TYR
Chi-restraints excluded: chain D residue 2408 CYS
Chi-restraints excluded: chain D residue 2420 VAL
Chi-restraints excluded: chain D residue 2470 VAL
Chi-restraints excluded: chain D residue 2490 CYS
Chi-restraints excluded: chain D residue 2603 ILE
Chi-restraints excluded: chain D residue 2636 THR
Chi-restraints excluded: chain D residue 2695 THR
Chi-restraints excluded: chain D residue 2703 LEU
Chi-restraints excluded: chain D residue 2745 LEU
Chi-restraints excluded: chain D residue 2795 ASN
Chi-restraints excluded: chain E residue 2393 TYR
Chi-restraints excluded: chain E residue 2470 VAL
Chi-restraints excluded: chain E residue 2490 CYS
Chi-restraints excluded: chain E residue 2552 SER
Chi-restraints excluded: chain E residue 2659 GLU
Chi-restraints excluded: chain E residue 2705 ILE
Chi-restraints excluded: chain E residue 2731 LEU
Chi-restraints excluded: chain F residue 2395 LEU
Chi-restraints excluded: chain F residue 2408 CYS
Chi-restraints excluded: chain F residue 2420 VAL
Chi-restraints excluded: chain F residue 2479 THR
Chi-restraints excluded: chain F residue 2497 MET
Chi-restraints excluded: chain F residue 2549 SER
Chi-restraints excluded: chain F residue 2649 ILE
Chi-restraints excluded: chain F residue 2705 ILE
Chi-restraints excluded: chain G residue 2393 TYR
Chi-restraints excluded: chain G residue 2408 CYS
Chi-restraints excluded: chain G residue 2479 THR
Chi-restraints excluded: chain G residue 2538 THR
Chi-restraints excluded: chain G residue 2617 ASP
Chi-restraints excluded: chain G residue 2626 VAL
Chi-restraints excluded: chain G residue 2636 THR
Chi-restraints excluded: chain G residue 2637 THR
Chi-restraints excluded: chain G residue 2745 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 287
   random chunks:
   chunk 230 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 161 optimal weight:    2.9990
   chunk 176 optimal weight:    0.0870
   chunk 177 optimal weight:    0.0870
   chunk 26 optimal weight:    5.9990
   chunk 133 optimal weight:    3.9990
   chunk 189 optimal weight:    0.1980
   chunk 249 optimal weight:    5.9990
   chunk 155 optimal weight:    3.9990
   chunk 93 optimal weight:    0.5980
   overall best weight:    0.3938

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

Flipped N/Q/H residues before XYZ refinement:
** A2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F2569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F2733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G2461 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.137537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.098601 restraints weight = 25719.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.100016 restraints weight = 40292.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.101067 restraints weight = 33949.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.101365 restraints weight = 20602.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.102015 restraints weight = 18741.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.4740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  21280  Z= 0.090
  Angle     :  0.486   6.244  29491  Z= 0.252
  Chirality :  0.045   0.149   3703
  Planarity :  0.004   0.036   3864
  Dihedral  :  3.913  18.177   3010
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 12.66 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.15), residues: 2891
  helix:  None (None), residues: 0
  sheet:  0.69 (0.15), residues: 1050
  loop :  0.01 (0.14), residues: 1841

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A2755 
 TYR   0.005   0.000   TYR G2672 
 PHE   0.016   0.001   PHE E2704 
 TRP   0.016   0.001   TRP C2674 
 HIS   0.002   0.001   HIS D2641 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 (21266)
  covalent geometry    : angle       0.48474 (29463)
  SS BOND              : bond        0.00104 (   14)
  SS BOND              : angle       1.18883 (   28)
  hydrogen bonds       : bond        0.02959 (  623)
  hydrogen bonds       : angle       4.94649 ( 1512)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2159.74 seconds
wall clock time: 38 minutes 32.70 seconds (2312.70 seconds total)