Starting phenix.real_space_refine
on Sun Aug 24 00:15:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ss5_40744/08_2025/8ss5_40744.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ss5_40744/08_2025/8ss5_40744.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ss5_40744/08_2025/8ss5_40744.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ss5_40744/08_2025/8ss5_40744.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ss5_40744/08_2025/8ss5_40744.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ss5_40744/08_2025/8ss5_40744.map"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.075
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S     104      5.16       5
     Na      1      4.78       5
     C   10182      2.51       5
     N    2524      2.21       5
     O    2826      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s

  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: 15637
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 595, 4662
          Classifications: {'peptide': 595}
          Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 577}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 3156
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 404, 3156
          Classifications: {'peptide': 404}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 390}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' NA': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, D
  Time building chain proxies: 5.48, per 1000 atoms: 0.35
  Number of scatterers: 15637
  At special positions: 0
  Unit cell: (120.84, 124.02, 135.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S     104     16.00
     Na      1     11.00
     O    2826      8.00
     N    2524      7.00
     C   10182      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 718 " - pdb=" SG  CYS A 773 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 890 " - pdb=" SG  CYS A 900 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 718 " - pdb=" SG  CYS B 773 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 718 " - pdb=" SG  CYS C 773 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 890 " - pdb=" SG  CYS C 900 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 718 " - pdb=" SG  CYS D 773 " 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: 1.30
  Conformation dependent library (CDL) restraints added in 610.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3656

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 22 sheets defined
      54.0% alpha, 5.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 423 through 437
      removed outlier: 3.724A  pdb=" N   LYS A 434 " --> pdb=" O   ALA A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 469
      removed outlier: 3.632A  pdb=" N   TYR A 469 " --> pdb=" O   GLY A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 487
      removed outlier: 3.502A  pdb=" N   GLU A 486 " --> pdb=" O   THR A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 546
      removed outlier: 3.509A  pdb=" N   VAL A 530 " --> pdb=" O   TRP A 526 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   SER A 544 " --> pdb=" O   LEU A 540 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ARG A 545 " --> pdb=" O   PHE A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 585
      removed outlier: 3.886A  pdb=" N   TRP A 578 " --> pdb=" O   PHE A 574 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   MET A 585 " --> pdb=" O   LEU A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 630
      removed outlier: 3.668A  pdb=" N   ILE A 600 " --> pdb=" O   LEU A 596 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL A 601 " --> pdb=" O   SER A 597 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLY A 602 " --> pdb=" O   GLY A 598 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   TRP A 606 " --> pdb=" O   GLY A 602 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   PHE A 607 " --> pdb=" O   GLY A 603 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   LEU A 610 " --> pdb=" O   TRP A 606 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE A 611 " --> pdb=" O   PHE A 607 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   SER A 614 " --> pdb=" O   LEU A 610 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ALA A 618 " --> pdb=" O   SER A 614 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   THR A 625 " --> pdb=" O   ALA A 621 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL A 626 " --> pdb=" O   ALA A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 642
      removed outlier: 3.789A  pdb=" N   LYS A 641 " --> pdb=" O   GLU A 637 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLN A 642 " --> pdb=" O   ASP A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 661
      removed outlier: 3.873A  pdb=" N   PHE A 659 " --> pdb=" O   THR A 655 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ARG A 660 " --> pdb=" O   LYS A 656 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   ARG A 661 " --> pdb=" O   GLU A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 664 through 676
    Processing helix  chain 'A' and resid 686 through 695
    Processing helix  chain 'A' and resid 706 through 714
      removed outlier: 3.865A  pdb=" N   TYR A 711 " --> pdb=" O   THR A 707 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLN A 714 " --> pdb=" O   GLU A 710 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 752
      removed outlier: 3.547A  pdb=" N   ASN A 747 " --> pdb=" O   GLY A 743 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   LEU A 751 " --> pdb=" O   ASN A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 757 through 767
      removed outlier: 3.845A  pdb=" N   LYS A 763 " --> pdb=" O   LEU A 759 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ASN A 764 " --> pdb=" O   ASP A 760 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 793 through 822
      removed outlier: 3.524A  pdb=" N   LEU A 805 " --> pdb=" O   GLY A 801 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU A 808 " --> pdb=" O   GLY A 804 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LEU A 811 " --> pdb=" O   MET A 807 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ILE A 812 " --> pdb=" O   LEU A 808 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   PHE A 814 " --> pdb=" O   ALA A 810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 858
      removed outlier: 3.611A  pdb=" N   LEU A 852 " --> pdb=" O   GLY A 848 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ALA A 855 " --> pdb=" O   LEU A 851 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 922 through 928
      removed outlier: 4.169A  pdb=" N   ARG A 926 " --> pdb=" O   LEU A 922 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 929 through 952
      removed outlier: 3.761A  pdb=" N   SER A 935 " --> pdb=" O   PHE A 931 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ILE A 941 " --> pdb=" O   PHE A 937 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ILE A 944 " --> pdb=" O   PHE A 940 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ARG A 952 " --> pdb=" O   ILE A 948 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 956 through 990
      removed outlier: 3.655A  pdb=" N   PHE A 965 " --> pdb=" O   VAL A 961 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ILE A 967 " --> pdb=" O   GLY A 963 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LEU A 968 " --> pdb=" O   ILE A 964 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   SER A 969 " --> pdb=" O   PHE A 965 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1004 through 1033
      removed outlier: 3.645A  pdb=" N   LEU A1015 " --> pdb=" O   ALA A1011 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   MET A1023 " --> pdb=" O   SER A1019 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   VAL A1025 " --> pdb=" O   GLY A1021 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 419
    Processing helix  chain 'B' and resid 423 through 436
    Processing helix  chain 'B' and resid 461 through 470
      removed outlier: 3.575A  pdb=" N   TYR B 469 " --> pdb=" O   GLY B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 487
    Processing helix  chain 'B' and resid 515 through 519
      removed outlier: 3.549A  pdb=" N   LEU B 518 " --> pdb=" O   PHE B 515 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 522 through 547
      removed outlier: 3.504A  pdb=" N   MET B 527 " --> pdb=" O   TYR B 523 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   PHE B 546 " --> pdb=" O   LEU B 542 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 585
      removed outlier: 3.717A  pdb=" N   LEU B 577 " --> pdb=" O   ILE B 573 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   TRP B 578 " --> pdb=" O   PHE B 574 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   SER B 580 " --> pdb=" O   SER B 576 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LEU B 581 " --> pdb=" O   LEU B 577 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 595 through 626
      removed outlier: 3.882A  pdb=" N   TRP B 605 " --> pdb=" O   VAL B 601 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   PHE B 608 " --> pdb=" O   VAL B 604 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU B 610 " --> pdb=" O   TRP B 606 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE B 611 " --> pdb=" O   PHE B 607 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ILE B 612 " --> pdb=" O   PHE B 608 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL B 626 " --> pdb=" O   ALA B 622 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 635 through 642
      removed outlier: 3.666A  pdb=" N   GLN B 642 " --> pdb=" O   ASP B 638 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 653 through 662
      removed outlier: 3.619A  pdb=" N   PHE B 659 " --> pdb=" O   THR B 655 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ARG B 660 " --> pdb=" O   LYS B 656 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 666 through 677
      removed outlier: 3.606A  pdb=" N   MET B 674 " --> pdb=" O   MET B 670 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   SER B 676 " --> pdb=" O   THR B 672 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 686 through 696
      removed outlier: 3.525A  pdb=" N   ALA B 691 " --> pdb=" O   ALA B 687 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 707 through 713
    Processing helix  chain 'B' and resid 742 through 757
      removed outlier: 3.534A  pdb=" N   ASN B 747 " --> pdb=" O   GLY B 743 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LEU B 751 " --> pdb=" O   ASN B 747 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 757 through 767
    Processing helix  chain 'B' and resid 793 through 820
      removed outlier: 3.589A  pdb=" N   TYR B 797 " --> pdb=" O   ALA B 793 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   TYR B 816 " --> pdb=" O   ILE B 812 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 423 through 437
      removed outlier: 3.724A  pdb=" N   LYS C 434 " --> pdb=" O   ALA C 430 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 462 through 469
      removed outlier: 3.632A  pdb=" N   TYR C 469 " --> pdb=" O   GLY C 465 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 482 through 487
      removed outlier: 3.502A  pdb=" N   GLU C 486 " --> pdb=" O   THR C 482 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 522 through 546
      removed outlier: 3.510A  pdb=" N   VAL C 530 " --> pdb=" O   TRP C 526 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   SER C 544 " --> pdb=" O   LEU C 540 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ARG C 545 " --> pdb=" O   PHE C 541 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 572 through 585
      removed outlier: 3.886A  pdb=" N   TRP C 578 " --> pdb=" O   PHE C 574 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   MET C 585 " --> pdb=" O   LEU C 581 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 595 through 630
      removed outlier: 3.667A  pdb=" N   ILE C 600 " --> pdb=" O   LEU C 596 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL C 601 " --> pdb=" O   SER C 597 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLY C 602 " --> pdb=" O   GLY C 598 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   TRP C 606 " --> pdb=" O   GLY C 602 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   PHE C 607 " --> pdb=" O   GLY C 603 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   LEU C 610 " --> pdb=" O   TRP C 606 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ILE C 611 " --> pdb=" O   PHE C 607 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER C 614 " --> pdb=" O   LEU C 610 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ALA C 618 " --> pdb=" O   SER C 614 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   THR C 625 " --> pdb=" O   ALA C 621 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL C 626 " --> pdb=" O   ALA C 622 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 635 through 642
      removed outlier: 3.789A  pdb=" N   LYS C 641 " --> pdb=" O   GLU C 637 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLN C 642 " --> pdb=" O   ASP C 638 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 653 through 661
      removed outlier: 3.874A  pdb=" N   PHE C 659 " --> pdb=" O   THR C 655 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ARG C 660 " --> pdb=" O   LYS C 656 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ARG C 661 " --> pdb=" O   GLU C 657 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 664 through 676
    Processing helix  chain 'C' and resid 686 through 695
    Processing helix  chain 'C' and resid 706 through 714
      removed outlier: 3.865A  pdb=" N   TYR C 711 " --> pdb=" O   THR C 707 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLN C 714 " --> pdb=" O   GLU C 710 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 743 through 752
      removed outlier: 3.547A  pdb=" N   ASN C 747 " --> pdb=" O   GLY C 743 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   LEU C 751 " --> pdb=" O   ASN C 747 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 757 through 767
      removed outlier: 3.845A  pdb=" N   LYS C 763 " --> pdb=" O   LEU C 759 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ASN C 764 " --> pdb=" O   ASP C 760 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 793 through 822
      removed outlier: 3.525A  pdb=" N   LEU C 805 " --> pdb=" O   GLY C 801 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LEU C 808 " --> pdb=" O   GLY C 804 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LEU C 811 " --> pdb=" O   MET C 807 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE C 812 " --> pdb=" O   LEU C 808 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   PHE C 814 " --> pdb=" O   ALA C 810 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 834 through 858
      removed outlier: 3.610A  pdb=" N   LEU C 852 " --> pdb=" O   GLY C 848 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ALA C 855 " --> pdb=" O   LEU C 851 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 922 through 928
      removed outlier: 4.170A  pdb=" N   ARG C 926 " --> pdb=" O   LEU C 922 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 929 through 952
      removed outlier: 3.761A  pdb=" N   SER C 935 " --> pdb=" O   PHE C 931 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ILE C 941 " --> pdb=" O   PHE C 937 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ILE C 944 " --> pdb=" O   PHE C 940 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ARG C 952 " --> pdb=" O   ILE C 948 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 956 through 990
      removed outlier: 3.656A  pdb=" N   PHE C 965 " --> pdb=" O   VAL C 961 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ILE C 967 " --> pdb=" O   GLY C 963 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU C 968 " --> pdb=" O   ILE C 964 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   SER C 969 " --> pdb=" O   PHE C 965 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1004 through 1033
      removed outlier: 3.644A  pdb=" N   LEU C1015 " --> pdb=" O   ALA C1011 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   MET C1023 " --> pdb=" O   SER C1019 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   VAL C1025 " --> pdb=" O   GLY C1021 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 416 through 419
    Processing helix  chain 'D' and resid 423 through 436
    Processing helix  chain 'D' and resid 461 through 470
      removed outlier: 3.575A  pdb=" N   TYR D 469 " --> pdb=" O   GLY D 465 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 482 through 487
    Processing helix  chain 'D' and resid 515 through 519
      removed outlier: 3.549A  pdb=" N   LEU D 518 " --> pdb=" O   PHE D 515 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 522 through 547
      removed outlier: 3.503A  pdb=" N   MET D 527 " --> pdb=" O   TYR D 523 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   PHE D 546 " --> pdb=" O   LEU D 542 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 572 through 585
      removed outlier: 3.718A  pdb=" N   LEU D 577 " --> pdb=" O   ILE D 573 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   TRP D 578 " --> pdb=" O   PHE D 574 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   SER D 580 " --> pdb=" O   SER D 576 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU D 581 " --> pdb=" O   LEU D 577 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 595 through 626
      removed outlier: 3.883A  pdb=" N   TRP D 605 " --> pdb=" O   VAL D 601 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   PHE D 608 " --> pdb=" O   VAL D 604 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU D 610 " --> pdb=" O   TRP D 606 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE D 611 " --> pdb=" O   PHE D 607 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ILE D 612 " --> pdb=" O   PHE D 608 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL D 626 " --> pdb=" O   ALA D 622 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 635 through 642
      removed outlier: 3.666A  pdb=" N   GLN D 642 " --> pdb=" O   ASP D 638 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 653 through 662
      removed outlier: 3.619A  pdb=" N   PHE D 659 " --> pdb=" O   THR D 655 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ARG D 660 " --> pdb=" O   LYS D 656 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 666 through 677
      removed outlier: 3.605A  pdb=" N   MET D 674 " --> pdb=" O   MET D 670 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   SER D 676 " --> pdb=" O   THR D 672 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 686 through 696
      removed outlier: 3.524A  pdb=" N   ALA D 691 " --> pdb=" O   ALA D 687 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 707 through 713
    Processing helix  chain 'D' and resid 742 through 757
      removed outlier: 3.534A  pdb=" N   ASN D 747 " --> pdb=" O   GLY D 743 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LEU D 751 " --> pdb=" O   ASN D 747 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 757 through 767
    Processing helix  chain 'D' and resid 793 through 820
      removed outlier: 3.591A  pdb=" N   TYR D 797 " --> pdb=" O   ALA D 793 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   TYR D 816 " --> pdb=" O   ILE D 812 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 399
      removed outlier: 6.240A  pdb=" N   VAL A 397 " --> pdb=" O   THR A 443 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408
    Processing sheet with id=AA3, first strand: chain 'A' and resid 490 through 491
    Processing sheet with id=AA4, first strand: chain 'A' and resid 702 through 705
      removed outlier: 3.939A  pdb=" N   ILE A 502 " --> pdb=" O   VAL A 723 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 649 through 650
      removed outlier: 5.957A  pdb=" N   THR A 649 " --> pdb=" O   VAL A 683 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 863 through 867
    Processing sheet with id=AA7, first strand: chain 'B' and resid 395 through 397
      removed outlier: 6.899A  pdb=" N   VAL B 395 " --> pdb=" O   LYS B 441 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 407 through 408
    Processing sheet with id=AA9, first strand: chain 'B' and resid 489 through 490
    Processing sheet with id=AB1, first strand: chain 'B' and resid 497 through 498
    Processing sheet with id=AB2, first strand: chain 'B' and resid 702 through 705
      removed outlier: 4.156A  pdb=" N   ILE B 502 " --> pdb=" O   VAL B 723 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 396 through 399
      removed outlier: 6.239A  pdb=" N   VAL C 397 " --> pdb=" O   THR C 443 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'C' and resid 407 through 408
    Processing sheet with id=AB5, first strand: chain 'C' and resid 490 through 491
    Processing sheet with id=AB6, first strand: chain 'C' and resid 702 through 705
      removed outlier: 3.940A  pdb=" N   ILE C 502 " --> pdb=" O   VAL C 723 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 649 through 650
      removed outlier: 5.956A  pdb=" N   THR C 649 " --> pdb=" O   VAL C 683 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'C' and resid 863 through 867
    Processing sheet with id=AB9, first strand: chain 'D' and resid 395 through 397
      removed outlier: 6.899A  pdb=" N   VAL D 395 " --> pdb=" O   LYS D 441 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9
    Processing sheet with id=AC1, first strand: chain 'D' and resid 407 through 408
    Processing sheet with id=AC2, first strand: chain 'D' and resid 489 through 490
    Processing sheet with id=AC3, first strand: chain 'D' and resid 497 through 498
    Processing sheet with id=AC4, first strand: chain 'D' and resid 702 through 705
      removed outlier: 4.155A  pdb=" N   ILE D 502 " --> pdb=" O   VAL D 723 " (cutoff:3.500A)

    716 hydrogen bonds defined for protein.
    2082 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.20

  Time building geometry restraints manager: 1.66 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 4742
        1.35 -     1.47: 4120
        1.47 -     1.59: 6942
        1.59 -     1.71: 0
        1.71 -     1.84: 174
  Bond restraints: 15978
  Sorted by residual:
  bond pdb=" C   THR C 929 "
       pdb=" N   PRO C 930 "
    ideal  model  delta    sigma   weight residual
    1.336  1.394 -0.058 1.25e-02 6.40e+03 2.13e+01
  bond pdb=" C   THR A 929 "
       pdb=" N   PRO A 930 "
    ideal  model  delta    sigma   weight residual
    1.336  1.393 -0.057 1.25e-02 6.40e+03 2.11e+01
  bond pdb=" C   THR B 744 "
       pdb=" N   PRO B 745 "
    ideal  model  delta    sigma   weight residual
    1.336  1.390 -0.055 1.23e-02 6.61e+03 1.99e+01
  bond pdb=" C   THR D 744 "
       pdb=" N   PRO D 745 "
    ideal  model  delta    sigma   weight residual
    1.336  1.390 -0.055 1.23e-02 6.61e+03 1.98e+01
  bond pdb=" C   ASP D 519 "
       pdb=" N   PRO D 520 "
    ideal  model  delta    sigma   weight residual
    1.335  1.380 -0.045 1.30e-02 5.92e+03 1.18e+01
  ... (remaining 15973 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.18: 20203
        2.18 -     4.36: 1064
        4.36 -     6.54: 203
        6.54 -     8.73: 87
        8.73 -    10.91: 13
  Bond angle restraints: 21570
  Sorted by residual:
  angle pdb=" N   LEU C 862 "
        pdb=" CA  LEU C 862 "
        pdb=" C   LEU C 862 "
      ideal   model   delta    sigma   weight residual
     110.42  118.07   -7.65 1.46e+00 4.69e-01 2.74e+01
  angle pdb=" N   LEU A 862 "
        pdb=" CA  LEU A 862 "
        pdb=" C   LEU A 862 "
      ideal   model   delta    sigma   weight residual
     110.42  118.03   -7.61 1.46e+00 4.69e-01 2.71e+01
  angle pdb=" C   GLU D 416 "
        pdb=" N   GLY D 417 "
        pdb=" CA  GLY D 417 "
      ideal   model   delta    sigma   weight residual
     119.99  125.64   -5.65 1.13e+00 7.83e-01 2.50e+01
  angle pdb=" C   GLY C 894 "
        pdb=" N   GLU C 895 "
        pdb=" CA  GLU C 895 "
      ideal   model   delta    sigma   weight residual
     121.54  131.06   -9.52 1.91e+00 2.74e-01 2.48e+01
  angle pdb=" C   GLU B 416 "
        pdb=" N   GLY B 417 "
        pdb=" CA  GLY B 417 "
      ideal   model   delta    sigma   weight residual
     119.99  125.61   -5.62 1.13e+00 7.83e-01 2.47e+01
  ... (remaining 21565 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.25: 8664
       14.25 -    28.51: 544
       28.51 -    42.76: 196
       42.76 -    57.02: 22
       57.02 -    71.27: 14
  Dihedral angle restraints: 9440
    sinusoidal: 3710
      harmonic: 5730
  Sorted by residual:
  dihedral pdb=" CA  LYS C 716 "
           pdb=" C   LYS C 716 "
           pdb=" N   PRO C 717 "
           pdb=" CA  PRO C 717 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -119.81  -60.19     0      5.00e+00 4.00e-02 1.45e+02
  dihedral pdb=" CA  LYS A 716 "
           pdb=" C   LYS A 716 "
           pdb=" N   PRO A 717 "
           pdb=" CA  PRO A 717 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -119.83  -60.17     0      5.00e+00 4.00e-02 1.45e+02
  dihedral pdb=" CA  GLU B 678 "
           pdb=" C   GLU B 678 "
           pdb=" N   PRO B 679 "
           pdb=" CA  PRO B 679 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  133.79   46.21     0      5.00e+00 4.00e-02 8.54e+01
  ... (remaining 9437 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1751
       0.057 -    0.113: 551
       0.113 -    0.170: 104
       0.170 -    0.226: 20
       0.226 -    0.283: 2
  Chirality restraints: 2428
  Sorted by residual:
  chirality pdb=" CB  ILE B 591 "
            pdb=" CA  ILE B 591 "
            pdb=" CG1 ILE B 591 "
            pdb=" CG2 ILE B 591 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.93   -0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" CB  ILE D 591 "
            pdb=" CA  ILE D 591 "
            pdb=" CG1 ILE D 591 "
            pdb=" CG2 ILE D 591 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.92   -0.28 2.00e-01 2.50e+01 1.94e+00
  chirality pdb=" CA  PRO B 494 "
            pdb=" N   PRO B 494 "
            pdb=" C   PRO B 494 "
            pdb=" CB  PRO B 494 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.22 2.00e-01 2.50e+01 1.26e+00
  ... (remaining 2425 not shown)

  Planarity restraints: 2654
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D 678 "   -0.079 5.00e-02 4.00e+02   1.21e-01 2.33e+01
        pdb=" N   PRO D 679 "    0.209 5.00e-02 4.00e+02
        pdb=" CA  PRO D 679 "   -0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO D 679 "   -0.069 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 678 "   -0.079 5.00e-02 4.00e+02   1.20e-01 2.32e+01
        pdb=" N   PRO B 679 "    0.208 5.00e-02 4.00e+02
        pdb=" CA  PRO B 679 "   -0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO B 679 "   -0.069 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 878 "    0.018 2.00e-02 2.50e+03   3.59e-02 1.29e+01
        pdb=" C   VAL C 878 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   VAL C 878 "    0.023 2.00e-02 2.50e+03
        pdb=" N   LYS C 879 "    0.021 2.00e-02 2.50e+03
  ... (remaining 2651 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 2117
        2.75 -     3.29: 14750
        3.29 -     3.83: 24692
        3.83 -     4.36: 29132
        4.36 -     4.90: 50296
  Nonbonded interactions: 120987
  Sorted by model distance:
  nonbonded pdb=" O   ILE C 925 "
            pdb=" OG1 THR C 929 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" O   ILE A 925 "
            pdb=" OG1 THR A 929 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   PHE C 966 "
            pdb=" OG  SER C 969 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" O   PHE A 966 "
            pdb=" OG  SER A 969 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   TRP B 606 "
            pdb=" OG1 THR B 609 "
     model   vdw
     2.313 3.040
  ... (remaining 120982 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 392 through 1035)
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

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:             2.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     15.200
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7142
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066  15984  Z= 0.278
  Angle     :  1.226  10.908  21582  Z= 0.730
  Chirality :  0.057   0.283   2428
  Planarity :  0.008   0.121   2654
  Dihedral  : 11.205  71.275   5766
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  1.12 %
    Allowed  : 10.63 %
    Favored  : 88.25 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  6.58 %
    Favored  : 93.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 10.00 %
    Twisted General : 0.42 %

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: -5.78 (0.13), residues: 1966
  helix: -3.64 (0.10), residues: 1010
  sheet: -3.71 (0.29), residues: 198
  loop : -3.92 (0.17), residues: 758

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG C 897 
 TYR   0.021   0.003   TYR C 533 
 PHE   0.049   0.003   PHE C 891 
 TRP   0.022   0.003   TRP A 861 
 HIS   0.005   0.001   HIS C 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00562 (15978)
  covalent geometry    : angle       1.22393 (21570)
  SS BOND              : bond        0.00267 (    6)
  SS BOND              : angle       2.91911 (   12)
  hydrogen bonds       : bond        0.29569 (  716)
  hydrogen bonds       : angle      10.32248 ( 2082)

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

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

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  396 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 392
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  527 MET cc_start: 0.7378 (ptm) cc_final: 0.5895 (mmt)
REVERT: A  669 LYS cc_start: 0.8209 (mtpm) cc_final: 0.7398 (tmtt)
REVERT: A  888 ARG cc_start: 0.6140 (mmp80) cc_final: 0.5806 (ttm-80)
REVERT: A 1001 TYR cc_start: 0.5863 (p90) cc_final: 0.5556 (p90)
REVERT: B  438 PHE cc_start: 0.8323 (p90) cc_final: 0.8008 (p90)
REVERT: B  695 LYS cc_start: 0.7623 (mtmp) cc_final: 0.7256 (mmpt)
REVERT: B  803 LEU cc_start: 0.8074 (mt) cc_final: 0.7812 (mp)
REVERT: C  500 ILE cc_start: 0.8878 (mt) cc_final: 0.8654 (mt)
REVERT: C  527 MET cc_start: 0.6397 (ptm) cc_final: 0.4304 (mmt)
REVERT: C  619 ASN cc_start: 0.8508 (t0) cc_final: 0.8253 (t0)
REVERT: C  814 PHE cc_start: 0.7335 (t80) cc_final: 0.7061 (t80)
REVERT: D  527 MET cc_start: 0.6718 (mtp) cc_final: 0.6501 (mmt)
  outliers start: 4
  outliers final: 2
  residues processed: 394
  average time/residue: 0.1266
  time to fit residues: 71.6084
Evaluate side-chains
  246 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 244
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain C residue  399 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 194 optimal weight:    7.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    6.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 435 HIS
** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 950 HIS
A1000 ASN
B 575 ASN
B 764 ASN
C 435 HIS
C 726 ASN
C 747 ASN
C 950 HIS
C 990 ASN
C1000 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.208446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.182759 restraints weight = 17999.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.172922 restraints weight = 23412.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.168580 restraints weight = 27749.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.167325 restraints weight = 28289.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.165857 restraints weight = 26260.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.3107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  15984  Z= 0.200
  Angle     :  0.762   9.196  21582  Z= 0.401
  Chirality :  0.045   0.211   2428
  Planarity :  0.007   0.087   2654
  Dihedral  :  6.562  48.612   2154
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  : 10.58 %
    Favored  : 88.81 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 11.03 %
    Favored  : 86.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.10 %

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: -3.56 (0.16), residues: 1966
  helix: -1.42 (0.14), residues: 1044
  sheet: -3.58 (0.36), residues: 148
  loop : -3.36 (0.19), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 594 
 TYR   0.027   0.002   TYR A 533 
 PHE   0.024   0.002   PHE A1028 
 TRP   0.015   0.002   TRP D 606 
 HIS   0.004   0.001   HIS B 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 (15978)
  covalent geometry    : angle       0.76048 (21570)
  SS BOND              : bond        0.00291 (    6)
  SS BOND              : angle       1.98502 (   12)
  hydrogen bonds       : bond        0.04672 (  716)
  hydrogen bonds       : angle       5.13052 ( 2082)

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

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

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 249
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  527 MET cc_start: 0.7198 (ptm) cc_final: 0.5886 (mmt)
REVERT: A  669 LYS cc_start: 0.8062 (mtpm) cc_final: 0.7483 (tmtt)
REVERT: A  695 LYS cc_start: 0.7857 (pptt) cc_final: 0.7358 (ptpt)
REVERT: A  975 VAL cc_start: 0.8698 (m) cc_final: 0.8211 (t)
REVERT: A 1029 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.5416 (tmm)
REVERT: C  527 MET cc_start: 0.6956 (ptm) cc_final: 0.5320 (mmt)
REVERT: C  634 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7399 (tm-30)
  outliers start: 46
  outliers final: 20
  residues processed: 282
  average time/residue: 0.1086
  time to fit residues: 47.2857
Evaluate side-chains
  238 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 217
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  519 ASP
Chi-restraints excluded: chain A residue  533 TYR
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  704 LEU
Chi-restraints excluded: chain A residue 1029 MET
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  456 ASP
Chi-restraints excluded: chain C residue  399 THR
Chi-restraints excluded: chain C residue  412 HIS
Chi-restraints excluded: chain C residue  447 ASP
Chi-restraints excluded: chain C residue  459 ILE
Chi-restraints excluded: chain C residue  533 TYR
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  742 LEU
Chi-restraints excluded: chain D residue  406 VAL
Chi-restraints excluded: chain D residue  445 VAL
Chi-restraints excluded: chain D residue  456 ASP
Chi-restraints excluded: chain D residue  482 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 116 optimal weight:    5.9990
   chunk 74 optimal weight:    9.9990
   chunk 120 optimal weight:    0.9980
   chunk 187 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0370
   chunk 144 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 103 optimal weight:    0.7980
   chunk 137 optimal weight:    1.9990
   overall best weight:    0.9662

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

Flipped N/Q/H residues before XYZ refinement:
A 435 HIS
A 747 ASN
A 990 ASN
C 508 GLN
D 418 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.209264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.181945 restraints weight = 18241.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.173499 restraints weight = 26881.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.171391 restraints weight = 31670.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.171398 restraints weight = 28218.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.170101 restraints weight = 25861.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.3847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  15984  Z= 0.154
  Angle     :  0.663   9.906  21582  Z= 0.346
  Chirality :  0.042   0.176   2428
  Planarity :  0.005   0.075   2654
  Dihedral  :  6.056  44.599   2154
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 10.43 %
    Favored  : 89.22 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 12.63 %
    Favored  : 84.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.10 %

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: -2.46 (0.18), residues: 1966
  helix: -0.28 (0.16), residues: 1048
  sheet: -3.29 (0.34), residues: 176
  loop : -3.20 (0.20), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 594 
 TYR   0.018   0.001   TYR C 702 
 PHE   0.023   0.002   PHE D 623 
 TRP   0.011   0.001   TRP D 606 
 HIS   0.003   0.001   HIS D 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (15978)
  covalent geometry    : angle       0.66054 (21570)
  SS BOND              : bond        0.00243 (    6)
  SS BOND              : angle       2.34668 (   12)
  hydrogen bonds       : bond        0.04019 (  716)
  hydrogen bonds       : angle       4.59220 ( 2082)

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

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

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 237
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  440 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.7667 (p90)
REVERT: A  527 MET cc_start: 0.7178 (ptm) cc_final: 0.5845 (mmt)
REVERT: A  663 LYS cc_start: 0.8045 (mmtm) cc_final: 0.7697 (mmtp)
REVERT: A  669 LYS cc_start: 0.7987 (mtpm) cc_final: 0.7448 (tmtt)
REVERT: A  674 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7564 (mtp)
REVERT: A  975 VAL cc_start: 0.8666 (m) cc_final: 0.8205 (t)
REVERT: A  988 MET cc_start: 0.5648 (mmm) cc_final: 0.5255 (mpp)
REVERT: A 1028 PHE cc_start: 0.5369 (t80) cc_final: 0.5136 (t80)
REVERT: C  518 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8194 (pp)
REVERT: C  527 MET cc_start: 0.6752 (ptm) cc_final: 0.5542 (mmt)
REVERT: C  634 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7470 (tm-30)
REVERT: C  669 LYS cc_start: 0.7604 (mtpm) cc_final: 0.7093 (tmtt)
REVERT: D  633 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8015 (pp)
REVERT: D  639 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8442 (tt)
  outliers start: 55
  outliers final: 27
  residues processed: 277
  average time/residue: 0.1162
  time to fit residues: 50.3831
Evaluate side-chains
  238 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 206
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  440 TYR
Chi-restraints excluded: chain A residue  447 ASP
Chi-restraints excluded: chain A residue  519 ASP
Chi-restraints excluded: chain A residue  533 TYR
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  674 MET
Chi-restraints excluded: chain B residue  456 ASP
Chi-restraints excluded: chain B residue  633 ILE
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  741 SER
Chi-restraints excluded: chain B residue  785 SER
Chi-restraints excluded: chain C residue  399 THR
Chi-restraints excluded: chain C residue  412 HIS
Chi-restraints excluded: chain C residue  442 LEU
Chi-restraints excluded: chain C residue  447 ASP
Chi-restraints excluded: chain C residue  459 ILE
Chi-restraints excluded: chain C residue  518 LEU
Chi-restraints excluded: chain C residue  519 ASP
Chi-restraints excluded: chain C residue  533 TYR
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  645 ILE
Chi-restraints excluded: chain C residue  742 LEU
Chi-restraints excluded: chain C residue  811 LEU
Chi-restraints excluded: chain C residue  975 VAL
Chi-restraints excluded: chain D residue  445 VAL
Chi-restraints excluded: chain D residue  456 ASP
Chi-restraints excluded: chain D residue  482 THR
Chi-restraints excluded: chain D residue  633 ILE
Chi-restraints excluded: chain D residue  639 LEU
Chi-restraints excluded: chain D residue  790 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 123 optimal weight:    2.9990
   chunk 160 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 93 optimal weight:    0.0980
   chunk 183 optimal weight:    6.9990
   chunk 33 optimal weight:    0.2980
   chunk 82 optimal weight:    5.9990
   chunk 54 optimal weight:    7.9990
   chunk 155 optimal weight:   10.0000
   chunk 118 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
D 418 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.210891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.186431 restraints weight = 18238.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.176829 restraints weight = 23814.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.173661 restraints weight = 29670.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.172301 restraints weight = 28444.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.171245 restraints weight = 24854.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
moved from start:          0.4262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15984  Z= 0.130
  Angle     :  0.622   8.231  21582  Z= 0.324
  Chirality :  0.041   0.181   2428
  Planarity :  0.005   0.083   2654
  Dihedral  :  5.744  42.430   2154
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.82 %
    Favored  : 89.98 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 14.71 %
    Favored  : 82.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.05 %

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: -1.88 (0.19), residues: 1966
  helix:  0.31 (0.16), residues: 1044
  sheet: -3.20 (0.34), residues: 176
  loop : -3.05 (0.20), residues: 746

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 594 
 TYR   0.019   0.001   TYR A 980 
 PHE   0.022   0.001   PHE D 623 
 TRP   0.016   0.001   TRP D 606 
 HIS   0.002   0.001   HIS D 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (15978)
  covalent geometry    : angle       0.62089 (21570)
  SS BOND              : bond        0.00342 (    6)
  SS BOND              : angle       1.80460 (   12)
  hydrogen bonds       : bond        0.03519 (  716)
  hydrogen bonds       : angle       4.35077 ( 2082)

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

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

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 227
  time to evaluate  : 0.717 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  440 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7602 (p90)
REVERT: A  527 MET cc_start: 0.7064 (ptm) cc_final: 0.5680 (mmt)
REVERT: A  669 LYS cc_start: 0.7839 (mtpm) cc_final: 0.7430 (tmtt)
REVERT: A  674 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7609 (mtp)
REVERT: A  975 VAL cc_start: 0.8529 (m) cc_final: 0.8093 (t)
REVERT: C  440 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.7600 (p90)
REVERT: C  527 MET cc_start: 0.6675 (ptm) cc_final: 0.5440 (mmt)
REVERT: C  634 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7490 (tm-30)
REVERT: C  669 LYS cc_start: 0.7742 (mtpm) cc_final: 0.7222 (tmtt)
REVERT: D  633 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8052 (pp)
  outliers start: 49
  outliers final: 27
  residues processed: 263
  average time/residue: 0.1138
  time to fit residues: 47.3668
Evaluate side-chains
  237 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 206
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  440 TYR
Chi-restraints excluded: chain A residue  447 ASP
Chi-restraints excluded: chain A residue  519 ASP
Chi-restraints excluded: chain A residue  533 TYR
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  674 MET
Chi-restraints excluded: chain A residue  889 VAL
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  456 ASP
Chi-restraints excluded: chain B residue  633 ILE
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  741 SER
Chi-restraints excluded: chain C residue  399 THR
Chi-restraints excluded: chain C residue  407 MET
Chi-restraints excluded: chain C residue  440 TYR
Chi-restraints excluded: chain C residue  447 ASP
Chi-restraints excluded: chain C residue  533 TYR
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  645 ILE
Chi-restraints excluded: chain C residue  734 ILE
Chi-restraints excluded: chain C residue  742 LEU
Chi-restraints excluded: chain C residue  811 LEU
Chi-restraints excluded: chain C residue  889 VAL
Chi-restraints excluded: chain D residue  445 VAL
Chi-restraints excluded: chain D residue  456 ASP
Chi-restraints excluded: chain D residue  482 THR
Chi-restraints excluded: chain D residue  633 ILE
Chi-restraints excluded: chain D residue  790 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 188 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 133 optimal weight:    0.9980
   chunk 128 optimal weight:    1.9990
   chunk 130 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 148 optimal weight:    1.9990
   chunk 164 optimal weight:    0.9980
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
C 642 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.206305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.178534 restraints weight = 18249.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.173235 restraints weight = 27999.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.170661 restraints weight = 24274.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.166908 restraints weight = 28613.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.164740 restraints weight = 32127.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.4620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  15984  Z= 0.184
  Angle     :  0.662   8.753  21582  Z= 0.344
  Chirality :  0.044   0.180   2428
  Planarity :  0.005   0.089   2654
  Dihedral  :  5.775  42.568   2154
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.19 %
    Favored  : 88.61 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 15.18 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.05 %

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: -1.74 (0.19), residues: 1966
  helix:  0.43 (0.16), residues: 1048
  sheet: -3.10 (0.35), residues: 170
  loop : -3.05 (0.21), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 675 
 TYR   0.019   0.002   TYR A 533 
 PHE   0.021   0.002   PHE D 623 
 TRP   0.009   0.001   TRP D 526 
 HIS   0.003   0.001   HIS B 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (15978)
  covalent geometry    : angle       0.65962 (21570)
  SS BOND              : bond        0.00490 (    6)
  SS BOND              : angle       2.27010 (   12)
  hydrogen bonds       : bond        0.03686 (  716)
  hydrogen bonds       : angle       4.46231 ( 2082)

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

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

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 211
  time to evaluate  : 0.624 
Fit side-chains
   revert: symmetry clash
REVERT: A  440 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7688 (p90)
REVERT: A  527 MET cc_start: 0.7185 (ptm) cc_final: 0.6003 (mmt)
REVERT: A  669 LYS cc_start: 0.7718 (mtpm) cc_final: 0.7331 (tmtt)
REVERT: A  674 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7897 (mtp)
REVERT: A  975 VAL cc_start: 0.8558 (m) cc_final: 0.8311 (p)
REVERT: B  591 ILE cc_start: 0.3579 (OUTLIER) cc_final: 0.3100 (pt)
REVERT: B  634 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6567 (mt-10)
REVERT: B  674 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7733 (mtp)
REVERT: C  527 MET cc_start: 0.7116 (ptm) cc_final: 0.5931 (mmt)
REVERT: C  634 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7706 (tm-30)
REVERT: C  669 LYS cc_start: 0.7603 (mtpm) cc_final: 0.7267 (tmtt)
REVERT: D  606 TRP cc_start: 0.6213 (m-10) cc_final: 0.5932 (m-90)
REVERT: D  633 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8055 (pp)
  outliers start: 52
  outliers final: 30
  residues processed: 245
  average time/residue: 0.1132
  time to fit residues: 43.7779
Evaluate side-chains
  235 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 199
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  407 MET
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  440 TYR
Chi-restraints excluded: chain A residue  447 ASP
Chi-restraints excluded: chain A residue  519 ASP
Chi-restraints excluded: chain A residue  533 TYR
Chi-restraints excluded: chain A residue  542 LEU
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  674 MET
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  456 ASP
Chi-restraints excluded: chain B residue  591 ILE
Chi-restraints excluded: chain B residue  633 ILE
Chi-restraints excluded: chain B residue  634 GLU
Chi-restraints excluded: chain B residue  674 MET
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  741 SER
Chi-restraints excluded: chain B residue  785 SER
Chi-restraints excluded: chain B residue  790 SER
Chi-restraints excluded: chain C residue  399 THR
Chi-restraints excluded: chain C residue  406 VAL
Chi-restraints excluded: chain C residue  407 MET
Chi-restraints excluded: chain C residue  447 ASP
Chi-restraints excluded: chain C residue  533 TYR
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  645 ILE
Chi-restraints excluded: chain C residue  742 LEU
Chi-restraints excluded: chain C residue  811 LEU
Chi-restraints excluded: chain C residue  889 VAL
Chi-restraints excluded: chain D residue  445 VAL
Chi-restraints excluded: chain D residue  456 ASP
Chi-restraints excluded: chain D residue  482 THR
Chi-restraints excluded: chain D residue  633 ILE
Chi-restraints excluded: chain D residue  741 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 178 optimal weight:    0.9980
   chunk 119 optimal weight:    0.5980
   chunk 58 optimal weight:    4.9990
   chunk 116 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 166 optimal weight:    0.5980
   chunk 17 optimal weight:    7.9990
   chunk 93 optimal weight:    0.9990
   chunk 112 optimal weight:    0.0770
   chunk 5 optimal weight:    0.6980
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
C 642 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.210707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.175606 restraints weight = 18150.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.174650 restraints weight = 29212.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.173744 restraints weight = 27121.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.172193 restraints weight = 26193.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.171616 restraints weight = 25079.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7123
moved from start:          0.4827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15984  Z= 0.123
  Angle     :  0.605   7.840  21582  Z= 0.314
  Chirality :  0.041   0.182   2428
  Planarity :  0.005   0.076   2654
  Dihedral  :  5.533  39.678   2154
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.97 %
    Favored  : 89.88 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 16.79 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    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: -1.38 (0.19), residues: 1966
  helix:  0.76 (0.17), residues: 1046
  sheet: -3.03 (0.35), residues: 174
  loop : -2.90 (0.21), residues: 746

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 675 
 TYR   0.015   0.001   TYR A 980 
 PHE   0.029   0.001   PHE A1028 
 TRP   0.011   0.001   TRP D 766 
 HIS   0.001   0.001   HIS C 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (15978)
  covalent geometry    : angle       0.60369 (21570)
  SS BOND              : bond        0.00168 (    6)
  SS BOND              : angle       2.02775 (   12)
  hydrogen bonds       : bond        0.03305 (  716)
  hydrogen bonds       : angle       4.25152 ( 2082)

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

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

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 227
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.6817 (ptp) cc_final: 0.6398 (ptp)
REVERT: A  527 MET cc_start: 0.7069 (ptm) cc_final: 0.5669 (mmt)
REVERT: A  585 MET cc_start: 0.5328 (mmt) cc_final: 0.4858 (mmt)
REVERT: A  669 LYS cc_start: 0.7800 (mtpm) cc_final: 0.7382 (tmtt)
REVERT: A  674 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7918 (mtp)
REVERT: A  936 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6511 (mt)
REVERT: A  975 VAL cc_start: 0.8568 (m) cc_final: 0.8316 (p)
REVERT: B  591 ILE cc_start: 0.3232 (OUTLIER) cc_final: 0.2792 (pt)
REVERT: C  440 TYR cc_start: 0.8168 (p90) cc_final: 0.7803 (p90)
REVERT: C  527 MET cc_start: 0.6847 (ptm) cc_final: 0.5343 (mmt)
REVERT: C  634 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7707 (tm-30)
REVERT: C  669 LYS cc_start: 0.7688 (mtpm) cc_final: 0.7276 (tmtt)
REVERT: C 1028 PHE cc_start: 0.5855 (t80) cc_final: 0.5642 (t80)
REVERT: D  633 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7988 (pp)
  outliers start: 41
  outliers final: 28
  residues processed: 250
  average time/residue: 0.1185
  time to fit residues: 46.0605
Evaluate side-chains
  243 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 211
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  407 MET
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  447 ASP
Chi-restraints excluded: chain A residue  533 TYR
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  674 MET
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  889 VAL
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  456 ASP
Chi-restraints excluded: chain B residue  591 ILE
Chi-restraints excluded: chain B residue  633 ILE
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  741 SER
Chi-restraints excluded: chain B residue  785 SER
Chi-restraints excluded: chain B residue  790 SER
Chi-restraints excluded: chain C residue  399 THR
Chi-restraints excluded: chain C residue  406 VAL
Chi-restraints excluded: chain C residue  407 MET
Chi-restraints excluded: chain C residue  447 ASP
Chi-restraints excluded: chain C residue  533 TYR
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  889 VAL
Chi-restraints excluded: chain C residue  966 PHE
Chi-restraints excluded: chain D residue  445 VAL
Chi-restraints excluded: chain D residue  456 ASP
Chi-restraints excluded: chain D residue  482 THR
Chi-restraints excluded: chain D residue  633 ILE
Chi-restraints excluded: chain D residue  741 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 147 optimal weight:   10.0000
   chunk 187 optimal weight:    2.9990
   chunk 96 optimal weight:    3.9990
   chunk 106 optimal weight:    0.9980
   chunk 83 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0270
   chunk 151 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 56 optimal weight:   10.0000
   overall best weight:    1.8044

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

Flipped N/Q/H residues before XYZ refinement:
C 435 HIS
C 642 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.204857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.178279 restraints weight = 18157.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.170908 restraints weight = 28223.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.167888 restraints weight = 28704.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.166085 restraints weight = 30311.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.163556 restraints weight = 28992.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.5002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  15984  Z= 0.219
  Angle     :  0.680   9.620  21582  Z= 0.353
  Chirality :  0.045   0.250   2428
  Planarity :  0.005   0.092   2654
  Dihedral  :  5.696  41.662   2154
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 11.09 %
    Favored  : 88.61 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 16.55 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    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: -1.57 (0.19), residues: 1966
  helix:  0.52 (0.16), residues: 1048
  sheet: -3.04 (0.36), residues: 172
  loop : -2.86 (0.21), residues: 746

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 675 
 TYR   0.025   0.002   TYR A 980 
 PHE   0.024   0.002   PHE D 623 
 TRP   0.042   0.002   TRP D 606 
 HIS   0.003   0.001   HIS B 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 (15978)
  covalent geometry    : angle       0.67729 (21570)
  SS BOND              : bond        0.00370 (    6)
  SS BOND              : angle       2.63650 (   12)
  hydrogen bonds       : bond        0.03703 (  716)
  hydrogen bonds       : angle       4.47857 ( 2082)

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

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

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 210
  time to evaluate  : 0.608 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.6798 (ptp) cc_final: 0.6402 (ptp)
REVERT: A  527 MET cc_start: 0.7238 (ptm) cc_final: 0.6093 (mmt)
REVERT: A  585 MET cc_start: 0.6148 (mmt) cc_final: 0.5563 (mmt)
REVERT: A  663 LYS cc_start: 0.7862 (mmtm) cc_final: 0.7554 (mmtp)
REVERT: A  669 LYS cc_start: 0.7706 (mtpm) cc_final: 0.7360 (tmtt)
REVERT: A  674 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8283 (mtp)
REVERT: A  936 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6486 (mt)
REVERT: A  975 VAL cc_start: 0.8564 (m) cc_final: 0.8314 (p)
REVERT: B  591 ILE cc_start: 0.3669 (OUTLIER) cc_final: 0.3152 (pt)
REVERT: B  634 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6560 (mt-10)
REVERT: B  674 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7679 (mtt)
REVERT: C  527 MET cc_start: 0.7088 (ptm) cc_final: 0.5956 (mmt)
REVERT: C  634 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7750 (tm-30)
REVERT: C  638 ASP cc_start: 0.7523 (m-30) cc_final: 0.7306 (m-30)
REVERT: C  669 LYS cc_start: 0.7616 (mtpm) cc_final: 0.7225 (tmtt)
REVERT: C  880 MET cc_start: 0.2596 (mpp) cc_final: 0.2041 (mmp)
REVERT: C  936 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.6121 (mt)
REVERT: C 1028 PHE cc_start: 0.5825 (t80) cc_final: 0.5614 (t80)
REVERT: D  408 MET cc_start: 0.7386 (mmm) cc_final: 0.7023 (mmt)
REVERT: D  606 TRP cc_start: 0.6461 (m-10) cc_final: 0.6191 (m-90)
REVERT: D  633 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8068 (pp)
  outliers start: 54
  outliers final: 29
  residues processed: 244
  average time/residue: 0.1157
  time to fit residues: 44.2852
Evaluate side-chains
  234 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 198
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  447 ASP
Chi-restraints excluded: chain A residue  533 TYR
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  674 MET
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  456 ASP
Chi-restraints excluded: chain B residue  591 ILE
Chi-restraints excluded: chain B residue  633 ILE
Chi-restraints excluded: chain B residue  634 GLU
Chi-restraints excluded: chain B residue  674 MET
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  741 SER
Chi-restraints excluded: chain B residue  785 SER
Chi-restraints excluded: chain B residue  790 SER
Chi-restraints excluded: chain C residue  399 THR
Chi-restraints excluded: chain C residue  406 VAL
Chi-restraints excluded: chain C residue  447 ASP
Chi-restraints excluded: chain C residue  533 TYR
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  645 ILE
Chi-restraints excluded: chain C residue  742 LEU
Chi-restraints excluded: chain C residue  889 VAL
Chi-restraints excluded: chain C residue  936 LEU
Chi-restraints excluded: chain C residue  966 PHE
Chi-restraints excluded: chain D residue  445 VAL
Chi-restraints excluded: chain D residue  456 ASP
Chi-restraints excluded: chain D residue  482 THR
Chi-restraints excluded: chain D residue  543 VAL
Chi-restraints excluded: chain D residue  633 ILE
Chi-restraints excluded: chain D residue  741 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 187 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 114 optimal weight:    9.9990
   chunk 51 optimal weight:   30.0000
   chunk 15 optimal weight:   10.0000
   chunk 129 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 954 HIS
C 642 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.203464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.178224 restraints weight = 18380.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.169113 restraints weight = 26151.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.165931 restraints weight = 30643.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.164860 restraints weight = 29590.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.162929 restraints weight = 29955.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.5213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062  15984  Z= 0.234
  Angle     :  0.708  15.724  21582  Z= 0.365
  Chirality :  0.046   0.258   2428
  Planarity :  0.005   0.094   2654
  Dihedral  :  5.841  41.515   2154
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 11.80 %
    Favored  : 87.89 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 17.62 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    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: -1.72 (0.19), residues: 1966
  helix:  0.42 (0.16), residues: 1034
  sheet: -3.37 (0.36), residues: 154
  loop : -2.89 (0.21), residues: 778

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 675 
 TYR   0.027   0.002   TYR A 980 
 PHE   0.026   0.002   PHE D 623 
 TRP   0.031   0.002   TRP D 606 
 HIS   0.003   0.001   HIS B 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00575 (15978)
  covalent geometry    : angle       0.70610 (21570)
  SS BOND              : bond        0.00293 (    6)
  SS BOND              : angle       2.55084 (   12)
  hydrogen bonds       : bond        0.03794 (  716)
  hydrogen bonds       : angle       4.55817 ( 2082)

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

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

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 206
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.6848 (ptp) cc_final: 0.6430 (ptp)
REVERT: A  527 MET cc_start: 0.7383 (ptm) cc_final: 0.6050 (mmt)
REVERT: A  570 GLU cc_start: 0.5571 (tt0) cc_final: 0.5236 (tt0)
REVERT: A  585 MET cc_start: 0.6343 (mmt) cc_final: 0.5808 (mmt)
REVERT: A  669 LYS cc_start: 0.7905 (mtpm) cc_final: 0.7377 (tmtt)
REVERT: A  674 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8328 (mtp)
REVERT: A  936 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6310 (mt)
REVERT: A  975 VAL cc_start: 0.8640 (m) cc_final: 0.8380 (p)
REVERT: B  634 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6685 (mt-10)
REVERT: B  674 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7797 (mtp)
REVERT: C  440 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.7911 (p90)
REVERT: C  527 MET cc_start: 0.7293 (ptm) cc_final: 0.6110 (mmt)
REVERT: C  627 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7716 (tm-30)
REVERT: C  634 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7776 (tm-30)
REVERT: C  669 LYS cc_start: 0.7851 (mtpm) cc_final: 0.7262 (tmtt)
REVERT: C  936 LEU cc_start: 0.6483 (OUTLIER) cc_final: 0.6137 (mt)
REVERT: D  408 MET cc_start: 0.7505 (mmm) cc_final: 0.7153 (mmt)
REVERT: D  606 TRP cc_start: 0.6919 (m-10) cc_final: 0.6600 (m-90)
REVERT: D  633 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8115 (pp)
  outliers start: 42
  outliers final: 28
  residues processed: 228
  average time/residue: 0.1179
  time to fit residues: 42.2157
Evaluate side-chains
  239 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 204
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  447 ASP
Chi-restraints excluded: chain A residue  533 TYR
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  674 MET
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  456 ASP
Chi-restraints excluded: chain B residue  633 ILE
Chi-restraints excluded: chain B residue  634 GLU
Chi-restraints excluded: chain B residue  674 MET
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  741 SER
Chi-restraints excluded: chain B residue  785 SER
Chi-restraints excluded: chain B residue  790 SER
Chi-restraints excluded: chain C residue  399 THR
Chi-restraints excluded: chain C residue  440 TYR
Chi-restraints excluded: chain C residue  447 ASP
Chi-restraints excluded: chain C residue  476 ILE
Chi-restraints excluded: chain C residue  533 TYR
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  645 ILE
Chi-restraints excluded: chain C residue  742 LEU
Chi-restraints excluded: chain C residue  889 VAL
Chi-restraints excluded: chain C residue  936 LEU
Chi-restraints excluded: chain D residue  445 VAL
Chi-restraints excluded: chain D residue  456 ASP
Chi-restraints excluded: chain D residue  482 THR
Chi-restraints excluded: chain D residue  543 VAL
Chi-restraints excluded: chain D residue  633 ILE
Chi-restraints excluded: chain D residue  741 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 104 optimal weight:    0.7980
   chunk 197 optimal weight:   10.0000
   chunk 144 optimal weight:    5.9990
   chunk 8 optimal weight:    0.2980
   chunk 52 optimal weight:    0.9990
   chunk 183 optimal weight:    6.9990
   chunk 88 optimal weight:    1.9990
   chunk 116 optimal weight:    0.6980
   chunk 140 optimal weight:    9.9990
   chunk 182 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
C 642 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.208625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.174260 restraints weight = 18195.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.173347 restraints weight = 34117.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.169303 restraints weight = 29713.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.163278 restraints weight = 32087.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.163392 restraints weight = 31274.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
moved from start:          0.5349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  15984  Z= 0.131
  Angle     :  0.620  10.705  21582  Z= 0.321
  Chirality :  0.042   0.182   2428
  Planarity :  0.005   0.083   2654
  Dihedral  :  5.550  39.253   2154
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.38 %
    Favored  : 89.42 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 18.27 %
    Favored  : 79.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    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: -1.39 (0.19), residues: 1966
  helix:  0.72 (0.17), residues: 1046
  sheet: -3.07 (0.36), residues: 176
  loop : -2.82 (0.21), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 675 
 TYR   0.023   0.001   TYR A 980 
 PHE   0.025   0.001   PHE D 623 
 TRP   0.036   0.001   TRP D 606 
 HIS   0.002   0.001   HIS C 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (15978)
  covalent geometry    : angle       0.61774 (21570)
  SS BOND              : bond        0.00221 (    6)
  SS BOND              : angle       2.36193 (   12)
  hydrogen bonds       : bond        0.03307 (  716)
  hydrogen bonds       : angle       4.29752 ( 2082)

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

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

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 216
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.6726 (ptp) cc_final: 0.6326 (ptp)
REVERT: A  527 MET cc_start: 0.7150 (ptm) cc_final: 0.5846 (mmt)
REVERT: A  585 MET cc_start: 0.5964 (mmt) cc_final: 0.5692 (mmt)
REVERT: A  669 LYS cc_start: 0.7919 (mtpm) cc_final: 0.7476 (tmtt)
REVERT: A  936 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.6203 (mt)
REVERT: A  975 VAL cc_start: 0.8611 (m) cc_final: 0.8349 (p)
REVERT: B  634 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.6451 (mt-10)
REVERT: C  527 MET cc_start: 0.6970 (ptm) cc_final: 0.5735 (mmt)
REVERT: C  627 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7643 (tm-30)
REVERT: C  634 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7750 (tm-30)
REVERT: C  669 LYS cc_start: 0.7747 (mtpm) cc_final: 0.7284 (tmtt)
REVERT: C  936 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.6062 (mt)
REVERT: D  408 MET cc_start: 0.7263 (mmm) cc_final: 0.6918 (mmt)
  outliers start: 40
  outliers final: 26
  residues processed: 241
  average time/residue: 0.1161
  time to fit residues: 43.4578
Evaluate side-chains
  231 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 202
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  407 MET
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  447 ASP
Chi-restraints excluded: chain A residue  533 TYR
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  936 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  456 ASP
Chi-restraints excluded: chain B residue  633 ILE
Chi-restraints excluded: chain B residue  634 GLU
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  741 SER
Chi-restraints excluded: chain B residue  785 SER
Chi-restraints excluded: chain B residue  790 SER
Chi-restraints excluded: chain C residue  406 VAL
Chi-restraints excluded: chain C residue  407 MET
Chi-restraints excluded: chain C residue  447 ASP
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain C residue  533 TYR
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  889 VAL
Chi-restraints excluded: chain C residue  936 LEU
Chi-restraints excluded: chain D residue  445 VAL
Chi-restraints excluded: chain D residue  456 ASP
Chi-restraints excluded: chain D residue  482 THR
Chi-restraints excluded: chain D residue  741 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 112 optimal weight:    0.0980
   chunk 49 optimal weight:    8.9990
   chunk 164 optimal weight:    0.1980
   chunk 38 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 183 optimal weight:    7.9990
   chunk 172 optimal weight:    6.9990
   chunk 129 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    1.0586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.206896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.179187 restraints weight = 18208.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.175345 restraints weight = 30355.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.174116 restraints weight = 24401.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.172376 restraints weight = 25899.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.170534 restraints weight = 26288.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.5450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  15984  Z= 0.160
  Angle     :  0.664  16.543  21582  Z= 0.342
  Chirality :  0.043   0.235   2428
  Planarity :  0.005   0.083   2654
  Dihedral  :  5.429  39.272   2152
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.73 %
    Favored  : 89.06 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 18.56 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    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: -1.39 (0.19), residues: 1966
  helix:  0.70 (0.17), residues: 1046
  sheet: -3.05 (0.36), residues: 176
  loop : -2.81 (0.22), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 660 
 TYR   0.024   0.001   TYR A 980 
 PHE   0.026   0.002   PHE C1028 
 TRP   0.069   0.002   TRP D 606 
 HIS   0.002   0.001   HIS B 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (15978)
  covalent geometry    : angle       0.66230 (21570)
  SS BOND              : bond        0.00214 (    6)
  SS BOND              : angle       2.27431 (   12)
  hydrogen bonds       : bond        0.03486 (  716)
  hydrogen bonds       : angle       4.37785 ( 2082)

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

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

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3932 Ramachandran restraints generated.
    1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 213
  time to evaluate  : 0.636 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.6721 (ptp) cc_final: 0.6331 (ptp)
REVERT: A  527 MET cc_start: 0.7227 (ptm) cc_final: 0.5693 (mmt)
REVERT: A  669 LYS cc_start: 0.7898 (mtpm) cc_final: 0.7525 (tmtt)
REVERT: A  975 VAL cc_start: 0.8594 (m) cc_final: 0.8329 (p)
REVERT: B  634 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6533 (mt-10)
REVERT: C  527 MET cc_start: 0.7102 (ptm) cc_final: 0.5705 (mmt)
REVERT: C  627 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7660 (tm-30)
REVERT: C  634 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7723 (tm-30)
REVERT: C  669 LYS cc_start: 0.8045 (mtpm) cc_final: 0.7434 (tmtt)
REVERT: C  880 MET cc_start: 0.3118 (mpp) cc_final: 0.1660 (mmp)
REVERT: C  936 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5959 (mt)
REVERT: D  408 MET cc_start: 0.7295 (mmm) cc_final: 0.6974 (mmt)
REVERT: D  606 TRP cc_start: 0.6880 (m-90) cc_final: 0.6310 (m-90)
  outliers start: 32
  outliers final: 22
  residues processed: 234
  average time/residue: 0.1215
  time to fit residues: 43.8112
Evaluate side-chains
  231 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 207
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  411 ASN
Chi-restraints excluded: chain A residue  447 ASP
Chi-restraints excluded: chain A residue  533 TYR
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  456 ASP
Chi-restraints excluded: chain B residue  633 ILE
Chi-restraints excluded: chain B residue  634 GLU
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  741 SER
Chi-restraints excluded: chain B residue  785 SER
Chi-restraints excluded: chain B residue  790 SER
Chi-restraints excluded: chain C residue  447 ASP
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain C residue  533 TYR
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  645 ILE
Chi-restraints excluded: chain C residue  889 VAL
Chi-restraints excluded: chain C residue  936 LEU
Chi-restraints excluded: chain D residue  445 VAL
Chi-restraints excluded: chain D residue  456 ASP
Chi-restraints excluded: chain D residue  482 THR
Chi-restraints excluded: chain D residue  741 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 160 optimal weight:    7.9990
   chunk 58 optimal weight:    7.9990
   chunk 116 optimal weight:    2.9990
   chunk 185 optimal weight:    4.9990
   chunk 142 optimal weight:   20.0000
   chunk 69 optimal weight:    0.5980
   chunk 84 optimal weight:    0.4980
   chunk 145 optimal weight:    0.4980
   chunk 93 optimal weight:    0.8980
   chunk 121 optimal weight:    0.0980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 586 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.210283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.183562 restraints weight = 18310.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.177259 restraints weight = 27829.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.174153 restraints weight = 33742.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.174190 restraints weight = 31667.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.173325 restraints weight = 25356.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
moved from start:          0.5634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  15984  Z= 0.125
  Angle     :  0.637  10.007  21582  Z= 0.329
  Chirality :  0.042   0.227   2428
  Planarity :  0.005   0.092   2654
  Dihedral  :  5.302  39.034   2152
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.87 %
    Favored  : 89.98 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 19.16 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    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: -1.17 (0.20), residues: 1966
  helix:  0.98 (0.17), residues: 1040
  sheet: -2.97 (0.36), residues: 174
  loop : -2.84 (0.21), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG D 661 
 TYR   0.025   0.001   TYR A 980 
 PHE   0.037   0.001   PHE C1028 
 TRP   0.070   0.001   TRP D 606 
 HIS   0.002   0.001   HIS A 883 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (15978)
  covalent geometry    : angle       0.63375 (21570)
  SS BOND              : bond        0.00704 (    6)
  SS BOND              : angle       2.96221 (   12)
  hydrogen bonds       : bond        0.03256 (  716)
  hydrogen bonds       : angle       4.23614 ( 2082)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2464.59 seconds
wall clock time: 43 minutes 53.41 seconds (2633.41 seconds total)