Starting phenix.real_space_refine
on Sat Jun 14 02:12:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ss5_40744/06_2025/8ss5_40744.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ss5_40744/06_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ss5_40744/06_2025/8ss5_40744.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ss5_40744/06_2025/8ss5_40744.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ss5_40744/06_2025/8ss5_40744.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ss5_40744/06_2025/8ss5_40744.cif"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.91, per 1000 atoms: 0.83
  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: 3.69
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  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: 1.64
  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: 4.65

  Time building geometry restraints manager: 4.45 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:             1.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.600
  Check model and map are aligned:         0.100
  Set scattering table:                    0.150
  Process input model:                     39.630
  Find NCS groups from input model:        0.510
  Set up NCS constraints:                  0.110
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.000
-------------------------------------------------------------------------------
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 : 3.90
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.022   0.003   TRP A 861 
 HIS   0.005   0.001   HIS C 412 
 PHE   0.049   0.003   PHE C 891 
 TYR   0.021   0.003   TYR C 533 
 ARG   0.014   0.001   ARG C 897 

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

*********************** 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  : 1.606 
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: 0.3152
  time to fit residues: 178.6621
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  : 1.802 
-------------------------------------------------------------------------------
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 167 optimal weight:    1.9990
   chunk 150 optimal weight:    0.0670
   chunk 83 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 101 optimal weight:    4.9990
   chunk 80 optimal weight:    0.0970
   chunk 155 optimal weight:   10.0000
   chunk 60 optimal weight:    0.4980
   chunk 94 optimal weight:    3.9990
   chunk 115 optimal weight:    2.9990
   chunk 179 optimal weight:    0.9980
   overall best weight:    0.7318

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

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

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.213305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.191527 restraints weight = 18145.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.184006 restraints weight = 24720.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.182168 restraints weight = 25196.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6948
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  15984  Z= 0.160
  Angle     :  0.721   8.671  21582  Z= 0.381
  Chirality :  0.043   0.194   2428
  Planarity :  0.006   0.083   2654
  Dihedral  :  6.424  47.148   2154
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.56 %
    Allowed  :  9.82 %
    Favored  : 89.62 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 11.45 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.52 (0.16), residues: 1966
  helix: -1.36 (0.14), residues: 1048
  sheet: -3.49 (0.34), residues: 176
  loop : -3.40 (0.19), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 766 
 HIS   0.003   0.001   HIS A 435 
 PHE   0.023   0.002   PHE A1028 
 TYR   0.023   0.002   TYR A 533 
 ARG   0.005   0.001   ARG B 594 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04532 (  716)
  hydrogen bonds       : angle       5.03309 ( 2082)
  SS BOND              : bond        0.00248 (    6)
  SS BOND              : angle       2.08242 (   12)
  covalent geometry    : bond        0.00343 (15978)
  covalent geometry    : angle       0.71929 (21570)

*********************** 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
  301 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 259
  time to evaluate  : 2.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  443 THR cc_start: 0.8696 (p) cc_final: 0.8257 (t)
REVERT: A  527 MET cc_start: 0.7163 (ptm) cc_final: 0.5851 (mmt)
REVERT: A  669 LYS cc_start: 0.7778 (mtpm) cc_final: 0.7388 (tmtt)
REVERT: A  695 LYS cc_start: 0.7722 (pptt) cc_final: 0.7345 (ptpt)
REVERT: A  975 VAL cc_start: 0.8590 (m) cc_final: 0.8144 (t)
REVERT: A 1029 MET cc_start: 0.6600 (OUTLIER) cc_final: 0.5287 (tmm)
REVERT: C  527 MET cc_start: 0.6801 (ptm) cc_final: 0.5238 (mmt)
REVERT: C  714 GLN cc_start: 0.7825 (mm110) cc_final: 0.7580 (mm-40)
REVERT: D  606 TRP cc_start: 0.5782 (m-10) cc_final: 0.5571 (m-10)
  outliers start: 42
  outliers final: 16
  residues processed: 289
  average time/residue: 0.3640
  time to fit residues: 164.7386
Evaluate side-chains
  232 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 215
  time to evaluate  : 4.082 
-------------------------------------------------------------------------------
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  519 ASP
Chi-restraints excluded: chain A residue  533 TYR
Chi-restraints excluded: chain A residue  744 THR
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  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  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 152 optimal weight:    4.9990
   chunk 41 optimal weight:   20.0000
   chunk 122 optimal weight:    9.9990
   chunk 124 optimal weight:    0.9990
   chunk 177 optimal weight:    0.7980
   chunk 43 optimal weight:   20.0000
   chunk 18 optimal weight:    0.9980
   chunk 155 optimal weight:    9.9990
   chunk 166 optimal weight:    0.6980
   chunk 142 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 990 ASN
C 726 ASN
D 418 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.210985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.185311 restraints weight = 18166.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.176297 restraints weight = 24302.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.173937 restraints weight = 30449.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.3736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  15984  Z= 0.152
  Angle     :  0.662  10.141  21582  Z= 0.346
  Chirality :  0.042   0.177   2428
  Planarity :  0.005   0.083   2654
  Dihedral  :  5.951  43.899   2153
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.82 %
    Favored  : 89.88 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 12.34 %
    Favored  : 84.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.41 (0.18), residues: 1966
  helix: -0.23 (0.15), residues: 1040
  sheet: -3.30 (0.34), residues: 176
  loop : -3.16 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 766 
 HIS   0.003   0.001   HIS D 435 
 PHE   0.022   0.002   PHE D 623 
 TYR   0.018   0.001   TYR A 533 
 ARG   0.004   0.000   ARG B 594 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04069 (  716)
  hydrogen bonds       : angle       4.57457 ( 2082)
  SS BOND              : bond        0.00178 (    6)
  SS BOND              : angle       2.33072 (   12)
  covalent geometry    : bond        0.00351 (15978)
  covalent geometry    : angle       0.66020 (21570)

*********************** 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
  280 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 229
  time to evaluate  : 1.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  440 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.7739 (p90)
REVERT: A  527 MET cc_start: 0.7200 (ptm) cc_final: 0.5821 (mmt)
REVERT: A  669 LYS cc_start: 0.7975 (mtpm) cc_final: 0.7459 (tmtt)
REVERT: A  674 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7546 (mtp)
REVERT: A  975 VAL cc_start: 0.8660 (m) cc_final: 0.8245 (t)
REVERT: A  988 MET cc_start: 0.5596 (mmm) cc_final: 0.4955 (mpp)
REVERT: C  518 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8167 (pp)
REVERT: C  527 MET cc_start: 0.6741 (ptm) cc_final: 0.5383 (mmt)
REVERT: C  634 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7397 (tm-30)
REVERT: D  639 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8464 (tt)
  outliers start: 51
  outliers final: 27
  residues processed: 264
  average time/residue: 0.2370
  time to fit residues: 97.7504
Evaluate side-chains
  240 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 209
  time to evaluate  : 2.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  528 CYS
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 A residue  744 THR
Chi-restraints excluded: chain A residue  889 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  412 HIS
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  639 LEU
Chi-restraints excluded: chain C residue  645 ILE
Chi-restraints excluded: chain C residue  742 LEU
Chi-restraints excluded: chain C residue  975 VAL
Chi-restraints excluded: chain D residue  401 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  639 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 192 optimal weight:    0.8980
   chunk 129 optimal weight:    0.5980
   chunk 144 optimal weight:   30.0000
   chunk 49 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 114 optimal weight:    9.9990
   chunk 194 optimal weight:    9.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 747 ASN
D 418 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.210503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.186938 restraints weight = 18129.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.175759 restraints weight = 21649.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.172860 restraints weight = 27353.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.4213

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= 0.143
  Angle     :  0.626  10.971  21582  Z= 0.326
  Chirality :  0.041   0.142   2428
  Planarity :  0.005   0.083   2654
  Dihedral  :  5.684  41.682   2153
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.43 %
    Favored  : 89.37 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 14.29 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.05 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.89 (0.19), residues: 1966
  helix:  0.29 (0.16), residues: 1044
  sheet: -3.21 (0.34), residues: 176
  loop : -3.03 (0.20), residues: 746

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 606 
 HIS   0.002   0.001   HIS B 435 
 PHE   0.027   0.002   PHE A1028 
 TYR   0.018   0.001   TYR A 980 
 ARG   0.003   0.000   ARG A 545 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03596 (  716)
  hydrogen bonds       : angle       4.38981 ( 2082)
  SS BOND              : bond        0.00218 (    6)
  SS BOND              : angle       1.70496 (   12)
  covalent geometry    : bond        0.00331 (15978)
  covalent geometry    : angle       0.62488 (21570)

*********************** 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
  277 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 225
  time to evaluate  : 1.664 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  527 MET cc_start: 0.7086 (ptm) cc_final: 0.5821 (mmt)
REVERT: A  669 LYS cc_start: 0.7810 (mtpm) cc_final: 0.7433 (tmtt)
REVERT: A  674 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7628 (mtp)
REVERT: A  975 VAL cc_start: 0.8574 (m) cc_final: 0.8128 (t)
REVERT: C  518 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8218 (pp)
REVERT: C  527 MET cc_start: 0.6754 (ptm) cc_final: 0.5463 (mmt)
REVERT: C  634 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7436 (tm-30)
REVERT: C  669 LYS cc_start: 0.7573 (mtpm) cc_final: 0.7148 (tmtt)
REVERT: C  714 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7630 (mm-40)
REVERT: D  606 TRP cc_start: 0.6018 (m-10) cc_final: 0.5649 (m-90)
REVERT: D  633 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8047 (pp)
  outliers start: 52
  outliers final: 26
  residues processed: 262
  average time/residue: 0.3109
  time to fit residues: 127.7716
Evaluate side-chains
  234 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 205
  time to evaluate  : 3.815 
-------------------------------------------------------------------------------
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  519 ASP
Chi-restraints excluded: chain A residue  528 CYS
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 A residue  744 THR
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  785 SER
Chi-restraints excluded: chain C residue  399 THR
Chi-restraints excluded: chain C residue  447 ASP
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  705 GLU
Chi-restraints excluded: chain C residue  742 LEU
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  790 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 180 optimal weight:    0.0670
   chunk 135 optimal weight:    7.9990
   chunk 184 optimal weight:    0.8980
   chunk 41 optimal weight:   20.0000
   chunk 175 optimal weight:    0.9990
   chunk 43 optimal weight:    9.9990
   chunk 127 optimal weight:    0.9980
   chunk 173 optimal weight:    9.9990
   chunk 20 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    0.7520

-------------------------------------------------------------------------------
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 = 0.4304 r_free = 0.4304 target = 0.211172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.187048 restraints weight = 18337.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.175473 restraints weight = 22645.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.172439 restraints weight = 29714.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
moved from start:          0.4526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  15984  Z= 0.133
  Angle     :  0.614  15.584  21582  Z= 0.318
  Chirality :  0.041   0.154   2428
  Planarity :  0.005   0.084   2654
  Dihedral  :  5.524  40.295   2153
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.07 %
    Favored  : 89.73 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 15.01 %
    Favored  : 82.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.05 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.19), residues: 1966
  helix:  0.64 (0.16), residues: 1052
  sheet: -3.11 (0.35), residues: 174
  loop : -2.98 (0.21), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 766 
 HIS   0.002   0.001   HIS C 412 
 PHE   0.022   0.001   PHE A1028 
 TYR   0.018   0.001   TYR A 980 
 ARG   0.005   0.000   ARG A 675 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03375 (  716)
  hydrogen bonds       : angle       4.25559 ( 2082)
  SS BOND              : bond        0.00131 (    6)
  SS BOND              : angle       2.37399 (   12)
  covalent geometry    : bond        0.00309 (15978)
  covalent geometry    : angle       0.61181 (21570)

*********************** 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
  268 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 221
  time to evaluate  : 2.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.6861 (ptp) cc_final: 0.6437 (ptp)
REVERT: A  440 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7687 (p90)
REVERT: A  527 MET cc_start: 0.7049 (ptm) cc_final: 0.5805 (mmt)
REVERT: A  669 LYS cc_start: 0.7783 (mtpm) cc_final: 0.7389 (tmtt)
REVERT: A  674 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7735 (mtp)
REVERT: A  975 VAL cc_start: 0.8568 (m) cc_final: 0.8363 (p)
REVERT: B  591 ILE cc_start: 0.3399 (OUTLIER) cc_final: 0.2994 (pt)
REVERT: C  518 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8244 (pp)
REVERT: C  527 MET cc_start: 0.6721 (ptm) cc_final: 0.5396 (mmt)
REVERT: C  634 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7507 (tm-30)
REVERT: C  669 LYS cc_start: 0.7681 (mtpm) cc_final: 0.7181 (tmtt)
REVERT: C  714 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7694 (mm-40)
REVERT: D  633 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7961 (pp)
  outliers start: 47
  outliers final: 30
  residues processed: 251
  average time/residue: 0.2546
  time to fit residues: 99.6880
Evaluate side-chains
  240 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 205
  time to evaluate  : 1.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  528 CYS
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  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 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  518 LEU
Chi-restraints excluded: chain C residue  533 TYR
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  705 GLU
Chi-restraints excluded: chain C residue  734 ILE
Chi-restraints excluded: chain C residue  742 LEU
Chi-restraints excluded: chain C residue  889 VAL
Chi-restraints excluded: chain C residue  966 PHE
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  790 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 76 optimal weight:    8.9990
   chunk 56 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 110 optimal weight:    3.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
B 714 GLN
C 642 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.204000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.175773 restraints weight = 18186.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.168155 restraints weight = 28920.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.165655 restraints weight = 29255.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7227
moved from start:          0.4854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  15984  Z= 0.240
  Angle     :  0.701  15.397  21582  Z= 0.363
  Chirality :  0.045   0.208   2428
  Planarity :  0.006   0.094   2654
  Dihedral  :  5.756  41.725   2153
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 11.44 %
    Favored  : 88.20 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 15.66 %
    Favored  : 81.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.69 (0.19), residues: 1966
  helix:  0.47 (0.16), residues: 1048
  sheet: -3.28 (0.37), residues: 150
  loop : -2.99 (0.21), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 526 
 HIS   0.004   0.001   HIS D 435 
 PHE   0.021   0.002   PHE D 623 
 TYR   0.021   0.002   TYR A 533 
 ARG   0.005   0.000   ARG A 675 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03839 (  716)
  hydrogen bonds       : angle       4.54460 ( 2082)
  SS BOND              : bond        0.00284 (    6)
  SS BOND              : angle       1.99809 (   12)
  covalent geometry    : bond        0.00586 (15978)
  covalent geometry    : angle       0.69988 (21570)

*********************** 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
  262 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 206
  time to evaluate  : 1.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  440 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.7888 (p90)
REVERT: A  527 MET cc_start: 0.7146 (ptm) cc_final: 0.5916 (mmt)
REVERT: A  585 MET cc_start: 0.6390 (mmt) cc_final: 0.6009 (mmt)
REVERT: A  663 LYS cc_start: 0.8007 (mmtm) cc_final: 0.7698 (mmtp)
REVERT: A  669 LYS cc_start: 0.7754 (mtpm) cc_final: 0.7345 (tmtt)
REVERT: A  674 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8181 (mtp)
REVERT: A  975 VAL cc_start: 0.8642 (m) cc_final: 0.8413 (p)
REVERT: A  981 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6722 (mm)
REVERT: B  591 ILE cc_start: 0.3661 (OUTLIER) cc_final: 0.3191 (pt)
REVERT: C  440 TYR cc_start: 0.8159 (p90) cc_final: 0.7912 (p90)
REVERT: C  518 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8457 (pp)
REVERT: C  527 MET cc_start: 0.7141 (ptm) cc_final: 0.5898 (mmt)
REVERT: C  634 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7786 (tm-30)
REVERT: C  638 ASP cc_start: 0.7781 (m-30) cc_final: 0.7554 (m-30)
REVERT: C  669 LYS cc_start: 0.7766 (mtpm) cc_final: 0.7281 (tmtt)
REVERT: C  714 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7768 (mm110)
REVERT: C  981 ILE cc_start: 0.6733 (mm) cc_final: 0.6189 (mm)
REVERT: C 1028 PHE cc_start: 0.5189 (t80) cc_final: 0.4933 (t80)
REVERT: D  633 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8114 (pp)
  outliers start: 56
  outliers final: 29
  residues processed: 238
  average time/residue: 0.2500
  time to fit residues: 93.2360
Evaluate side-chains
  229 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 194
  time to evaluate  : 1.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  528 CYS
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 A residue  981 ILE
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  447 ASP
Chi-restraints excluded: chain C residue  518 LEU
Chi-restraints excluded: chain C residue  533 TYR
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  705 GLU
Chi-restraints excluded: chain C residue  742 LEU
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  543 VAL
Chi-restraints excluded: chain D residue  633 ILE
Chi-restraints excluded: chain D residue  741 SER
Chi-restraints excluded: chain D residue  790 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 8 optimal weight:    0.0070
   chunk 156 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 103 optimal weight:    0.8980
   chunk 18 optimal weight:   10.0000
   chunk 186 optimal weight:    0.4980
   chunk 76 optimal weight:    6.9990
   chunk 162 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 169 optimal weight:    0.0060
   chunk 175 optimal weight:    6.9990
   overall best weight:    0.4014

-------------------------------------------------------------------------------
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 = 0.4296 r_free = 0.4296 target = 0.210564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.184578 restraints weight = 18215.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.175560 restraints weight = 23232.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.172233 restraints weight = 25825.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.5042

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= 0.118
  Angle     :  0.604  14.083  21582  Z= 0.312
  Chirality :  0.040   0.158   2428
  Planarity :  0.005   0.079   2654
  Dihedral  :  5.414  38.681   2153
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.66 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 16.90 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.19), residues: 1966
  helix:  0.88 (0.17), residues: 1054
  sheet: -3.06 (0.35), residues: 176
  loop : -2.91 (0.21), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 766 
 HIS   0.002   0.001   HIS C 435 
 PHE   0.019   0.001   PHE D 623 
 TYR   0.024   0.001   TYR A 980 
 ARG   0.003   0.000   ARG A 675 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03182 (  716)
  hydrogen bonds       : angle       4.20626 ( 2082)
  SS BOND              : bond        0.00216 (    6)
  SS BOND              : angle       2.67649 (   12)
  covalent geometry    : bond        0.00263 (15978)
  covalent geometry    : angle       0.60069 (21570)

*********************** 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
  262 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 225
  time to evaluate  : 1.474 
Fit side-chains
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.6695 (ptp) cc_final: 0.6333 (ptp)
REVERT: A  527 MET cc_start: 0.6864 (ptm) cc_final: 0.5600 (mmt)
REVERT: A  585 MET cc_start: 0.6034 (mmt) cc_final: 0.5626 (mmt)
REVERT: A  669 LYS cc_start: 0.7677 (mtpm) cc_final: 0.7297 (tmtt)
REVERT: A  936 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6477 (mt)
REVERT: B  591 ILE cc_start: 0.3830 (OUTLIER) cc_final: 0.3308 (pt)
REVERT: C  527 MET cc_start: 0.6785 (ptm) cc_final: 0.5478 (mmt)
REVERT: C  634 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7802 (tm-30)
REVERT: C  669 LYS cc_start: 0.7755 (mtpm) cc_final: 0.7302 (tmtt)
REVERT: C  714 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7566 (mm110)
REVERT: C  880 MET cc_start: 0.2496 (mpp) cc_final: 0.1971 (mmp)
REVERT: C  936 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6143 (mt)
REVERT: D  633 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7993 (pp)
  outliers start: 37
  outliers final: 22
  residues processed: 246
  average time/residue: 0.2640
  time to fit residues: 103.6240
Evaluate side-chains
  229 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 203
  time to evaluate  : 1.724 
-------------------------------------------------------------------------------
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  542 LEU
Chi-restraints excluded: chain A residue  630 VAL
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  591 ILE
Chi-restraints excluded: chain B residue  633 ILE
Chi-restraints excluded: chain B residue  681 VAL
Chi-restraints excluded: chain B residue  785 SER
Chi-restraints excluded: chain B residue  790 SER
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 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  790 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 140 optimal weight:   10.0000
   chunk 20 optimal weight:    0.5980
   chunk 119 optimal weight:    1.9990
   chunk 135 optimal weight:    6.9990
   chunk 196 optimal weight:    0.8980
   chunk 41 optimal weight:   20.0000
   chunk 43 optimal weight:   20.0000
   chunk 188 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 147 optimal weight:    4.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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 = 0.4268 r_free = 0.4268 target = 0.207092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.179235 restraints weight = 18091.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.172203 restraints weight = 28315.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.169544 restraints weight = 35426.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7182
moved from start:          0.5158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  15984  Z= 0.178
  Angle     :  0.655  16.284  21582  Z= 0.337
  Chirality :  0.043   0.225   2428
  Planarity :  0.005   0.092   2654
  Dihedral  :  5.399  39.473   2152
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.68 %
    Favored  : 89.11 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 16.67 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.19), residues: 1966
  helix:  0.80 (0.17), residues: 1038
  sheet: -3.05 (0.36), residues: 174
  loop : -2.86 (0.21), residues: 754

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.060   0.002   TRP D 606 
 HIS   0.003   0.001   HIS A 412 
 PHE   0.025   0.002   PHE D 623 
 TYR   0.022   0.001   TYR A 980 
 ARG   0.003   0.000   ARG A 675 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03482 (  716)
  hydrogen bonds       : angle       4.36074 ( 2082)
  SS BOND              : bond        0.00219 (    6)
  SS BOND              : angle       2.50798 (   12)
  covalent geometry    : bond        0.00432 (15978)
  covalent geometry    : angle       0.65269 (21570)

*********************** 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
  255 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 211
  time to evaluate  : 2.816 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.6632 (ptp) cc_final: 0.6196 (ptp)
REVERT: A  527 MET cc_start: 0.7016 (ptm) cc_final: 0.5812 (mmt)
REVERT: A  669 LYS cc_start: 0.7559 (mtpm) cc_final: 0.7280 (tmtt)
REVERT: A  674 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8123 (mtp)
REVERT: A  936 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6412 (mt)
REVERT: B  591 ILE cc_start: 0.3750 (OUTLIER) cc_final: 0.3327 (pt)
REVERT: C  527 MET cc_start: 0.7055 (ptm) cc_final: 0.5925 (mmt)
REVERT: C  634 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7741 (tm-30)
REVERT: C  669 LYS cc_start: 0.7614 (mtpm) cc_final: 0.7287 (tmtt)
REVERT: C  714 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7631 (mm110)
REVERT: C  880 MET cc_start: 0.2304 (mpp) cc_final: 0.1735 (mmp)
REVERT: C  936 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6169 (mt)
REVERT: C 1029 MET cc_start: 0.6301 (mmm) cc_final: 0.5358 (mmm)
REVERT: D  606 TRP cc_start: 0.6490 (m-90) cc_final: 0.6284 (m-90)
REVERT: D  633 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8052 (pp)
REVERT: D  639 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8450 (tt)
  outliers start: 44
  outliers final: 25
  residues processed: 240
  average time/residue: 0.2905
  time to fit residues: 109.3821
Evaluate side-chains
  236 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 205
  time to evaluate  : 1.715 
-------------------------------------------------------------------------------
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  542 LEU
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  681 VAL
Chi-restraints excluded: chain B residue  785 SER
Chi-restraints excluded: chain B residue  790 SER
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  705 GLU
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  639 LEU
Chi-restraints excluded: chain D residue  790 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 191 optimal weight:    0.6980
   chunk 83 optimal weight:    2.9990
   chunk 147 optimal weight:    7.9990
   chunk 193 optimal weight:    3.9990
   chunk 123 optimal weight:    1.9990
   chunk 165 optimal weight:    0.7980
   chunk 122 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 91 optimal weight:    0.2980
   chunk 44 optimal weight:    5.9990
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.4296 r_free = 0.4296 target = 0.210064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.179213 restraints weight = 18180.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.173457 restraints weight = 33345.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.172150 restraints weight = 31864.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
moved from start:          0.5317

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= 0.135
  Angle     :  0.634  16.091  21582  Z= 0.324
  Chirality :  0.042   0.184   2428
  Planarity :  0.005   0.089   2654
  Dihedral  :  5.322  38.384   2152
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.02 %
    Favored  : 89.78 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 17.44 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.19), residues: 1966
  helix:  0.95 (0.17), residues: 1038
  sheet: -3.03 (0.36), residues: 178
  loop : -2.82 (0.21), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.001   TRP D 606 
 HIS   0.002   0.001   HIS C 883 
 PHE   0.029   0.001   PHE C1028 
 TYR   0.021   0.001   TYR A 980 
 ARG   0.003   0.000   ARG A 675 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03325 (  716)
  hydrogen bonds       : angle       4.24651 ( 2082)
  SS BOND              : bond        0.00211 (    6)
  SS BOND              : angle       2.32367 (   12)
  covalent geometry    : bond        0.00314 (15978)
  covalent geometry    : angle       0.63147 (21570)

*********************** 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
  254 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 216
  time to evaluate  : 1.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 MET cc_start: 0.7995 (mmm) cc_final: 0.7391 (mmm)
REVERT: A  414 MET cc_start: 0.6716 (ptp) cc_final: 0.6304 (ptp)
REVERT: A  527 MET cc_start: 0.7011 (ptm) cc_final: 0.5587 (mmt)
REVERT: A  669 LYS cc_start: 0.7700 (mtpm) cc_final: 0.7326 (tmtt)
REVERT: A  674 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8263 (mtp)
REVERT: A  936 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6385 (mt)
REVERT: B  591 ILE cc_start: 0.3738 (OUTLIER) cc_final: 0.3195 (pt)
REVERT: C  527 MET cc_start: 0.7016 (ptm) cc_final: 0.5668 (mmt)
REVERT: C  634 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7767 (tm-30)
REVERT: C  669 LYS cc_start: 0.7958 (mtpm) cc_final: 0.7419 (tmtt)
REVERT: C  714 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7661 (mm110)
REVERT: C  936 LEU cc_start: 0.6356 (OUTLIER) cc_final: 0.6078 (mt)
REVERT: D  633 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7996 (pp)
  outliers start: 38
  outliers final: 26
  residues processed: 241
  average time/residue: 0.2569
  time to fit residues: 95.8166
Evaluate side-chains
  234 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 203
  time to evaluate  : 2.128 
-------------------------------------------------------------------------------
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  649 THR
Chi-restraints excluded: chain A residue  674 MET
Chi-restraints excluded: chain A residue  789 LEU
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  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  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  643 THR
Chi-restraints excluded: chain C residue  645 ILE
Chi-restraints excluded: chain C residue  705 GLU
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  633 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 23 optimal weight:    0.0570
   chunk 185 optimal weight:    0.8980
   chunk 149 optimal weight:    9.9990
   chunk 134 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0870
   chunk 49 optimal weight:    0.6980
   chunk 147 optimal weight:    2.9990
   chunk 188 optimal weight:    5.9990
   chunk 163 optimal weight:    0.0170
   chunk 114 optimal weight:    9.9990
   overall best weight:    0.3514

-------------------------------------------------------------------------------
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 = 0.4318 r_free = 0.4318 target = 0.212334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 95)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.177518 restraints weight = 18237.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.175561 restraints weight = 30670.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.168936 restraints weight = 28179.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7243
moved from start:          0.5485

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= 0.118
  Angle     :  0.626  15.743  21582  Z= 0.318
  Chirality :  0.041   0.151   2428
  Planarity :  0.005   0.091   2654
  Dihedral  :  5.157  38.655   2152
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.77 %
    Favored  : 90.08 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 17.56 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.20), residues: 1966
  helix:  1.16 (0.17), residues: 1048
  sheet: -2.89 (0.37), residues: 174
  loop : -2.93 (0.21), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.001   TRP D 606 
 HIS   0.002   0.001   HIS C 883 
 PHE   0.029   0.001   PHE C1028 
 TYR   0.017   0.001   TYR A 980 
 ARG   0.012   0.000   ARG D 661 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03080 (  716)
  hydrogen bonds       : angle       4.12212 ( 2082)
  SS BOND              : bond        0.00261 (    6)
  SS BOND              : angle       2.96982 (   12)
  covalent geometry    : bond        0.00263 (15978)
  covalent geometry    : angle       0.62267 (21570)

********************** 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
  247 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 217
  time to evaluate  : 1.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 MET cc_start: 0.8097 (mmm) cc_final: 0.7372 (mmm)
REVERT: A  414 MET cc_start: 0.6794 (ptp) cc_final: 0.6400 (ptp)
REVERT: A  527 MET cc_start: 0.6565 (ptm) cc_final: 0.5183 (mmt)
REVERT: A  669 LYS cc_start: 0.8026 (mtpm) cc_final: 0.7457 (tmtt)
REVERT: A  936 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6560 (mt)
REVERT: B  591 ILE cc_start: 0.3512 (OUTLIER) cc_final: 0.2998 (pt)
REVERT: C  527 MET cc_start: 0.6757 (ptm) cc_final: 0.5289 (mmt)
REVERT: C  634 GLU cc_start: 0.8503 (tm-30) cc_final: 0.7978 (tm-30)
REVERT: C  669 LYS cc_start: 0.8189 (mtpm) cc_final: 0.7478 (tmtt)
REVERT: C  714 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7670 (mm110)
REVERT: C  936 LEU cc_start: 0.6092 (OUTLIER) cc_final: 0.5707 (mt)
REVERT: C 1029 MET cc_start: 0.6700 (mmm) cc_final: 0.5919 (mmm)
  outliers start: 30
  outliers final: 21
  residues processed: 235
  average time/residue: 0.2823
  time to fit residues: 103.3104
Evaluate side-chains
  229 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 205
  time to evaluate  : 2.926 
-------------------------------------------------------------------------------
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  645 ILE
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  789 LEU
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  681 VAL
Chi-restraints excluded: chain B residue  785 SER
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 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 152 optimal weight:    0.0050
   chunk 128 optimal weight:    0.9990
   chunk 137 optimal weight:    1.9990
   chunk 176 optimal weight:    9.9990
   chunk 192 optimal weight:    0.9990
   chunk 154 optimal weight:    9.9990
   chunk 3 optimal weight:    2.9990
   chunk 145 optimal weight:    0.8980
   chunk 188 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.7198

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.210403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.184033 restraints weight = 18082.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.177811 restraints weight = 25850.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.174072 restraints weight = 23965.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          0.5575

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= 0.135
  Angle     :  0.641  15.735  21582  Z= 0.325
  Chirality :  0.041   0.178   2428
  Planarity :  0.005   0.092   2654
  Dihedral  :  5.172  38.517   2152
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.97 %
    Favored  : 89.83 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 18.33 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.67 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.20), residues: 1966
  helix:  1.15 (0.17), residues: 1056
  sheet: -2.88 (0.37), residues: 174
  loop : -2.86 (0.21), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.001   TRP D 606 
 HIS   0.002   0.001   HIS C 883 
 PHE   0.025   0.001   PHE D 623 
 TYR   0.020   0.001   TYR D 647 
 ARG   0.013   0.000   ARG D 661 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03151 (  716)
  hydrogen bonds       : angle       4.17872 ( 2082)
  SS BOND              : bond        0.00258 (    6)
  SS BOND              : angle       2.99408 (   12)
  covalent geometry    : bond        0.00317 (15978)
  covalent geometry    : angle       0.63711 (21570)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5116.44 seconds
wall clock time: 92 minutes 35.13 seconds (5555.13 seconds total)