Starting phenix.real_space_refine
on Thu Sep 18 12:00:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/3j9p_6267/09_2025/3j9p_6267.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/3j9p_6267/09_2025/3j9p_6267.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/3j9p_6267/09_2025/3j9p_6267.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/3j9p_6267/09_2025/3j9p_6267.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/3j9p_6267/09_2025/3j9p_6267.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/3j9p_6267/09_2025/3j9p_6267.cif"
  }
  resolution = 4.24
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     120      5.16       5
     C   11100      2.51       5
     N    2844      2.21       5
     O    2888      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16952
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "D"
      Number of atoms: 4238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 560, 4238
          Classifications: {'peptide': 560}
          Incomplete info: {'truncation_to_alanine': 90}
          Link IDs: {'CIS': 22, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 519}
          Chain breaks: 4
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 302
          Unresolved non-hydrogen angles: 383
          Unresolved non-hydrogen dihedrals: 240
          Unresolved non-hydrogen chiralities: 27
          Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 7, 'ASN:plan1': 9, 'GLU:plan': 13, 'PHE:plan': 1, 'HIS:plan': 3, 'TYR:plan': 2, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 163
  Restraints were copied for chains:
    A, B, C
  Time building chain proxies: 3.26, per 1000 atoms: 0.19
  Number of scatterers: 16952
  At special positions: 0
  Unit cell: (115.482, 115.482, 142.225, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     120     16.00
     O    2888      8.00
     N    2844      7.00
     C   11100      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.43
  Conformation dependent library (CDL) restraints added in 955.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  4400 Ramachandran restraints generated.
    2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4296

  Finding SS restraints...
    Secondary structure from input PDB file:
      100 helices and 0 sheets defined
      65.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'D' and resid 448 through 457
      removed outlier: 3.976A  pdb=" N   PHE D 452 " --> pdb=" O   SER D 448 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 458 through 467
    Processing helix  chain 'D' and resid 484 through 492
      removed outlier: 3.533A  pdb=" N   ALA D 490 " --> pdb=" O   LEU D 486 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASN D 492 " --> pdb=" O   LEU D 488 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 494 through 505
    Processing helix  chain 'D' and resid 516 through 522
      removed outlier: 4.207A  pdb=" N   HIS D 520 " --> pdb=" O   THR D 516 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 527 through 537
      removed outlier: 3.740A  pdb=" N   LEU D 534 " --> pdb=" O   MET D 530 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ASN D 537 " --> pdb=" O   ILE D 533 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 550 through 556
    Processing helix  chain 'D' and resid 560 through 569
      removed outlier: 4.355A  pdb=" N   VAL D 564 " --> pdb=" O   HIS D 560 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 582 through 589
    Processing helix  chain 'D' and resid 592 through 602
      removed outlier: 4.150A  pdb=" N   VAL D 596 " --> pdb=" O   ARG D 592 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   ILE D 600 " --> pdb=" O   VAL D 596 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   ARG D 601 " --> pdb=" O   LEU D 597 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   SER D 602 " --> pdb=" O   THR D 598 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 620 through 627
    Processing helix  chain 'D' and resid 629 through 637
      removed outlier: 3.575A  pdb=" N   CYS D 633 " --> pdb=" O   TYR D 629 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 684 through 691
    Processing helix  chain 'D' and resid 703 through 740
      removed outlier: 3.763A  pdb=" N   TYR D 714 " --> pdb=" O   LYS D 710 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   MET D 721 " --> pdb=" O   ARG D 717 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   GLY D 729 " --> pdb=" O   SER D 725 " (cutoff:3.500A)
      Proline residue:  D 732  - end of helix
    Processing helix  chain 'D' and resid 766 through 783
      removed outlier: 3.548A  pdb=" N   ILE D 770 " --> pdb=" O   ASN D 766 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ILE D 782 " --> pdb=" O   PHE D 778 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   PHE D 783 " --> pdb=" O   LEU D 779 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 804 through 820
      removed outlier: 3.753A  pdb=" N   TYR D 812 " --> pdb=" O   GLU D 808 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 821 through 823
      No H-bonds generated for 'chain 'D' and resid 821 through 823'
    Processing helix  chain 'D' and resid 828 through 850
      removed outlier: 3.694A  pdb=" N   ALA D 836 " --> pdb=" O   TRP D 832 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ILE D 837 " --> pdb=" O   GLN D 833 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   LEU D 848 " --> pdb=" O   MET D 844 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   TYR D 849 " --> pdb=" O   ASN D 845 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 858 through 892
      removed outlier: 3.904A  pdb=" N   ARG D 872 " --> pdb=" O   LYS D 868 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   SER D 873 " --> pdb=" O   THR D 869 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   LEU D 882 " --> pdb=" O   ILE D 878 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 900 through 913
      removed outlier: 4.276A  pdb=" N   LEU D 913 " --> pdb=" O   PHE D 909 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 922 through 929
    Processing helix  chain 'D' and resid 933 through 948
      removed outlier: 4.001A  pdb=" N   ALA D 939 " --> pdb=" O   VAL D 935 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 950 through 970
      removed outlier: 3.965A  pdb=" N   HIS D 970 " --> pdb=" O   ASP D 966 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 970 through 988
      removed outlier: 4.264A  pdb=" N   LYS D 974 " --> pdb=" O   HIS D 970 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1040 through 1071
      removed outlier: 4.217A  pdb=" N   ILE D1044 " --> pdb=" O   LEU D1040 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   TYR D1049 " --> pdb=" O   LEU D1045 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ARG D1050 " --> pdb=" O   LYS D1046 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   LYS D1060 " --> pdb=" O   PHE D1056 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   GLN D1061 " --> pdb=" O   LEU D1057 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   LYS D1071 " --> pdb=" O   LEU D1067 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 457
      removed outlier: 3.977A  pdb=" N   PHE A 452 " --> pdb=" O   SER A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 467
    Processing helix  chain 'A' and resid 484 through 492
      removed outlier: 3.533A  pdb=" N   ALA A 490 " --> pdb=" O   LEU A 486 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ASN A 492 " --> pdb=" O   LEU A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 505
    Processing helix  chain 'A' and resid 516 through 522
      removed outlier: 4.207A  pdb=" N   HIS A 520 " --> pdb=" O   THR A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 537
      removed outlier: 3.740A  pdb=" N   LEU A 534 " --> pdb=" O   MET A 530 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   ASN A 537 " --> pdb=" O   ILE A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 556
    Processing helix  chain 'A' and resid 560 through 569
      removed outlier: 4.356A  pdb=" N   VAL A 564 " --> pdb=" O   HIS A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 589
    Processing helix  chain 'A' and resid 592 through 602
      removed outlier: 4.150A  pdb=" N   VAL A 596 " --> pdb=" O   ARG A 592 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   ILE A 600 " --> pdb=" O   VAL A 596 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   ARG A 601 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   SER A 602 " --> pdb=" O   THR A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 627
    Processing helix  chain 'A' and resid 629 through 637
      removed outlier: 3.574A  pdb=" N   CYS A 633 " --> pdb=" O   TYR A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 684 through 691
    Processing helix  chain 'A' and resid 703 through 740
      removed outlier: 3.764A  pdb=" N   TYR A 714 " --> pdb=" O   LYS A 710 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   MET A 721 " --> pdb=" O   ARG A 717 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   GLY A 729 " --> pdb=" O   SER A 725 " (cutoff:3.500A)
      Proline residue:  A 732  - end of helix
    Processing helix  chain 'A' and resid 766 through 783
      removed outlier: 3.547A  pdb=" N   ILE A 770 " --> pdb=" O   ASN A 766 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ILE A 782 " --> pdb=" O   PHE A 778 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   PHE A 783 " --> pdb=" O   LEU A 779 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 804 through 820
      removed outlier: 3.752A  pdb=" N   TYR A 812 " --> pdb=" O   GLU A 808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 821 through 823
      No H-bonds generated for 'chain 'A' and resid 821 through 823'
    Processing helix  chain 'A' and resid 828 through 850
      removed outlier: 3.695A  pdb=" N   ALA A 836 " --> pdb=" O   TRP A 832 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ILE A 837 " --> pdb=" O   GLN A 833 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   LEU A 848 " --> pdb=" O   MET A 844 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   TYR A 849 " --> pdb=" O   ASN A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 858 through 892
      removed outlier: 3.904A  pdb=" N   ARG A 872 " --> pdb=" O   LYS A 868 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   SER A 873 " --> pdb=" O   THR A 869 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   LEU A 882 " --> pdb=" O   ILE A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 900 through 913
      removed outlier: 4.278A  pdb=" N   LEU A 913 " --> pdb=" O   PHE A 909 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 922 through 929
    Processing helix  chain 'A' and resid 933 through 948
      removed outlier: 4.003A  pdb=" N   ALA A 939 " --> pdb=" O   VAL A 935 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 950 through 970
      removed outlier: 3.964A  pdb=" N   HIS A 970 " --> pdb=" O   ASP A 966 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 988
      removed outlier: 4.264A  pdb=" N   LYS A 974 " --> pdb=" O   HIS A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1040 through 1071
      removed outlier: 4.217A  pdb=" N   ILE A1044 " --> pdb=" O   LEU A1040 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   TYR A1049 " --> pdb=" O   LEU A1045 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ARG A1050 " --> pdb=" O   LYS A1046 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   LYS A1060 " --> pdb=" O   PHE A1056 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   GLN A1061 " --> pdb=" O   LEU A1057 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LYS A1071 " --> pdb=" O   LEU A1067 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 457
      removed outlier: 3.975A  pdb=" N   PHE B 452 " --> pdb=" O   SER B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 467
    Processing helix  chain 'B' and resid 484 through 492
      removed outlier: 3.533A  pdb=" N   ALA B 490 " --> pdb=" O   LEU B 486 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASN B 492 " --> pdb=" O   LEU B 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 494 through 505
    Processing helix  chain 'B' and resid 516 through 522
      removed outlier: 4.208A  pdb=" N   HIS B 520 " --> pdb=" O   THR B 516 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 527 through 537
      removed outlier: 3.741A  pdb=" N   LEU B 534 " --> pdb=" O   MET B 530 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ASN B 537 " --> pdb=" O   ILE B 533 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 550 through 556
    Processing helix  chain 'B' and resid 560 through 569
      removed outlier: 4.355A  pdb=" N   VAL B 564 " --> pdb=" O   HIS B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 582 through 589
    Processing helix  chain 'B' and resid 592 through 602
      removed outlier: 4.151A  pdb=" N   VAL B 596 " --> pdb=" O   ARG B 592 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   ILE B 600 " --> pdb=" O   VAL B 596 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   ARG B 601 " --> pdb=" O   LEU B 597 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   SER B 602 " --> pdb=" O   THR B 598 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 620 through 627
    Processing helix  chain 'B' and resid 629 through 637
      removed outlier: 3.575A  pdb=" N   CYS B 633 " --> pdb=" O   TYR B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 684 through 691
    Processing helix  chain 'B' and resid 703 through 740
      removed outlier: 3.763A  pdb=" N   TYR B 714 " --> pdb=" O   LYS B 710 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   MET B 721 " --> pdb=" O   ARG B 717 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   GLY B 729 " --> pdb=" O   SER B 725 " (cutoff:3.500A)
      Proline residue:  B 732  - end of helix
    Processing helix  chain 'B' and resid 766 through 783
      removed outlier: 3.546A  pdb=" N   ILE B 770 " --> pdb=" O   ASN B 766 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ILE B 782 " --> pdb=" O   PHE B 778 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   PHE B 783 " --> pdb=" O   LEU B 779 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 804 through 820
      removed outlier: 3.753A  pdb=" N   TYR B 812 " --> pdb=" O   GLU B 808 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 821 through 823
      No H-bonds generated for 'chain 'B' and resid 821 through 823'
    Processing helix  chain 'B' and resid 828 through 850
      removed outlier: 3.696A  pdb=" N   ALA B 836 " --> pdb=" O   TRP B 832 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ILE B 837 " --> pdb=" O   GLN B 833 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   LEU B 848 " --> pdb=" O   MET B 844 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   TYR B 849 " --> pdb=" O   ASN B 845 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 858 through 892
      removed outlier: 3.904A  pdb=" N   ARG B 872 " --> pdb=" O   LYS B 868 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   SER B 873 " --> pdb=" O   THR B 869 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   LEU B 882 " --> pdb=" O   ILE B 878 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 900 through 913
      removed outlier: 4.277A  pdb=" N   LEU B 913 " --> pdb=" O   PHE B 909 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 922 through 929
    Processing helix  chain 'B' and resid 933 through 948
      removed outlier: 4.002A  pdb=" N   ALA B 939 " --> pdb=" O   VAL B 935 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 950 through 970
      removed outlier: 3.964A  pdb=" N   HIS B 970 " --> pdb=" O   ASP B 966 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 970 through 988
      removed outlier: 4.265A  pdb=" N   LYS B 974 " --> pdb=" O   HIS B 970 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1040 through 1071
      removed outlier: 4.217A  pdb=" N   ILE B1044 " --> pdb=" O   LEU B1040 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   TYR B1049 " --> pdb=" O   LEU B1045 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ARG B1050 " --> pdb=" O   LYS B1046 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   LYS B1060 " --> pdb=" O   PHE B1056 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   GLN B1061 " --> pdb=" O   LEU B1057 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LYS B1071 " --> pdb=" O   LEU B1067 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 448 through 457
      removed outlier: 3.976A  pdb=" N   PHE C 452 " --> pdb=" O   SER C 448 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 458 through 467
    Processing helix  chain 'C' and resid 484 through 492
      removed outlier: 3.533A  pdb=" N   ALA C 490 " --> pdb=" O   LEU C 486 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASN C 492 " --> pdb=" O   LEU C 488 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 494 through 505
    Processing helix  chain 'C' and resid 516 through 522
      removed outlier: 4.207A  pdb=" N   HIS C 520 " --> pdb=" O   THR C 516 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 527 through 537
      removed outlier: 3.740A  pdb=" N   LEU C 534 " --> pdb=" O   MET C 530 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ASN C 537 " --> pdb=" O   ILE C 533 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 550 through 556
    Processing helix  chain 'C' and resid 560 through 569
      removed outlier: 4.356A  pdb=" N   VAL C 564 " --> pdb=" O   HIS C 560 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 582 through 589
    Processing helix  chain 'C' and resid 592 through 602
      removed outlier: 4.151A  pdb=" N   VAL C 596 " --> pdb=" O   ARG C 592 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   ILE C 600 " --> pdb=" O   VAL C 596 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   ARG C 601 " --> pdb=" O   LEU C 597 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   SER C 602 " --> pdb=" O   THR C 598 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 620 through 627
    Processing helix  chain 'C' and resid 629 through 637
      removed outlier: 3.574A  pdb=" N   CYS C 633 " --> pdb=" O   TYR C 629 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 684 through 691
    Processing helix  chain 'C' and resid 703 through 740
      removed outlier: 3.764A  pdb=" N   TYR C 714 " --> pdb=" O   LYS C 710 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   MET C 721 " --> pdb=" O   ARG C 717 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   GLY C 729 " --> pdb=" O   SER C 725 " (cutoff:3.500A)
      Proline residue:  C 732  - end of helix
    Processing helix  chain 'C' and resid 766 through 783
      removed outlier: 3.548A  pdb=" N   ILE C 770 " --> pdb=" O   ASN C 766 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ILE C 782 " --> pdb=" O   PHE C 778 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   PHE C 783 " --> pdb=" O   LEU C 779 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 804 through 820
      removed outlier: 3.752A  pdb=" N   TYR C 812 " --> pdb=" O   GLU C 808 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 821 through 823
      No H-bonds generated for 'chain 'C' and resid 821 through 823'
    Processing helix  chain 'C' and resid 828 through 850
      removed outlier: 3.694A  pdb=" N   ALA C 836 " --> pdb=" O   TRP C 832 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   ILE C 837 " --> pdb=" O   GLN C 833 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   LEU C 848 " --> pdb=" O   MET C 844 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   TYR C 849 " --> pdb=" O   ASN C 845 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 858 through 892
      removed outlier: 3.904A  pdb=" N   ARG C 872 " --> pdb=" O   LYS C 868 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   SER C 873 " --> pdb=" O   THR C 869 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   LEU C 882 " --> pdb=" O   ILE C 878 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 900 through 913
      removed outlier: 4.278A  pdb=" N   LEU C 913 " --> pdb=" O   PHE C 909 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 922 through 929
    Processing helix  chain 'C' and resid 933 through 948
      removed outlier: 4.001A  pdb=" N   ALA C 939 " --> pdb=" O   VAL C 935 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 950 through 970
      removed outlier: 3.963A  pdb=" N   HIS C 970 " --> pdb=" O   ASP C 966 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 970 through 988
      removed outlier: 4.265A  pdb=" N   LYS C 974 " --> pdb=" O   HIS C 970 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1040 through 1071
      removed outlier: 4.217A  pdb=" N   ILE C1044 " --> pdb=" O   LEU C1040 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   TYR C1049 " --> pdb=" O   LEU C1045 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ARG C1050 " --> pdb=" O   LYS C1046 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   LYS C1060 " --> pdb=" O   PHE C1056 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   GLN C1061 " --> pdb=" O   LEU C1057 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   LYS C1071 " --> pdb=" O   LEU C1067 " (cutoff:3.500A)

    904 hydrogen bonds defined for protein.
    2712 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.16

  Time building geometry restraints manager: 1.88 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 2661
        1.32 -     1.44: 4574
        1.44 -     1.57: 9837
        1.57 -     1.69: 36
        1.69 -     1.82: 196
  Bond restraints: 17304
  Sorted by residual:
  bond pdb=" CA  VAL C 824 "
       pdb=" CB  VAL C 824 "
    ideal  model  delta    sigma   weight residual
    1.540  1.612 -0.072 1.36e-02 5.41e+03 2.82e+01
  bond pdb=" CA  VAL B 824 "
       pdb=" CB  VAL B 824 "
    ideal  model  delta    sigma   weight residual
    1.540  1.612 -0.072 1.36e-02 5.41e+03 2.81e+01
  bond pdb=" CA  VAL D 824 "
       pdb=" CB  VAL D 824 "
    ideal  model  delta    sigma   weight residual
    1.540  1.612 -0.072 1.36e-02 5.41e+03 2.80e+01
  bond pdb=" CA  VAL A 824 "
       pdb=" CB  VAL A 824 "
    ideal  model  delta    sigma   weight residual
    1.540  1.612 -0.071 1.36e-02 5.41e+03 2.76e+01
  bond pdb=" CA  LEU D 480 "
       pdb=" C   LEU D 480 "
    ideal  model  delta    sigma   weight residual
    1.524  1.578 -0.055 1.26e-02 6.30e+03 1.89e+01
  ... (remaining 17299 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.90: 21057
        2.90 -     5.79: 2065
        5.79 -     8.69: 298
        8.69 -    11.58: 60
       11.58 -    14.48: 8
  Bond angle restraints: 23488
  Sorted by residual:
  angle pdb=" C   GLU C 681 "
        pdb=" N   PRO C 682 "
        pdb=" CA  PRO C 682 "
      ideal   model   delta    sigma   weight residual
     119.78  129.49   -9.71 1.03e+00 9.43e-01 8.89e+01
  angle pdb=" C   GLU D 681 "
        pdb=" N   PRO D 682 "
        pdb=" CA  PRO D 682 "
      ideal   model   delta    sigma   weight residual
     119.78  129.47   -9.69 1.03e+00 9.43e-01 8.84e+01
  angle pdb=" C   GLU A 681 "
        pdb=" N   PRO A 682 "
        pdb=" CA  PRO A 682 "
      ideal   model   delta    sigma   weight residual
     119.78  129.46   -9.68 1.03e+00 9.43e-01 8.83e+01
  angle pdb=" C   GLU B 681 "
        pdb=" N   PRO B 682 "
        pdb=" CA  PRO B 682 "
      ideal   model   delta    sigma   weight residual
     119.78  129.45   -9.67 1.03e+00 9.43e-01 8.81e+01
  angle pdb=" N   ASN A 766 "
        pdb=" CA  ASN A 766 "
        pdb=" CB  ASN A 766 "
      ideal   model   delta    sigma   weight residual
     112.41  126.89  -14.48 1.55e+00 4.16e-01 8.73e+01
  ... (remaining 23483 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.99: 9343
       22.99 -    45.98: 729
       45.98 -    68.97: 152
       68.97 -    91.97: 20
       91.97 -   114.96: 4
  Dihedral angle restraints: 10248
    sinusoidal: 3652
      harmonic: 6596
  Sorted by residual:
  dihedral pdb=" CA  PHE A 612 "
           pdb=" C   PHE A 612 "
           pdb=" N   SER A 613 "
           pdb=" CA  SER A 613 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -65.04 -114.96     0      5.00e+00 4.00e-02 5.29e+02
  dihedral pdb=" CA  PHE B 612 "
           pdb=" C   PHE B 612 "
           pdb=" N   SER B 613 "
           pdb=" CA  SER B 613 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -65.09 -114.91     0      5.00e+00 4.00e-02 5.28e+02
  dihedral pdb=" CA  PHE C 612 "
           pdb=" C   PHE C 612 "
           pdb=" N   SER C 613 "
           pdb=" CA  SER C 613 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00  -65.12 -114.88     0      5.00e+00 4.00e-02 5.28e+02
  ... (remaining 10245 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 2146
       0.077 -    0.155: 580
       0.155 -    0.232: 58
       0.232 -    0.309: 16
       0.309 -    0.386: 8
  Chirality restraints: 2808
  Sorted by residual:
  chirality pdb=" CA  VAL A 824 "
            pdb=" N   VAL A 824 "
            pdb=" C   VAL A 824 "
            pdb=" CB  VAL A 824 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.83   -0.39 2.00e-01 2.50e+01 3.73e+00
  chirality pdb=" CA  VAL C 824 "
            pdb=" N   VAL C 824 "
            pdb=" C   VAL C 824 "
            pdb=" CB  VAL C 824 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.83   -0.38 2.00e-01 2.50e+01 3.70e+00
  chirality pdb=" CA  VAL D 824 "
            pdb=" N   VAL D 824 "
            pdb=" C   VAL D 824 "
            pdb=" CB  VAL D 824 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.83   -0.38 2.00e-01 2.50e+01 3.69e+00
  ... (remaining 2805 not shown)

  Planarity restraints: 2888
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN D1047 "   -0.038 2.00e-02 2.50e+03   7.60e-02 5.77e+01
        pdb=" CD  GLN D1047 "    0.131 2.00e-02 2.50e+03
        pdb=" OE1 GLN D1047 "   -0.049 2.00e-02 2.50e+03
        pdb=" NE2 GLN D1047 "   -0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN C1047 "   -0.038 2.00e-02 2.50e+03   7.58e-02 5.75e+01
        pdb=" CD  GLN C1047 "    0.131 2.00e-02 2.50e+03
        pdb=" OE1 GLN C1047 "   -0.049 2.00e-02 2.50e+03
        pdb=" NE2 GLN C1047 "   -0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B1047 "    0.038 2.00e-02 2.50e+03   7.55e-02 5.71e+01
        pdb=" CD  GLN B1047 "   -0.131 2.00e-02 2.50e+03
        pdb=" OE1 GLN B1047 "    0.049 2.00e-02 2.50e+03
        pdb=" NE2 GLN B1047 "    0.044 2.00e-02 2.50e+03
  ... (remaining 2885 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 628
        2.67 -     3.23: 18247
        3.23 -     3.79: 25629
        3.79 -     4.34: 31485
        4.34 -     4.90: 48026
  Nonbonded interactions: 124015
  Sorted by model distance:
  nonbonded pdb=" O   MET A1072 "
            pdb=" NH2 ARG B 458 "
     model   vdw
     2.113 3.120
  nonbonded pdb=" O   HIS C 970 "
            pdb=" ND1 HIS C 970 "
     model   vdw
     2.123 3.120
  nonbonded pdb=" O   HIS D 970 "
            pdb=" ND1 HIS D 970 "
     model   vdw
     2.123 3.120
  nonbonded pdb=" O   HIS B 970 "
            pdb=" ND1 HIS B 970 "
     model   vdw
     2.123 3.120
  nonbonded pdb=" O   HIS A 970 "
            pdb=" ND1 HIS A 970 "
     model   vdw
     2.123 3.120
  ... (remaining 124010 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'D'
  selection = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:                  0.010
  Normalize map: mean=0, sd=1:             1.870
  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:          0.160
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     14.310
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
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      :  0.009   0.072  17304  Z= 0.547
  Angle     :  1.852  14.481  23488  Z= 1.228
  Chirality :  0.070   0.386   2808
  Planarity :  0.006   0.076   2888
  Dihedral  : 17.684 114.956   5952
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 26.35
  Ramachandran Plot:
    Outliers :  1.64 %
    Allowed  : 10.18 %
    Favored  : 88.18 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 24.04 %
    Favored  : 71.33 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 3.68 %
    Twisted Proline : 5.56 %
    Twisted General : 3.96 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.58 (0.15), residues: 2200
  helix: -1.89 (0.11), residues: 1412
  sheet:  None (None), residues: 0
  loop : -3.09 (0.20), residues: 788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 604 
 TYR   0.041   0.004   TYR B 842 
 PHE   0.041   0.004   PHE B 877 
 TRP   0.017   0.003   TRP C 605 
 HIS   0.055   0.005   HIS A 481 

Details of bonding type rmsd
  covalent geometry    : bond        0.00880 (17304)
  covalent geometry    : angle       1.85224 (23488)
  hydrogen bonds       : bond        0.13206 (  904)
  hydrogen bonds       : angle       9.13697 ( 2712)

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

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

  4400 Ramachandran restraints generated.
    2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4400 Ramachandran restraints generated.
    2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  520 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 443
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  819 VAL cc_start: 0.9191 (OUTLIER) cc_final: 0.8949 (m)
REVERT: D  844 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8206 (tmm)
REVERT: D  955 LEU cc_start: 0.9112 (tt) cc_final: 0.8701 (tt)
REVERT: D  959 LEU cc_start: 0.9194 (mp) cc_final: 0.8600 (mp)
REVERT: A  819 VAL cc_start: 0.9210 (OUTLIER) cc_final: 0.8969 (m)
REVERT: A  844 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8223 (tmm)
REVERT: A  955 LEU cc_start: 0.9055 (tt) cc_final: 0.8643 (tt)
REVERT: A  959 LEU cc_start: 0.9172 (mp) cc_final: 0.8575 (mp)
REVERT: A 1050 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7663 (mtt-85)
REVERT: B  819 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8973 (m)
REVERT: B  955 LEU cc_start: 0.9072 (tt) cc_final: 0.8641 (tt)
REVERT: B  959 LEU cc_start: 0.9196 (mp) cc_final: 0.8616 (mp)
REVERT: B 1050 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7664 (mtt-85)
REVERT: C  819 VAL cc_start: 0.9209 (OUTLIER) cc_final: 0.8961 (m)
REVERT: C  844 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8182 (tmm)
REVERT: C  959 LEU cc_start: 0.9197 (mp) cc_final: 0.8682 (mp)
REVERT: C 1050 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7722 (mtt-85)
  outliers start: 77
  outliers final: 20
  residues processed: 492
  average time/residue: 0.1256
  time to fit residues: 91.2760
Evaluate side-chains
  285 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 255
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 216 optimal weight:    1.9990
   chunk 98 optimal weight:    8.9990
   chunk 194 optimal weight:    5.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    4.9990
   chunk 200 optimal weight:   10.0000
   chunk 212 optimal weight:    7.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
D 570 HIS
D 766 ASN
** D 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D1047 GLN
A 570 HIS
A 766 ASN
** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 570 HIS
B 766 ASN
** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 570 HIS
C 766 ASN
** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.043453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.034677 restraints weight = 124532.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.035716 restraints weight = 87526.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.036530 restraints weight = 66044.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.037096 restraints weight = 52921.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.037506 restraints weight = 44761.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.5074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  17304  Z= 0.225
  Angle     :  1.018  12.708  23488  Z= 0.532
  Chirality :  0.049   0.192   2808
  Planarity :  0.005   0.040   2888
  Dihedral  :  8.105  47.120   2356
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 18.36
  Ramachandran Plot:
    Outliers :  1.09 %
    Allowed  :  7.68 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  5.72 %
    Favored  : 94.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 4.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.74 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.37 (0.17), residues: 2200
  helix: -0.80 (0.13), residues: 1428
  sheet:  None (None), residues: 0
  loop : -2.99 (0.21), residues: 772

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 604 
 TYR   0.029   0.002   TYR B 842 
 PHE   0.041   0.002   PHE D 877 
 TRP   0.016   0.002   TRP C 605 
 HIS   0.009   0.002   HIS D 933 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 (17304)
  covalent geometry    : angle       1.01753 (23488)
  hydrogen bonds       : bond        0.06204 (  904)
  hydrogen bonds       : angle       5.71358 ( 2712)

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

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

  4400 Ramachandran restraints generated.
    2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4400 Ramachandran restraints generated.
    2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  375 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 371
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  626 MET cc_start: 0.8544 (mtp) cc_final: 0.8339 (mtm)
REVERT: D  703 CYS cc_start: 0.9169 (t) cc_final: 0.8969 (m)
REVERT: D  706 TYR cc_start: 0.9105 (m-80) cc_final: 0.8632 (m-10)
REVERT: D  733 MET cc_start: 0.9273 (mmp) cc_final: 0.8996 (mmp)
REVERT: D  834 CYS cc_start: 0.9322 (m) cc_final: 0.9119 (m)
REVERT: D  844 MET cc_start: 0.9053 (ttm) cc_final: 0.8736 (tpt)
REVERT: D 1042 MET cc_start: 0.8898 (ppp) cc_final: 0.8677 (ppp)
REVERT: D 1056 PHE cc_start: 0.9308 (t80) cc_final: 0.9078 (t80)
REVERT: D 1059 GLU cc_start: 0.9164 (pt0) cc_final: 0.8882 (pp20)
REVERT: A  626 MET cc_start: 0.8533 (mtp) cc_final: 0.8318 (mtm)
REVERT: A  634 MET cc_start: 0.9333 (tmm) cc_final: 0.9125 (tmm)
REVERT: A  703 CYS cc_start: 0.9165 (t) cc_final: 0.8963 (m)
REVERT: A  706 TYR cc_start: 0.9105 (m-80) cc_final: 0.8629 (m-10)
REVERT: A  834 CYS cc_start: 0.9313 (m) cc_final: 0.9106 (m)
REVERT: A  844 MET cc_start: 0.9072 (ttm) cc_final: 0.8699 (tpt)
REVERT: A 1042 MET cc_start: 0.8908 (ppp) cc_final: 0.8687 (ppp)
REVERT: A 1059 GLU cc_start: 0.9174 (pt0) cc_final: 0.8896 (pp20)
REVERT: B  626 MET cc_start: 0.8541 (mtp) cc_final: 0.8331 (mtm)
REVERT: B  634 MET cc_start: 0.9334 (tmm) cc_final: 0.9128 (tmm)
REVERT: B  703 CYS cc_start: 0.9108 (t) cc_final: 0.8897 (m)
REVERT: B  706 TYR cc_start: 0.9104 (m-80) cc_final: 0.8631 (m-10)
REVERT: B  733 MET cc_start: 0.9285 (mmp) cc_final: 0.9011 (mmp)
REVERT: B  834 CYS cc_start: 0.9310 (m) cc_final: 0.9104 (m)
REVERT: B  844 MET cc_start: 0.8896 (tmm) cc_final: 0.8315 (tpt)
REVERT: B 1042 MET cc_start: 0.8910 (ppp) cc_final: 0.8693 (ppp)
REVERT: B 1059 GLU cc_start: 0.9182 (pt0) cc_final: 0.8908 (pp20)
REVERT: C  626 MET cc_start: 0.8547 (mtp) cc_final: 0.8338 (mtm)
REVERT: C  703 CYS cc_start: 0.9172 (t) cc_final: 0.8964 (m)
REVERT: C  706 TYR cc_start: 0.9141 (m-80) cc_final: 0.8669 (m-10)
REVERT: C  733 MET cc_start: 0.9295 (mmp) cc_final: 0.9022 (mmp)
REVERT: C  834 CYS cc_start: 0.9312 (m) cc_final: 0.9108 (m)
REVERT: C  844 MET cc_start: 0.9045 (ttm) cc_final: 0.8738 (tpt)
REVERT: C  915 ASP cc_start: 0.8022 (p0) cc_final: 0.7314 (p0)
REVERT: C 1042 MET cc_start: 0.8911 (ppp) cc_final: 0.8704 (ppp)
REVERT: C 1056 PHE cc_start: 0.9323 (t80) cc_final: 0.9081 (t80)
REVERT: C 1059 GLU cc_start: 0.9151 (pt0) cc_final: 0.8873 (pp20)
  outliers start: 4
  outliers final: 0
  residues processed: 371
  average time/residue: 0.1036
  time to fit residues: 61.3016
Evaluate side-chains
  244 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 174 optimal weight:    0.0770
   chunk 214 optimal weight:    0.8980
   chunk 187 optimal weight:    0.4980
   chunk 114 optimal weight:   10.0000
   chunk 132 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 177 optimal weight:    9.9990
   chunk 28 optimal weight:    6.9990
   chunk 208 optimal weight:    7.9990
   chunk 90 optimal weight:    0.9980
   chunk 72 optimal weight:    0.6980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
D 549 ASN
D 829 HIS
D 970 HIS
A 549 ASN
A 829 HIS
A 970 HIS
B 549 ASN
B 829 HIS
** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 549 ASN
C 829 HIS
** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.041727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2639 r_free = 0.2639 target = 0.032829 restraints weight = 122791.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.033856 restraints weight = 84865.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.034638 restraints weight = 64111.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.035261 restraints weight = 51314.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.035686 restraints weight = 42775.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.6071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  17304  Z= 0.171
  Angle     :  0.927  12.081  23488  Z= 0.478
  Chirality :  0.046   0.192   2808
  Planarity :  0.004   0.037   2888
  Dihedral  :  6.687  29.773   2356
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  1.09 %
    Allowed  :  7.59 %
    Favored  : 91.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 4.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.90 (0.17), residues: 2200
  helix: -0.34 (0.13), residues: 1404
  sheet:  None (None), residues: 0
  loop : -2.94 (0.21), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 604 
 TYR   0.017   0.001   TYR C 654 
 PHE   0.050   0.002   PHE A 716 
 TRP   0.011   0.001   TRP D 605 
 HIS   0.007   0.001   HIS C 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (17304)
  covalent geometry    : angle       0.92696 (23488)
  hydrogen bonds       : bond        0.05281 (  904)
  hydrogen bonds       : angle       5.05514 ( 2712)

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

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

  4400 Ramachandran restraints generated.
    2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4400 Ramachandran restraints generated.
    2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  373 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 373
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  502 LEU cc_start: 0.9332 (mm) cc_final: 0.9027 (pp)
REVERT: D  603 LYS cc_start: 0.8622 (tppt) cc_final: 0.8393 (tppt)
REVERT: D  703 CYS cc_start: 0.9119 (t) cc_final: 0.8649 (m)
REVERT: D  706 TYR cc_start: 0.9183 (m-80) cc_final: 0.8808 (m-80)
REVERT: D  711 TRP cc_start: 0.8971 (m100) cc_final: 0.8504 (m-10)
REVERT: D  727 CYS cc_start: 0.9110 (t) cc_final: 0.8890 (t)
REVERT: D  774 MET cc_start: 0.9271 (ttp) cc_final: 0.9056 (ptm)
REVERT: D  834 CYS cc_start: 0.9187 (m) cc_final: 0.8288 (p)
REVERT: D  844 MET cc_start: 0.9175 (ttm) cc_final: 0.8700 (tpt)
REVERT: D  850 LEU cc_start: 0.8932 (mt) cc_final: 0.8606 (mt)
REVERT: D  856 CYS cc_start: 0.8921 (m) cc_final: 0.8110 (p)
REVERT: D 1063 GLU cc_start: 0.9260 (tm-30) cc_final: 0.9044 (tm-30)
REVERT: D 1068 ILE cc_start: 0.9229 (mm) cc_final: 0.8950 (mm)
REVERT: A  502 LEU cc_start: 0.9326 (mm) cc_final: 0.9020 (pp)
REVERT: A  603 LYS cc_start: 0.8633 (tppt) cc_final: 0.8397 (tppt)
REVERT: A  703 CYS cc_start: 0.9099 (t) cc_final: 0.8725 (m)
REVERT: A  706 TYR cc_start: 0.9175 (m-80) cc_final: 0.8800 (m-80)
REVERT: A  711 TRP cc_start: 0.8975 (m100) cc_final: 0.8512 (m-10)
REVERT: A  727 CYS cc_start: 0.9107 (t) cc_final: 0.8885 (t)
REVERT: A  774 MET cc_start: 0.9277 (ttp) cc_final: 0.9058 (ptm)
REVERT: A  834 CYS cc_start: 0.9086 (m) cc_final: 0.8212 (p)
REVERT: A  844 MET cc_start: 0.9181 (ttm) cc_final: 0.8645 (tpt)
REVERT: A  850 LEU cc_start: 0.8875 (mt) cc_final: 0.8611 (mt)
REVERT: A  856 CYS cc_start: 0.9053 (m) cc_final: 0.8208 (p)
REVERT: A  877 PHE cc_start: 0.8929 (p90) cc_final: 0.8656 (p90)
REVERT: A 1063 GLU cc_start: 0.9250 (tm-30) cc_final: 0.9037 (tm-30)
REVERT: A 1068 ILE cc_start: 0.9250 (mm) cc_final: 0.8990 (mm)
REVERT: B  479 ASP cc_start: 0.8722 (p0) cc_final: 0.8489 (p0)
REVERT: B  502 LEU cc_start: 0.9344 (mm) cc_final: 0.9040 (pp)
REVERT: B  603 LYS cc_start: 0.8627 (tppt) cc_final: 0.8389 (tppt)
REVERT: B  606 ASP cc_start: 0.7340 (p0) cc_final: 0.6981 (p0)
REVERT: B  697 LEU cc_start: 0.8758 (mt) cc_final: 0.8552 (pp)
REVERT: B  703 CYS cc_start: 0.9099 (t) cc_final: 0.8726 (m)
REVERT: B  706 TYR cc_start: 0.9184 (m-80) cc_final: 0.8808 (m-80)
REVERT: B  711 TRP cc_start: 0.8987 (m100) cc_final: 0.8506 (m-10)
REVERT: B  774 MET cc_start: 0.9268 (ttp) cc_final: 0.9051 (ptm)
REVERT: B  834 CYS cc_start: 0.9093 (m) cc_final: 0.8219 (p)
REVERT: B  844 MET cc_start: 0.9102 (ttp) cc_final: 0.8562 (tpt)
REVERT: B  850 LEU cc_start: 0.8939 (mt) cc_final: 0.8627 (mt)
REVERT: B  856 CYS cc_start: 0.9061 (m) cc_final: 0.8205 (p)
REVERT: B  877 PHE cc_start: 0.8929 (p90) cc_final: 0.8668 (p90)
REVERT: B 1063 GLU cc_start: 0.9258 (tm-30) cc_final: 0.9046 (tm-30)
REVERT: B 1068 ILE cc_start: 0.9259 (mm) cc_final: 0.8997 (mm)
REVERT: C  479 ASP cc_start: 0.8735 (p0) cc_final: 0.8499 (p0)
REVERT: C  502 LEU cc_start: 0.9343 (mm) cc_final: 0.9039 (pp)
REVERT: C  603 LYS cc_start: 0.8617 (tppt) cc_final: 0.8385 (tppt)
REVERT: C  703 CYS cc_start: 0.9121 (t) cc_final: 0.8642 (m)
REVERT: C  706 TYR cc_start: 0.9187 (m-80) cc_final: 0.8808 (m-80)
REVERT: C  711 TRP cc_start: 0.8957 (m100) cc_final: 0.8496 (m-10)
REVERT: C  844 MET cc_start: 0.9185 (ttm) cc_final: 0.8695 (tpt)
REVERT: C  850 LEU cc_start: 0.8939 (mt) cc_final: 0.8618 (mt)
REVERT: C  856 CYS cc_start: 0.9059 (m) cc_final: 0.8204 (p)
REVERT: C  877 PHE cc_start: 0.8896 (p90) cc_final: 0.8563 (p90)
REVERT: C 1063 GLU cc_start: 0.9251 (tm-30) cc_final: 0.9045 (tm-30)
REVERT: C 1068 ILE cc_start: 0.9255 (mm) cc_final: 0.8997 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 373
  average time/residue: 0.0987
  time to fit residues: 58.9085
Evaluate side-chains
  283 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 283
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 92 optimal weight:    6.9990
   chunk 155 optimal weight:    0.4980
   chunk 148 optimal weight:    5.9990
   chunk 183 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9980
   chunk 104 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   chunk 67 optimal weight:    9.9990
   chunk 220 optimal weight:    9.9990
   chunk 222 optimal weight:    3.9990
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
D1062 HIS
** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1062 HIS
** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C1062 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.042321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2633 r_free = 0.2633 target = 0.033134 restraints weight = 120219.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.034127 restraints weight = 86306.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.034851 restraints weight = 66358.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.035403 restraints weight = 53823.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.035798 restraints weight = 45934.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.6654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  17304  Z= 0.177
  Angle     :  0.889  11.279  23488  Z= 0.463
  Chirality :  0.045   0.184   2808
  Planarity :  0.005   0.042   2888
  Dihedral  :  6.356  32.428   2356
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 16.59
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  9.14 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 3.91 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.75 (0.17), residues: 2200
  helix: -0.20 (0.13), residues: 1420
  sheet:  None (None), residues: 0
  loop : -2.98 (0.21), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 604 
 TYR   0.020   0.002   TYR A 629 
 PHE   0.039   0.002   PHE C 877 
 TRP   0.022   0.002   TRP B 711 
 HIS   0.006   0.001   HIS C 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (17304)
  covalent geometry    : angle       0.88873 (23488)
  hydrogen bonds       : bond        0.04964 (  904)
  hydrogen bonds       : angle       4.90814 ( 2712)

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

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

  4400 Ramachandran restraints generated.
    2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4400 Ramachandran restraints generated.
    2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 336
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  603 LYS cc_start: 0.8648 (tppt) cc_final: 0.8425 (tppt)
REVERT: D  640 PHE cc_start: 0.8970 (m-80) cc_final: 0.8670 (m-80)
REVERT: D  697 LEU cc_start: 0.9018 (pp) cc_final: 0.8203 (pp)
REVERT: D  706 TYR cc_start: 0.9179 (m-80) cc_final: 0.8748 (m-80)
REVERT: D  774 MET cc_start: 0.9333 (ttp) cc_final: 0.9099 (ptm)
REVERT: D  834 CYS cc_start: 0.9217 (m) cc_final: 0.8345 (p)
REVERT: D  844 MET cc_start: 0.9201 (ttm) cc_final: 0.8880 (tpt)
REVERT: D  850 LEU cc_start: 0.8958 (mt) cc_final: 0.8658 (mt)
REVERT: D  856 CYS cc_start: 0.8793 (m) cc_final: 0.7824 (p)
REVERT: D  878 ILE cc_start: 0.9197 (tp) cc_final: 0.8981 (pt)
REVERT: D 1059 GLU cc_start: 0.9065 (pt0) cc_final: 0.8719 (pp20)
REVERT: D 1063 GLU cc_start: 0.9292 (tm-30) cc_final: 0.9090 (tm-30)
REVERT: A  603 LYS cc_start: 0.8644 (tppt) cc_final: 0.8419 (tppt)
REVERT: A  640 PHE cc_start: 0.8976 (m-80) cc_final: 0.8665 (m-80)
REVERT: A  697 LEU cc_start: 0.8999 (pp) cc_final: 0.8553 (mp)
REVERT: A  703 CYS cc_start: 0.8778 (t) cc_final: 0.8550 (m)
REVERT: A  706 TYR cc_start: 0.9176 (m-80) cc_final: 0.8721 (m-80)
REVERT: A  733 MET cc_start: 0.9356 (mmp) cc_final: 0.9109 (mmp)
REVERT: A  774 MET cc_start: 0.9323 (ttp) cc_final: 0.9090 (ptm)
REVERT: A  834 CYS cc_start: 0.9221 (m) cc_final: 0.8345 (p)
REVERT: A  844 MET cc_start: 0.9177 (ttm) cc_final: 0.8880 (tpt)
REVERT: A  877 PHE cc_start: 0.8985 (p90) cc_final: 0.8672 (p90)
REVERT: A  878 ILE cc_start: 0.9199 (tp) cc_final: 0.8994 (pt)
REVERT: A 1063 GLU cc_start: 0.9273 (tm-30) cc_final: 0.9060 (tm-30)
REVERT: B  603 LYS cc_start: 0.8639 (tppt) cc_final: 0.8418 (tppt)
REVERT: B  640 PHE cc_start: 0.8932 (m-80) cc_final: 0.8698 (m-80)
REVERT: B  697 LEU cc_start: 0.8779 (mt) cc_final: 0.8081 (mt)
REVERT: B  706 TYR cc_start: 0.9189 (m-80) cc_final: 0.8770 (m-10)
REVERT: B  834 CYS cc_start: 0.9204 (m) cc_final: 0.8326 (p)
REVERT: B  844 MET cc_start: 0.9114 (ttp) cc_final: 0.8763 (tpt)
REVERT: B  850 LEU cc_start: 0.8933 (mt) cc_final: 0.8641 (mt)
REVERT: B  856 CYS cc_start: 0.8921 (m) cc_final: 0.7972 (p)
REVERT: B  860 ILE cc_start: 0.9172 (mp) cc_final: 0.8899 (mp)
REVERT: B  877 PHE cc_start: 0.9009 (p90) cc_final: 0.8699 (p90)
REVERT: B  878 ILE cc_start: 0.9214 (tp) cc_final: 0.9010 (pt)
REVERT: B 1063 GLU cc_start: 0.9293 (tm-30) cc_final: 0.9087 (tm-30)
REVERT: C  603 LYS cc_start: 0.8632 (tppt) cc_final: 0.8414 (tppt)
REVERT: C  640 PHE cc_start: 0.8935 (m-80) cc_final: 0.8703 (m-80)
REVERT: C  697 LEU cc_start: 0.9026 (pp) cc_final: 0.8217 (pp)
REVERT: C  706 TYR cc_start: 0.9171 (m-80) cc_final: 0.8753 (m-80)
REVERT: C  834 CYS cc_start: 0.9265 (m) cc_final: 0.8338 (p)
REVERT: C  844 MET cc_start: 0.9195 (ttm) cc_final: 0.8881 (tpt)
REVERT: C  850 LEU cc_start: 0.8945 (mt) cc_final: 0.8638 (mt)
REVERT: C  856 CYS cc_start: 0.8920 (m) cc_final: 0.7970 (p)
REVERT: C  860 ILE cc_start: 0.9220 (mp) cc_final: 0.8945 (mp)
REVERT: C  873 SER cc_start: 0.9085 (p) cc_final: 0.8870 (m)
REVERT: C  877 PHE cc_start: 0.8940 (p90) cc_final: 0.8675 (p90)
REVERT: C  878 ILE cc_start: 0.9169 (tp) cc_final: 0.8960 (pt)
REVERT: C  915 ASP cc_start: 0.7840 (p0) cc_final: 0.7630 (p0)
REVERT: C 1059 GLU cc_start: 0.9061 (pt0) cc_final: 0.8718 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 336
  average time/residue: 0.0949
  time to fit residues: 51.3252
Evaluate side-chains
  245 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 207 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 200 optimal weight:    0.9990
   chunk 28 optimal weight:    7.9990
   chunk 102 optimal weight:    2.9990
   chunk 83 optimal weight:   10.0000
   chunk 128 optimal weight:    0.5980
   chunk 103 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   chunk 153 optimal weight:    0.6980
   chunk 181 optimal weight:    0.7980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
D1062 HIS
B 970 HIS
B1062 HIS
C 970 HIS
C1062 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.042832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.033636 restraints weight = 119302.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.034627 restraints weight = 85411.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.035392 restraints weight = 65967.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.035972 restraints weight = 53424.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.036388 restraints weight = 45601.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.7134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  17304  Z= 0.164
  Angle     :  0.874  11.192  23488  Z= 0.450
  Chirality :  0.045   0.182   2808
  Planarity :  0.005   0.043   2888
  Dihedral  :  5.934  32.128   2356
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 16.11
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  9.91 %
    Favored  : 89.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 3.91 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.78 (0.17), residues: 2200
  helix: -0.23 (0.13), residues: 1420
  sheet:  None (None), residues: 0
  loop : -2.98 (0.21), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 652 
 TYR   0.032   0.002   TYR B 842 
 PHE   0.030   0.001   PHE A 716 
 TRP   0.007   0.001   TRP C 515 
 HIS   0.008   0.002   HIS D 933 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (17304)
  covalent geometry    : angle       0.87431 (23488)
  hydrogen bonds       : bond        0.04652 (  904)
  hydrogen bonds       : angle       4.90145 ( 2712)

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

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

  4400 Ramachandran restraints generated.
    2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4400 Ramachandran restraints generated.
    2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 327
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  515 TRP cc_start: 0.9075 (m-10) cc_final: 0.8834 (m-10)
REVERT: D  640 PHE cc_start: 0.8803 (m-80) cc_final: 0.8520 (m-80)
REVERT: D  697 LEU cc_start: 0.9155 (pp) cc_final: 0.8841 (pp)
REVERT: D  706 TYR cc_start: 0.9155 (m-80) cc_final: 0.8717 (m-10)
REVERT: D  817 ILE cc_start: 0.9328 (tp) cc_final: 0.9027 (pt)
REVERT: D  844 MET cc_start: 0.9233 (ttm) cc_final: 0.8923 (tpt)
REVERT: D 1063 GLU cc_start: 0.9286 (tm-30) cc_final: 0.9056 (tm-30)
REVERT: D 1068 ILE cc_start: 0.9037 (mm) cc_final: 0.8829 (mm)
REVERT: A  640 PHE cc_start: 0.8802 (m-80) cc_final: 0.8519 (m-80)
REVERT: A  697 LEU cc_start: 0.8932 (pp) cc_final: 0.8544 (pp)
REVERT: A  706 TYR cc_start: 0.9143 (m-80) cc_final: 0.8670 (m-80)
REVERT: A  733 MET cc_start: 0.9321 (mmp) cc_final: 0.9090 (mmp)
REVERT: A  773 CYS cc_start: 0.9477 (t) cc_final: 0.9130 (p)
REVERT: A  834 CYS cc_start: 0.9237 (m) cc_final: 0.8468 (p)
REVERT: A  844 MET cc_start: 0.9273 (ttm) cc_final: 0.8869 (tpt)
REVERT: A 1063 GLU cc_start: 0.9273 (tm-30) cc_final: 0.9036 (tm-30)
REVERT: B  467 GLN cc_start: 0.9169 (tm-30) cc_final: 0.8860 (pp30)
REVERT: B  640 PHE cc_start: 0.8773 (m-80) cc_final: 0.8571 (m-80)
REVERT: B  697 LEU cc_start: 0.8649 (mt) cc_final: 0.8016 (mt)
REVERT: B  706 TYR cc_start: 0.9175 (m-80) cc_final: 0.8727 (m-10)
REVERT: B  733 MET cc_start: 0.9394 (mmp) cc_final: 0.9112 (mmp)
REVERT: B  844 MET cc_start: 0.9059 (ttp) cc_final: 0.8698 (tpt)
REVERT: B 1063 GLU cc_start: 0.9314 (tm-30) cc_final: 0.9094 (tm-30)
REVERT: C  515 TRP cc_start: 0.9086 (m-10) cc_final: 0.8842 (m-10)
REVERT: C  640 PHE cc_start: 0.8822 (m-80) cc_final: 0.8618 (m-80)
REVERT: C  697 LEU cc_start: 0.9153 (pp) cc_final: 0.8863 (pp)
REVERT: C  706 TYR cc_start: 0.9185 (m-80) cc_final: 0.8771 (m-10)
REVERT: C  733 MET cc_start: 0.9350 (mmp) cc_final: 0.9041 (mmp)
REVERT: C  844 MET cc_start: 0.9249 (ttm) cc_final: 0.8919 (tpt)
REVERT: C  915 ASP cc_start: 0.7800 (p0) cc_final: 0.7572 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 327
  average time/residue: 0.1015
  time to fit residues: 52.7221
Evaluate side-chains
  241 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 111 optimal weight:    6.9990
   chunk 195 optimal weight:    8.9990
   chunk 30 optimal weight:    8.9990
   chunk 15 optimal weight:    4.9990
   chunk 121 optimal weight:    9.9990
   chunk 148 optimal weight:    6.9990
   chunk 129 optimal weight:    1.9990
   chunk 188 optimal weight:   20.0000
   chunk 156 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 170 optimal weight:    3.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
D 467 GLN
D 691 GLN
A 467 GLN
A 691 GLN
B 691 GLN
C 691 GLN
C 954 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.039803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2574 r_free = 0.2574 target = 0.031089 restraints weight = 128519.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.032026 restraints weight = 91050.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2633 r_free = 0.2633 target = 0.032814 restraints weight = 69238.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.033329 restraints weight = 55478.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.033701 restraints weight = 47380.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.2657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.7527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  17304  Z= 0.264
  Angle     :  0.938  10.171  23488  Z= 0.493
  Chirality :  0.047   0.197   2808
  Planarity :  0.005   0.043   2888
  Dihedral  :  6.447  35.808   2356
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 21.38
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  9.95 %
    Favored  : 89.50 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  3.01 %
    Favored  : 96.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 3.91 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.96 (0.17), residues: 2200
  helix: -0.42 (0.13), residues: 1424
  sheet:  None (None), residues: 0
  loop : -2.95 (0.21), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 694 
 TYR   0.042   0.003   TYR D 842 
 PHE   0.026   0.003   PHE A 716 
 TRP   0.015   0.002   TRP B 515 
 HIS   0.008   0.002   HIS B 933 

Details of bonding type rmsd
  covalent geometry    : bond        0.00546 (17304)
  covalent geometry    : angle       0.93835 (23488)
  hydrogen bonds       : bond        0.05247 (  904)
  hydrogen bonds       : angle       5.24150 ( 2712)

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

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

  4400 Ramachandran restraints generated.
    2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4400 Ramachandran restraints generated.
    2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 284
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  626 MET cc_start: 0.8116 (mtp) cc_final: 0.7562 (mtm)
REVERT: D  640 PHE cc_start: 0.9032 (m-80) cc_final: 0.8798 (m-80)
REVERT: D  706 TYR cc_start: 0.9137 (m-80) cc_final: 0.8609 (m-10)
REVERT: D  844 MET cc_start: 0.9221 (ttm) cc_final: 0.8993 (tpt)
REVERT: D  878 ILE cc_start: 0.9253 (tp) cc_final: 0.9047 (pt)
REVERT: D 1059 GLU cc_start: 0.9087 (pt0) cc_final: 0.8883 (tm-30)
REVERT: A  626 MET cc_start: 0.8141 (mtp) cc_final: 0.7608 (mtm)
REVERT: A  640 PHE cc_start: 0.9016 (m-80) cc_final: 0.8790 (m-80)
REVERT: A  706 TYR cc_start: 0.9116 (m-80) cc_final: 0.8688 (m-10)
REVERT: A  844 MET cc_start: 0.9249 (ttm) cc_final: 0.8928 (tpt)
REVERT: A  878 ILE cc_start: 0.9273 (tp) cc_final: 0.9069 (pt)
REVERT: B  467 GLN cc_start: 0.9135 (tm-30) cc_final: 0.8660 (pp30)
REVERT: B  626 MET cc_start: 0.8140 (mtp) cc_final: 0.7581 (mtm)
REVERT: B  706 TYR cc_start: 0.9128 (m-80) cc_final: 0.8674 (m-10)
REVERT: B  844 MET cc_start: 0.9120 (ttp) cc_final: 0.8841 (tpt)
REVERT: B  878 ILE cc_start: 0.9261 (tp) cc_final: 0.9060 (pt)
REVERT: C  626 MET cc_start: 0.8117 (mtp) cc_final: 0.7571 (mtm)
REVERT: C  706 TYR cc_start: 0.9142 (m-80) cc_final: 0.8613 (m-10)
REVERT: C  844 MET cc_start: 0.9189 (ttm) cc_final: 0.8941 (tpt)
REVERT: C  878 ILE cc_start: 0.9223 (tp) cc_final: 0.8962 (pt)
  outliers start: 6
  outliers final: 6
  residues processed: 290
  average time/residue: 0.1017
  time to fit residues: 46.6598
Evaluate side-chains
  229 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 223
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 193 optimal weight:    2.9990
   chunk 188 optimal weight:    1.9990
   chunk 161 optimal weight:    0.0170
   chunk 30 optimal weight:    3.9990
   chunk 146 optimal weight:    0.6980
   chunk 14 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 87 optimal weight:    1.9990
   chunk 137 optimal weight:    0.9990
   overall best weight:    0.8822

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

Flipped N/Q/H residues before XYZ refinement:
D 467 GLN
A 467 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.041479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.032264 restraints weight = 116607.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.033272 restraints weight = 81415.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.034060 restraints weight = 62050.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.034644 restraints weight = 49827.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.035145 restraints weight = 42325.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.7747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  17304  Z= 0.163
  Angle     :  0.874  10.709  23488  Z= 0.448
  Chirality :  0.044   0.186   2808
  Planarity :  0.005   0.044   2888
  Dihedral  :  5.874  33.844   2356
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 15.66
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  8.77 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 3.91 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.70 (0.17), residues: 2200
  helix: -0.16 (0.13), residues: 1396
  sheet:  None (None), residues: 0
  loop : -2.88 (0.21), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 458 
 TYR   0.037   0.002   TYR D 842 
 PHE   0.025   0.001   PHE C 877 
 TRP   0.006   0.001   TRP A 605 
 HIS   0.006   0.001   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (17304)
  covalent geometry    : angle       0.87378 (23488)
  hydrogen bonds       : bond        0.04717 (  904)
  hydrogen bonds       : angle       4.87997 ( 2712)

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

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

  4400 Ramachandran restraints generated.
    2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4400 Ramachandran restraints generated.
    2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 302
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  626 MET cc_start: 0.8117 (mtp) cc_final: 0.7560 (mtm)
REVERT: D  642 MET cc_start: 0.6322 (pmm) cc_final: 0.6048 (pmm)
REVERT: D  706 TYR cc_start: 0.9051 (m-80) cc_final: 0.8585 (m-10)
REVERT: D  733 MET cc_start: 0.9256 (mmp) cc_final: 0.8993 (mmp)
REVERT: D  840 TYR cc_start: 0.9068 (t80) cc_final: 0.8835 (t80)
REVERT: D  844 MET cc_start: 0.9203 (ttm) cc_final: 0.8996 (mtp)
REVERT: D  877 PHE cc_start: 0.9088 (p90) cc_final: 0.8658 (p90)
REVERT: D  878 ILE cc_start: 0.9202 (tp) cc_final: 0.8983 (pt)
REVERT: A  642 MET cc_start: 0.6308 (pmm) cc_final: 0.6042 (pmm)
REVERT: A  697 LEU cc_start: 0.8896 (pp) cc_final: 0.8463 (pp)
REVERT: A  698 LEU cc_start: 0.9109 (tp) cc_final: 0.8452 (tp)
REVERT: A  706 TYR cc_start: 0.9036 (m-80) cc_final: 0.8535 (m-10)
REVERT: A  733 MET cc_start: 0.9246 (mmp) cc_final: 0.8970 (mmp)
REVERT: A  840 TYR cc_start: 0.9215 (t80) cc_final: 0.8904 (t80)
REVERT: A  844 MET cc_start: 0.9167 (ttm) cc_final: 0.8708 (mmm)
REVERT: A  877 PHE cc_start: 0.9112 (p90) cc_final: 0.8688 (p90)
REVERT: A  878 ILE cc_start: 0.9260 (tp) cc_final: 0.9045 (pt)
REVERT: B  545 ASP cc_start: 0.8599 (m-30) cc_final: 0.8129 (p0)
REVERT: B  642 MET cc_start: 0.6641 (pmm) cc_final: 0.6396 (pmm)
REVERT: B  697 LEU cc_start: 0.8618 (mt) cc_final: 0.8219 (mt)
REVERT: B  706 TYR cc_start: 0.9072 (m-80) cc_final: 0.8607 (m-10)
REVERT: B  733 MET cc_start: 0.9223 (mmp) cc_final: 0.8945 (mmp)
REVERT: B  844 MET cc_start: 0.9066 (ttp) cc_final: 0.8769 (tpt)
REVERT: B  877 PHE cc_start: 0.9091 (p90) cc_final: 0.8652 (p90)
REVERT: B  878 ILE cc_start: 0.9230 (tp) cc_final: 0.9009 (pt)
REVERT: B 1059 GLU cc_start: 0.9198 (pt0) cc_final: 0.8975 (pt0)
REVERT: C  503 LYS cc_start: 0.9496 (ttpt) cc_final: 0.9285 (ptmt)
REVERT: C  626 MET cc_start: 0.8117 (mtp) cc_final: 0.7571 (mtm)
REVERT: C  642 MET cc_start: 0.6604 (pmm) cc_final: 0.6340 (pmm)
REVERT: C  706 TYR cc_start: 0.9061 (m-80) cc_final: 0.8617 (m-10)
REVERT: C  733 MET cc_start: 0.9251 (mmp) cc_final: 0.8976 (mmp)
REVERT: C  844 MET cc_start: 0.9193 (ttm) cc_final: 0.8933 (mtp)
REVERT: C  878 ILE cc_start: 0.9236 (tp) cc_final: 0.9003 (pt)
REVERT: C 1059 GLU cc_start: 0.9036 (pt0) cc_final: 0.8549 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 302
  average time/residue: 0.1046
  time to fit residues: 49.8954
Evaluate side-chains
  235 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 210 optimal weight:    0.9990
   chunk 135 optimal weight:    2.9990
   chunk 195 optimal weight:    6.9990
   chunk 157 optimal weight:    0.5980
   chunk 121 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 223 optimal weight:   10.0000
   chunk 90 optimal weight:    0.8980
   chunk 170 optimal weight:    9.9990
   chunk 214 optimal weight:    1.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
B 940 GLN
B 954 ASN
C 940 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.041313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.032180 restraints weight = 119882.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2657 r_free = 0.2657 target = 0.033163 restraints weight = 85178.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.033928 restraints weight = 65438.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.034527 restraints weight = 52952.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.034934 restraints weight = 44860.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.7966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  17304  Z= 0.166
  Angle     :  0.879  10.737  23488  Z= 0.454
  Chirality :  0.045   0.271   2808
  Planarity :  0.005   0.046   2888
  Dihedral  :  5.764  32.890   2356
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  : 10.14 %
    Favored  : 89.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 3.91 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.69 (0.17), residues: 2200
  helix: -0.13 (0.13), residues: 1400
  sheet:  None (None), residues: 0
  loop : -2.93 (0.21), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 601 
 TYR   0.034   0.002   TYR C 629 
 PHE   0.030   0.002   PHE A 877 
 TRP   0.012   0.001   TRP D 515 
 HIS   0.006   0.001   HIS B 933 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (17304)
  covalent geometry    : angle       0.87929 (23488)
  hydrogen bonds       : bond        0.04656 (  904)
  hydrogen bonds       : angle       4.85575 ( 2712)

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

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

  4400 Ramachandran restraints generated.
    2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4400 Ramachandran restraints generated.
    2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 309
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  642 MET cc_start: 0.6639 (pmm) cc_final: 0.6309 (pmm)
REVERT: D  706 TYR cc_start: 0.9152 (m-80) cc_final: 0.8680 (m-10)
REVERT: D  733 MET cc_start: 0.9242 (mmp) cc_final: 0.8941 (mmp)
REVERT: D  840 TYR cc_start: 0.9202 (t80) cc_final: 0.8883 (t80)
REVERT: D  844 MET cc_start: 0.9207 (ttm) cc_final: 0.8781 (mmm)
REVERT: D  878 ILE cc_start: 0.9217 (tp) cc_final: 0.9000 (pt)
REVERT: D  912 MET cc_start: 0.9361 (tmm) cc_final: 0.9099 (tmm)
REVERT: D  913 LEU cc_start: 0.8973 (tp) cc_final: 0.8538 (tp)
REVERT: D 1068 ILE cc_start: 0.9208 (mt) cc_final: 0.8903 (mm)
REVERT: A  642 MET cc_start: 0.6764 (pmm) cc_final: 0.6448 (pmm)
REVERT: A  698 LEU cc_start: 0.8843 (tp) cc_final: 0.8382 (tt)
REVERT: A  706 TYR cc_start: 0.9127 (m-80) cc_final: 0.8602 (m-10)
REVERT: A  733 MET cc_start: 0.9248 (mmp) cc_final: 0.8948 (mmp)
REVERT: A  840 TYR cc_start: 0.9251 (t80) cc_final: 0.9015 (t80)
REVERT: A  844 MET cc_start: 0.9189 (ttm) cc_final: 0.8838 (mmm)
REVERT: A  877 PHE cc_start: 0.9192 (p90) cc_final: 0.8742 (p90)
REVERT: A  878 ILE cc_start: 0.9273 (tp) cc_final: 0.9049 (pt)
REVERT: A 1059 GLU cc_start: 0.9093 (pt0) cc_final: 0.8614 (pp20)
REVERT: A 1063 GLU cc_start: 0.9291 (mm-30) cc_final: 0.9061 (mm-30)
REVERT: A 1068 ILE cc_start: 0.9200 (mt) cc_final: 0.8988 (mt)
REVERT: B  545 ASP cc_start: 0.8745 (m-30) cc_final: 0.8121 (p0)
REVERT: B  642 MET cc_start: 0.6941 (pmm) cc_final: 0.6640 (pmm)
REVERT: B  697 LEU cc_start: 0.8629 (mt) cc_final: 0.8171 (mt)
REVERT: B  706 TYR cc_start: 0.9139 (m-80) cc_final: 0.8671 (m-10)
REVERT: B  733 MET cc_start: 0.9267 (mmp) cc_final: 0.9019 (mmp)
REVERT: B  840 TYR cc_start: 0.9347 (t80) cc_final: 0.9054 (t80)
REVERT: B  878 ILE cc_start: 0.9238 (tp) cc_final: 0.9020 (pt)
REVERT: B  912 MET cc_start: 0.9349 (tmm) cc_final: 0.9015 (tmm)
REVERT: B  913 LEU cc_start: 0.8969 (tp) cc_final: 0.8547 (tp)
REVERT: B 1059 GLU cc_start: 0.9236 (pt0) cc_final: 0.9024 (pt0)
REVERT: B 1068 ILE cc_start: 0.9222 (mt) cc_final: 0.8893 (mm)
REVERT: C  642 MET cc_start: 0.6739 (pmm) cc_final: 0.6432 (pmm)
REVERT: C  706 TYR cc_start: 0.9202 (m-80) cc_final: 0.8741 (m-10)
REVERT: C  711 TRP cc_start: 0.8797 (m100) cc_final: 0.8582 (m100)
REVERT: C  733 MET cc_start: 0.9275 (mmp) cc_final: 0.9018 (mmp)
REVERT: C  840 TYR cc_start: 0.9139 (t80) cc_final: 0.8930 (t80)
REVERT: C  844 MET cc_start: 0.9210 (ttm) cc_final: 0.8763 (mmm)
REVERT: C  912 MET cc_start: 0.9367 (tmm) cc_final: 0.9141 (tmm)
REVERT: C  913 LEU cc_start: 0.8990 (tp) cc_final: 0.8706 (tp)
REVERT: C 1059 GLU cc_start: 0.9000 (pt0) cc_final: 0.8772 (pt0)
REVERT: C 1063 GLU cc_start: 0.9083 (mp0) cc_final: 0.8881 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 309
  average time/residue: 0.1004
  time to fit residues: 50.0520
Evaluate side-chains
  239 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 140 optimal weight:    7.9990
   chunk 3 optimal weight:    9.9990
   chunk 109 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 112 optimal weight:    0.0040
   chunk 7 optimal weight:    5.9990
   chunk 212 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   chunk 178 optimal weight:    8.9990
   chunk 59 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    3.4000

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

Flipped N/Q/H residues before XYZ refinement:
D 451 HIS
** D 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 451 HIS
A 691 GLN
B 451 HIS
B 691 GLN
C 691 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.040359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2597 r_free = 0.2597 target = 0.031696 restraints weight = 127847.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.032649 restraints weight = 90539.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.033446 restraints weight = 68553.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.033943 restraints weight = 54694.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.034452 restraints weight = 47069.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.8205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  17304  Z= 0.225
  Angle     :  0.941  10.298  23488  Z= 0.490
  Chirality :  0.048   0.273   2808
  Planarity :  0.005   0.046   2888
  Dihedral  :  6.175  34.173   2356
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 21.11
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  9.95 %
    Favored  : 89.32 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.75 %
    Favored  : 98.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 3.91 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.86 (0.17), residues: 2200
  helix: -0.30 (0.13), residues: 1404
  sheet:  None (None), residues: 0
  loop : -2.93 (0.21), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 694 
 TYR   0.040   0.002   TYR D 842 
 PHE   0.042   0.002   PHE C 877 
 TRP   0.016   0.002   TRP B 605 
 HIS   0.009   0.002   HIS B 933 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 (17304)
  covalent geometry    : angle       0.94094 (23488)
  hydrogen bonds       : bond        0.05008 (  904)
  hydrogen bonds       : angle       5.16292 ( 2712)

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

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

  4400 Ramachandran restraints generated.
    2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4400 Ramachandran restraints generated.
    2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 280
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  642 MET cc_start: 0.7020 (pmm) cc_final: 0.6679 (pmm)
REVERT: D  706 TYR cc_start: 0.9135 (m-80) cc_final: 0.8623 (m-10)
REVERT: D  733 MET cc_start: 0.9246 (mmp) cc_final: 0.8962 (mmp)
REVERT: D  840 TYR cc_start: 0.9205 (t80) cc_final: 0.8842 (t80)
REVERT: D  844 MET cc_start: 0.9180 (ttm) cc_final: 0.8752 (mmm)
REVERT: D 1059 GLU cc_start: 0.9257 (pt0) cc_final: 0.9047 (pt0)
REVERT: D 1068 ILE cc_start: 0.9366 (mt) cc_final: 0.9067 (mm)
REVERT: A  642 MET cc_start: 0.7003 (pmm) cc_final: 0.6671 (pmm)
REVERT: A  691 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8189 (pp30)
REVERT: A  706 TYR cc_start: 0.9054 (m-80) cc_final: 0.8557 (m-10)
REVERT: A  733 MET cc_start: 0.9265 (mmp) cc_final: 0.8990 (mmp)
REVERT: A  844 MET cc_start: 0.9137 (ttm) cc_final: 0.8839 (mmm)
REVERT: A 1059 GLU cc_start: 0.9055 (pt0) cc_final: 0.8250 (tm-30)
REVERT: A 1063 GLU cc_start: 0.9296 (mm-30) cc_final: 0.8582 (mm-30)
REVERT: A 1068 ILE cc_start: 0.9312 (mt) cc_final: 0.9003 (mm)
REVERT: B  642 MET cc_start: 0.7035 (pmm) cc_final: 0.6708 (pmm)
REVERT: B  691 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8236 (pp30)
REVERT: B  706 TYR cc_start: 0.9065 (m-80) cc_final: 0.8686 (m-10)
REVERT: B  733 MET cc_start: 0.9257 (mmp) cc_final: 0.8973 (mmp)
REVERT: B  844 MET cc_start: 0.8758 (mtp) cc_final: 0.8556 (mmm)
REVERT: B 1059 GLU cc_start: 0.9294 (pt0) cc_final: 0.9070 (pt0)
REVERT: B 1068 ILE cc_start: 0.9301 (mt) cc_final: 0.9002 (mm)
REVERT: C  503 LYS cc_start: 0.9328 (ptmt) cc_final: 0.9069 (ptpt)
REVERT: C  642 MET cc_start: 0.7037 (pmm) cc_final: 0.6687 (pmm)
REVERT: C  691 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8168 (pp30)
REVERT: C  706 TYR cc_start: 0.9133 (m-80) cc_final: 0.8560 (m-10)
REVERT: C  720 MET cc_start: 0.8859 (mtm) cc_final: 0.8654 (mpp)
REVERT: C  733 MET cc_start: 0.9266 (mmp) cc_final: 0.8975 (mmp)
REVERT: C  912 MET cc_start: 0.9445 (tmm) cc_final: 0.9134 (tmm)
REVERT: C 1059 GLU cc_start: 0.8940 (pt0) cc_final: 0.8702 (pt0)
REVERT: C 1068 ILE cc_start: 0.9344 (mt) cc_final: 0.9100 (mm)
  outliers start: 3
  outliers final: 0
  residues processed: 283
  average time/residue: 0.0968
  time to fit residues: 44.7481
Evaluate side-chains
  220 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 217
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 80 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9990
   chunk 118 optimal weight:   10.0000
   chunk 152 optimal weight:    0.5980
   chunk 26 optimal weight:    4.9990
   chunk 63 optimal weight:    9.9990
   chunk 178 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 113 optimal weight:    5.9990
   chunk 112 optimal weight:    0.0670
   chunk 138 optimal weight:    2.9990
   overall best weight:    1.0322

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

Flipped N/Q/H residues before XYZ refinement:
D 467 GLN
** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 467 GLN
C 467 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.041953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2642 r_free = 0.2642 target = 0.032833 restraints weight = 119743.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.033846 restraints weight = 84495.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.034587 restraints weight = 64565.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.035132 restraints weight = 52193.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.035671 restraints weight = 44632.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.8356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  17304  Z= 0.166
  Angle     :  0.916  10.854  23488  Z= 0.470
  Chirality :  0.046   0.317   2808
  Planarity :  0.005   0.045   2888
  Dihedral  :  5.847  32.681   2356
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 17.46
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  9.09 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 3.91 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.79 (0.17), residues: 2200
  helix: -0.25 (0.13), residues: 1400
  sheet:  None (None), residues: 0
  loop : -2.88 (0.21), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 601 
 TYR   0.036   0.002   TYR A 629 
 PHE   0.039   0.002   PHE C 877 
 TRP   0.007   0.001   TRP C 515 
 HIS   0.006   0.001   HIS A 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (17304)
  covalent geometry    : angle       0.91585 (23488)
  hydrogen bonds       : bond        0.04735 (  904)
  hydrogen bonds       : angle       4.97203 ( 2712)

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

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

  4400 Ramachandran restraints generated.
    2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4400 Ramachandran restraints generated.
    2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 298
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  642 MET cc_start: 0.6878 (pmm) cc_final: 0.6528 (pmm)
REVERT: D  706 TYR cc_start: 0.9210 (m-80) cc_final: 0.8684 (m-10)
REVERT: D  711 TRP cc_start: 0.9004 (m100) cc_final: 0.8784 (m100)
REVERT: D  720 MET cc_start: 0.8675 (mtm) cc_final: 0.8415 (mpp)
REVERT: D  733 MET cc_start: 0.9277 (mmp) cc_final: 0.9013 (mmp)
REVERT: D  840 TYR cc_start: 0.9221 (t80) cc_final: 0.8935 (t80)
REVERT: D  844 MET cc_start: 0.9218 (ttm) cc_final: 0.8880 (mmm)
REVERT: D  910 SER cc_start: 0.9521 (t) cc_final: 0.9307 (p)
REVERT: D  913 LEU cc_start: 0.8611 (tp) cc_final: 0.8370 (tp)
REVERT: D 1068 ILE cc_start: 0.9369 (mt) cc_final: 0.9041 (mm)
REVERT: A  642 MET cc_start: 0.6878 (pmm) cc_final: 0.6541 (pmm)
REVERT: A  706 TYR cc_start: 0.9116 (m-80) cc_final: 0.8582 (m-10)
REVERT: A  711 TRP cc_start: 0.8989 (m100) cc_final: 0.8751 (m100)
REVERT: A  733 MET cc_start: 0.9277 (mmp) cc_final: 0.9021 (mmp)
REVERT: A  840 TYR cc_start: 0.9282 (t80) cc_final: 0.9016 (t80)
REVERT: A  844 MET cc_start: 0.9180 (ttm) cc_final: 0.8876 (mmm)
REVERT: A 1059 GLU cc_start: 0.9077 (pt0) cc_final: 0.8653 (pp20)
REVERT: A 1068 ILE cc_start: 0.9283 (mt) cc_final: 0.8965 (mm)
REVERT: B  545 ASP cc_start: 0.8827 (m-30) cc_final: 0.8104 (p0)
REVERT: B  642 MET cc_start: 0.6850 (pmm) cc_final: 0.6541 (pmm)
REVERT: B  698 LEU cc_start: 0.9098 (tp) cc_final: 0.8867 (tt)
REVERT: B  706 TYR cc_start: 0.9117 (m-80) cc_final: 0.8635 (m-10)
REVERT: B  733 MET cc_start: 0.9279 (mmp) cc_final: 0.9020 (mmp)
REVERT: B  840 TYR cc_start: 0.9269 (t80) cc_final: 0.8747 (t80)
REVERT: B  844 MET cc_start: 0.8787 (mtp) cc_final: 0.8430 (mmm)
REVERT: B  878 ILE cc_start: 0.9321 (tp) cc_final: 0.9119 (pt)
REVERT: B  913 LEU cc_start: 0.8694 (tp) cc_final: 0.8429 (tp)
REVERT: B  936 LEU cc_start: 0.9269 (mp) cc_final: 0.8964 (tp)
REVERT: B 1063 GLU cc_start: 0.9321 (mm-30) cc_final: 0.9115 (mm-30)
REVERT: B 1068 ILE cc_start: 0.9306 (mt) cc_final: 0.8989 (mm)
REVERT: C  642 MET cc_start: 0.6902 (pmm) cc_final: 0.6564 (pmm)
REVERT: C  706 TYR cc_start: 0.9208 (m-80) cc_final: 0.8672 (m-10)
REVERT: C  733 MET cc_start: 0.9281 (mmp) cc_final: 0.9015 (mmp)
REVERT: C  840 TYR cc_start: 0.9212 (t80) cc_final: 0.8727 (t80)
REVERT: C  844 MET cc_start: 0.8909 (mtp) cc_final: 0.8516 (mmm)
REVERT: C  913 LEU cc_start: 0.8605 (tp) cc_final: 0.8326 (tp)
REVERT: C 1059 GLU cc_start: 0.8988 (pt0) cc_final: 0.8786 (pt0)
REVERT: C 1068 ILE cc_start: 0.9355 (mt) cc_final: 0.9034 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 298
  average time/residue: 0.0885
  time to fit residues: 43.5715
Evaluate side-chains
  237 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 117 optimal weight:    0.8980
   chunk 211 optimal weight:    0.0010
   chunk 199 optimal weight:    0.9990
   chunk 7 optimal weight:    0.4980
   chunk 168 optimal weight:    0.0570
   chunk 116 optimal weight:    0.9990
   chunk 179 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 181 optimal weight:    0.0060
   chunk 35 optimal weight:    0.9980
   chunk 220 optimal weight:    7.9990
   overall best weight:    0.2920

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

Flipped N/Q/H residues before XYZ refinement:
** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 940 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.043890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.034561 restraints weight = 117852.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.035564 restraints weight = 84665.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.036450 restraints weight = 64994.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.037018 restraints weight = 52255.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.037443 restraints weight = 44633.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.8547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  17304  Z= 0.163
  Angle     :  0.911  11.219  23488  Z= 0.463
  Chirality :  0.045   0.270   2808
  Planarity :  0.005   0.047   2888
  Dihedral  :  5.558  30.909   2356
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 15.66
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  8.45 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 3.96 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.81 (0.17), residues: 2200
  helix: -0.28 (0.13), residues: 1408
  sheet:  None (None), residues: 0
  loop : -2.89 (0.21), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 458 
 TYR   0.032   0.002   TYR A 629 
 PHE   0.041   0.001   PHE B 877 
 TRP   0.014   0.001   TRP B 711 
 HIS   0.006   0.001   HIS D 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (17304)
  covalent geometry    : angle       0.91088 (23488)
  hydrogen bonds       : bond        0.04419 (  904)
  hydrogen bonds       : angle       4.79356 ( 2712)

===============================================================================
Job complete
usr+sys time: 2200.31 seconds
wall clock time: 39 minutes 0.36 seconds (2340.36 seconds total)