Starting phenix.real_space_refine
on Sat Jun 14 21:40:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/3j9p_6267/06_2025/3j9p_6267.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/3j9p_6267/06_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_6267/06_2025/3j9p_6267.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/3j9p_6267/06_2025/3j9p_6267.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/3j9p_6267/06_2025/3j9p_6267.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/3j9p_6267/06_2025/3j9p_6267.cif"
  }
  resolution = 4.24
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
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): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 16952
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      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: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 163
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 9.68, per 1000 atoms: 0.57
  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: 4.40
  Conformation dependent library (CDL) restraints added in 2.4 seconds
  

  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: 1.69
  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: 4.47

  Time building geometry restraints manager: 5.15 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: 0.12
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.760
  Check model and map are aligned:         0.150
  Set scattering table:                    0.150
  Process input model:                     38.590
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.860
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.58 (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
 TRP   0.017   0.003   TRP C 605 
 HIS   0.055   0.005   HIS A 481 
 PHE   0.041   0.004   PHE B 877 
 TYR   0.041   0.004   TYR B 842 
 ARG   0.011   0.001   ARG C 604 

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

*********************** 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  : 2.101 
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: 0.8948 (m)
REVERT: D  844 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8205 (tmm)
REVERT: D  955 LEU cc_start: 0.9112 (tt) cc_final: 0.8700 (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: 0.8968 (m)
REVERT: A  844 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8222 (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: 0.8574 (mp)
REVERT: A 1050 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7698 (mtt-85)
REVERT: B  819 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8972 (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: 0.8615 (mp)
REVERT: B 1050 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7697 (mtt-85)
REVERT: C  819 VAL cc_start: 0.9209 (OUTLIER) cc_final: 0.8960 (m)
REVERT: C  844 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8181 (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: 0.7700 (mtt-85)
  outliers start: 77
  outliers final: 20
  residues processed: 492
  average time/residue: 0.3015
  time to fit residues: 217.7209
Evaluate side-chains
  297 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 267
  time to evaluate  : 1.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 189 optimal weight:    0.0570
   chunk 169 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   chunk 57 optimal weight:    8.9990
   chunk 114 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 175 optimal weight:    6.9990
   chunk 67 optimal weight:    0.0170
   chunk 106 optimal weight:    8.9990
   chunk 130 optimal weight:    7.9990
   chunk 203 optimal weight:    6.9990
   overall best weight:    1.1940

-------------------------------------------------------------------------------
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 = 0.2914 r_free = 0.2914 target = 0.043395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.034546 restraints weight = 119261.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.035550 restraints weight = 83687.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.036340 restraints weight = 63847.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.5004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  17304  Z= 0.197
  Angle     :  1.011  13.010  23488  Z= 0.524
  Chirality :  0.049   0.197   2808
  Planarity :  0.005   0.033   2888
  Dihedral  :  7.944  46.593   2356
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 17.13
  Ramachandran Plot:
    Outliers :  1.09 %
    Allowed  :  7.05 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  5.12 %
    Favored  : 94.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 4.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.56 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.17), residues: 2200
  helix: -0.71 (0.13), residues: 1400
  sheet:  None (None), residues: 0
  loop : -2.92 (0.20), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 605 
 HIS   0.007   0.002   HIS A 494 
 PHE   0.043   0.002   PHE C 877 
 TYR   0.026   0.002   TYR B 842 
 ARG   0.010   0.001   ARG B 604 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06059 (  904)
  hydrogen bonds       : angle       5.58861 ( 2712)
  covalent geometry    : bond        0.00400 (17304)
  covalent geometry    : angle       1.01063 (23488)

*********************** 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
  385 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 381
  time to evaluate  : 2.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  486 LEU cc_start: 0.9580 (mp) cc_final: 0.9369 (tp)
REVERT: D  593 LYS cc_start: 0.9216 (tptm) cc_final: 0.8993 (tppt)
REVERT: D  634 MET cc_start: 0.9322 (tmm) cc_final: 0.9121 (tmm)
REVERT: D  697 LEU cc_start: 0.8790 (mt) cc_final: 0.8520 (mt)
REVERT: D  711 TRP cc_start: 0.9013 (m100) cc_final: 0.8812 (m100)
REVERT: D  720 MET cc_start: 0.8772 (mmp) cc_final: 0.8544 (mmt)
REVERT: D  721 MET cc_start: 0.8703 (tmm) cc_final: 0.8495 (tmm)
REVERT: D  733 MET cc_start: 0.9301 (mmp) cc_final: 0.9065 (mmp)
REVERT: D  834 CYS cc_start: 0.9222 (m) cc_final: 0.8191 (p)
REVERT: D  844 MET cc_start: 0.9124 (ttm) cc_final: 0.8766 (tpt)
REVERT: D 1042 MET cc_start: 0.8755 (ppp) cc_final: 0.8527 (ppp)
REVERT: D 1056 PHE cc_start: 0.9245 (t80) cc_final: 0.9045 (t80)
REVERT: D 1059 GLU cc_start: 0.9140 (pt0) cc_final: 0.8817 (pp20)
REVERT: A  486 LEU cc_start: 0.9579 (mp) cc_final: 0.9362 (tp)
REVERT: A  697 LEU cc_start: 0.8788 (mt) cc_final: 0.8507 (mt)
REVERT: A  720 MET cc_start: 0.8785 (mmp) cc_final: 0.8553 (mmt)
REVERT: A  721 MET cc_start: 0.8702 (tmm) cc_final: 0.8494 (tmm)
REVERT: A  834 CYS cc_start: 0.9222 (m) cc_final: 0.8974 (m)
REVERT: A  844 MET cc_start: 0.9144 (ttm) cc_final: 0.8826 (tpt)
REVERT: A 1042 MET cc_start: 0.8775 (ppp) cc_final: 0.8522 (ppp)
REVERT: A 1059 GLU cc_start: 0.9116 (pt0) cc_final: 0.8826 (pp20)
REVERT: B  486 LEU cc_start: 0.9577 (mp) cc_final: 0.9369 (tp)
REVERT: B  593 LYS cc_start: 0.9247 (tptm) cc_final: 0.9025 (tppt)
REVERT: B  697 LEU cc_start: 0.8788 (mt) cc_final: 0.8508 (mt)
REVERT: B  720 MET cc_start: 0.8797 (mmp) cc_final: 0.8562 (mmt)
REVERT: B  721 MET cc_start: 0.8702 (tmm) cc_final: 0.8481 (tmm)
REVERT: B  727 CYS cc_start: 0.9012 (t) cc_final: 0.8810 (t)
REVERT: B  733 MET cc_start: 0.9299 (mmp) cc_final: 0.9008 (mmp)
REVERT: B  834 CYS cc_start: 0.9219 (m) cc_final: 0.8211 (p)
REVERT: B  844 MET cc_start: 0.8793 (tmm) cc_final: 0.8252 (tpt)
REVERT: B 1042 MET cc_start: 0.8874 (ppp) cc_final: 0.8611 (ppp)
REVERT: B 1059 GLU cc_start: 0.9145 (pt0) cc_final: 0.8867 (pp20)
REVERT: C  486 LEU cc_start: 0.9575 (mp) cc_final: 0.9367 (tp)
REVERT: C  593 LYS cc_start: 0.9235 (tptm) cc_final: 0.9016 (tppt)
REVERT: C  697 LEU cc_start: 0.8788 (mt) cc_final: 0.8510 (mt)
REVERT: C  720 MET cc_start: 0.8765 (mmp) cc_final: 0.8512 (mmt)
REVERT: C  721 MET cc_start: 0.8691 (tmm) cc_final: 0.8461 (tmm)
REVERT: C  733 MET cc_start: 0.9310 (mmp) cc_final: 0.9021 (mmp)
REVERT: C  834 CYS cc_start: 0.9218 (m) cc_final: 0.8202 (p)
REVERT: C  844 MET cc_start: 0.9105 (ttm) cc_final: 0.8751 (tpt)
REVERT: C  986 LEU cc_start: 0.9580 (tt) cc_final: 0.9364 (pp)
REVERT: C 1042 MET cc_start: 0.8789 (ppp) cc_final: 0.8532 (ppp)
REVERT: C 1059 GLU cc_start: 0.9118 (pt0) cc_final: 0.8800 (pp20)
  outliers start: 4
  outliers final: 0
  residues processed: 381
  average time/residue: 0.2446
  time to fit residues: 145.5830
Evaluate side-chains
  248 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 1.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 120 optimal weight:    5.9990
   chunk 118 optimal weight:   20.0000
   chunk 147 optimal weight:    9.9990
   chunk 45 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 102 optimal weight:    0.9990
   chunk 84 optimal weight:    0.8980
   chunk 111 optimal weight:    3.9990
   chunk 62 optimal weight:   20.0000
   chunk 81 optimal weight:    0.9980
   overall best weight:    2.1786

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 549 ASN
A 829 HIS
** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.042361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.033534 restraints weight = 121899.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.034532 restraints weight = 86277.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.035335 restraints weight = 65719.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.6107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  17304  Z= 0.189
  Angle     :  0.899  11.747  23488  Z= 0.471
  Chirality :  0.046   0.197   2808
  Planarity :  0.004   0.037   2888
  Dihedral  :  6.777  30.232   2356
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 17.31
  Ramachandran Plot:
    Outliers :  1.09 %
    Allowed  :  8.23 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  5.12 %
    Favored  : 94.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 4.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.17), residues: 2200
  helix: -0.30 (0.13), residues: 1404
  sheet:  None (None), residues: 0
  loop : -3.04 (0.20), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 605 
 HIS   0.007   0.001   HIS A 512 
 PHE   0.035   0.002   PHE A 877 
 TYR   0.020   0.002   TYR A 842 
 ARG   0.005   0.001   ARG D 604 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05314 (  904)
  hydrogen bonds       : angle       5.13626 ( 2712)
  covalent geometry    : bond        0.00391 (17304)
  covalent geometry    : angle       0.89919 (23488)

*********************** 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
  309 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 306
  time to evaluate  : 2.008 
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: D  502 LEU cc_start: 0.9472 (mm) cc_final: 0.9157 (pp)
REVERT: D  697 LEU cc_start: 0.8743 (mt) cc_final: 0.7900 (mp)
REVERT: D  706 TYR cc_start: 0.9193 (m-80) cc_final: 0.8794 (m-80)
REVERT: D  733 MET cc_start: 0.9369 (mmp) cc_final: 0.9135 (mmp)
REVERT: D  844 MET cc_start: 0.9169 (ttm) cc_final: 0.8621 (tpt)
REVERT: D  862 MET cc_start: 0.9340 (ttp) cc_final: 0.9114 (ptm)
REVERT: D 1068 ILE cc_start: 0.9247 (mm) cc_final: 0.9021 (mm)
REVERT: A  502 LEU cc_start: 0.9466 (mm) cc_final: 0.9153 (pp)
REVERT: A  697 LEU cc_start: 0.8753 (mt) cc_final: 0.8476 (mt)
REVERT: A  706 TYR cc_start: 0.9199 (m-80) cc_final: 0.8787 (m-10)
REVERT: A  733 MET cc_start: 0.9344 (mmp) cc_final: 0.9101 (mmp)
REVERT: A  844 MET cc_start: 0.9131 (ttm) cc_final: 0.8702 (tpt)
REVERT: A 1068 ILE cc_start: 0.9253 (mm) cc_final: 0.9025 (mm)
REVERT: B  502 LEU cc_start: 0.9469 (mm) cc_final: 0.9161 (pp)
REVERT: B  697 LEU cc_start: 0.8749 (mt) cc_final: 0.7886 (mp)
REVERT: B  706 TYR cc_start: 0.9193 (m-80) cc_final: 0.8791 (m-80)
REVERT: B  844 MET cc_start: 0.9136 (ttp) cc_final: 0.8566 (tpt)
REVERT: B  915 ASP cc_start: 0.8139 (p0) cc_final: 0.7555 (p0)
REVERT: B 1068 ILE cc_start: 0.9264 (mm) cc_final: 0.9037 (mm)
REVERT: C  502 LEU cc_start: 0.9477 (mm) cc_final: 0.9164 (pp)
REVERT: C  697 LEU cc_start: 0.8746 (mt) cc_final: 0.7893 (mp)
REVERT: C  706 TYR cc_start: 0.9193 (m-80) cc_final: 0.8791 (m-80)
REVERT: C  844 MET cc_start: 0.9175 (ttm) cc_final: 0.8623 (tpt)
REVERT: C  878 ILE cc_start: 0.9212 (tp) cc_final: 0.8998 (pt)
REVERT: C  915 ASP cc_start: 0.8153 (p0) cc_final: 0.7367 (p0)
REVERT: C  953 MET cc_start: 0.9197 (mmp) cc_final: 0.8956 (mmp)
REVERT: C 1068 ILE cc_start: 0.9259 (mm) cc_final: 0.9031 (mm)
  outliers start: 3
  outliers final: 0
  residues processed: 309
  average time/residue: 0.2474
  time to fit residues: 119.9861
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  : 1.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 158 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   chunk 146 optimal weight:    4.9990
   chunk 108 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 118 optimal weight:    0.0370
   chunk 90 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   chunk 135 optimal weight:    8.9990
   chunk 166 optimal weight:    0.7980
   chunk 30 optimal weight:    5.9990
   overall best weight:    0.7458

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

Flipped N/Q/H residues before XYZ refinement:
D 970 HIS
D1062 HIS
A 970 HIS
A1062 HIS
B 970 HIS
C 970 HIS
C1062 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.043727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.034195 restraints weight = 118968.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.035197 restraints weight = 86421.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.035943 restraints weight = 66804.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.6663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  17304  Z= 0.161
  Angle     :  0.862  11.582  23488  Z= 0.448
  Chirality :  0.044   0.189   2808
  Planarity :  0.004   0.040   2888
  Dihedral  :  6.177  31.182   2356
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 14.76
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  8.59 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 3.91 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.17), residues: 2200
  helix: -0.25 (0.13), residues: 1424
  sheet:  None (None), residues: 0
  loop : -2.96 (0.21), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 605 
 HIS   0.006   0.001   HIS C 512 
 PHE   0.037   0.001   PHE C 877 
 TYR   0.014   0.001   TYR A 456 
 ARG   0.002   0.000   ARG B 604 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04792 (  904)
  hydrogen bonds       : angle       4.79555 ( 2712)
  covalent geometry    : bond        0.00318 (17304)
  covalent geometry    : angle       0.86180 (23488)

*********************** 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
  329 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 329
  time to evaluate  : 2.130 
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  458 ARG cc_start: 0.8980 (ttm-80) cc_final: 0.8720 (mmm-85)
REVERT: D  697 LEU cc_start: 0.8702 (mt) cc_final: 0.8479 (mt)
REVERT: D  706 TYR cc_start: 0.9198 (m-80) cc_final: 0.8729 (m-10)
REVERT: D  720 MET cc_start: 0.8906 (mmp) cc_final: 0.8632 (mmp)
REVERT: D  733 MET cc_start: 0.9358 (mmp) cc_final: 0.9056 (mmp)
REVERT: D  844 MET cc_start: 0.9261 (ttm) cc_final: 0.8899 (tpt)
REVERT: D  877 PHE cc_start: 0.8995 (p90) cc_final: 0.8729 (p90)
REVERT: D  878 ILE cc_start: 0.9138 (tp) cc_final: 0.8932 (pt)
REVERT: D 1056 PHE cc_start: 0.9426 (t80) cc_final: 0.9169 (t80)
REVERT: D 1059 GLU cc_start: 0.9083 (pt0) cc_final: 0.8752 (pp20)
REVERT: D 1063 GLU cc_start: 0.9334 (tm-30) cc_final: 0.9118 (tm-30)
REVERT: D 1068 ILE cc_start: 0.9051 (mm) cc_final: 0.8704 (mm)
REVERT: A  697 LEU cc_start: 0.8774 (mt) cc_final: 0.8063 (mt)
REVERT: A  704 LYS cc_start: 0.9079 (mppt) cc_final: 0.8687 (mttt)
REVERT: A  706 TYR cc_start: 0.9188 (m-80) cc_final: 0.8797 (m-10)
REVERT: A  720 MET cc_start: 0.8911 (mmp) cc_final: 0.8678 (mmm)
REVERT: A  733 MET cc_start: 0.9360 (mmp) cc_final: 0.9043 (mmp)
REVERT: A  844 MET cc_start: 0.9237 (ttm) cc_final: 0.8861 (tpt)
REVERT: A  877 PHE cc_start: 0.9005 (p90) cc_final: 0.8757 (p90)
REVERT: A  878 ILE cc_start: 0.9194 (tp) cc_final: 0.8983 (pt)
REVERT: A  911 MET cc_start: 0.9284 (mtm) cc_final: 0.8759 (mtm)
REVERT: A 1063 GLU cc_start: 0.9351 (tm-30) cc_final: 0.9102 (tm-30)
REVERT: A 1068 ILE cc_start: 0.9053 (mm) cc_final: 0.8699 (mm)
REVERT: B  697 LEU cc_start: 0.8688 (mt) cc_final: 0.8488 (mt)
REVERT: B  706 TYR cc_start: 0.9198 (m-80) cc_final: 0.8810 (m-10)
REVERT: B  720 MET cc_start: 0.8820 (mmp) cc_final: 0.8576 (mmm)
REVERT: B  733 MET cc_start: 0.9167 (mmp) cc_final: 0.8912 (mmp)
REVERT: B  840 TYR cc_start: 0.9385 (t80) cc_final: 0.8980 (t80)
REVERT: B  844 MET cc_start: 0.9118 (ttp) cc_final: 0.8777 (tpt)
REVERT: B  877 PHE cc_start: 0.8996 (p90) cc_final: 0.8727 (p90)
REVERT: B  878 ILE cc_start: 0.9181 (tp) cc_final: 0.8977 (pt)
REVERT: B  915 ASP cc_start: 0.7788 (p0) cc_final: 0.7572 (p0)
REVERT: B 1063 GLU cc_start: 0.9349 (tm-30) cc_final: 0.9105 (tm-30)
REVERT: B 1068 ILE cc_start: 0.9063 (mm) cc_final: 0.8708 (mm)
REVERT: C  635 LYS cc_start: 0.8494 (ptpt) cc_final: 0.8163 (pttm)
REVERT: C  697 LEU cc_start: 0.8717 (mt) cc_final: 0.8212 (mp)
REVERT: C  706 TYR cc_start: 0.9187 (m-80) cc_final: 0.8743 (m-80)
REVERT: C  720 MET cc_start: 0.8890 (mmp) cc_final: 0.8664 (mmm)
REVERT: C  733 MET cc_start: 0.9175 (mmp) cc_final: 0.8946 (mmp)
REVERT: C  844 MET cc_start: 0.9267 (ttm) cc_final: 0.8875 (tpt)
REVERT: C  877 PHE cc_start: 0.8984 (p90) cc_final: 0.8720 (p90)
REVERT: C  915 ASP cc_start: 0.7804 (p0) cc_final: 0.7434 (p0)
REVERT: C 1063 GLU cc_start: 0.9327 (tm-30) cc_final: 0.9100 (tm-30)
REVERT: C 1068 ILE cc_start: 0.9060 (mm) cc_final: 0.8706 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 329
  average time/residue: 0.2752
  time to fit residues: 138.9006
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  : 1.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 65 optimal weight:    9.9990
   chunk 183 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 20 optimal weight:    6.9990
   chunk 169 optimal weight:    4.9990
   chunk 205 optimal weight:    0.7980
   chunk 76 optimal weight:    8.9990
   chunk 117 optimal weight:    1.9990
   chunk 177 optimal weight:    8.9990
   chunk 113 optimal weight:    1.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
D 691 GLN
** D 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D1062 HIS
A 691 GLN
A1062 HIS
B 691 GLN
** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 691 GLN
C1062 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.040044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2601 r_free = 0.2601 target = 0.031230 restraints weight = 123358.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.032203 restraints weight = 87449.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2659 r_free = 0.2659 target = 0.032904 restraints weight = 66915.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.7105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  17304  Z= 0.208
  Angle     :  0.902  10.726  23488  Z= 0.470
  Chirality :  0.045   0.187   2808
  Planarity :  0.005   0.042   2888
  Dihedral  :  6.408  33.738   2356
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 18.96
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  : 10.18 %
    Favored  : 89.27 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  4.88 %
    Favored  : 94.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 3.91 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.17), residues: 2200
  helix: -0.38 (0.13), residues: 1432
  sheet:  None (None), residues: 0
  loop : -3.04 (0.21), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 605 
 HIS   0.014   0.002   HIS B 700 
 PHE   0.015   0.002   PHE B 944 
 TYR   0.036   0.002   TYR B 842 
 ARG   0.005   0.000   ARG B 604 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05059 (  904)
  hydrogen bonds       : angle       5.08912 ( 2712)
  covalent geometry    : bond        0.00434 (17304)
  covalent geometry    : angle       0.90158 (23488)

*********************** 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
  293 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 289
  time to evaluate  : 1.892 
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: D  706 TYR cc_start: 0.9190 (m-80) cc_final: 0.8767 (m-10)
REVERT: D  720 MET cc_start: 0.8920 (mmp) cc_final: 0.8613 (mmm)
REVERT: D  774 MET cc_start: 0.9071 (ptp) cc_final: 0.8825 (ppp)
REVERT: D  844 MET cc_start: 0.9280 (ttm) cc_final: 0.9048 (tpt)
REVERT: D 1072 MET cc_start: 0.8049 (mtm) cc_final: 0.7718 (mtt)
REVERT: A  697 LEU cc_start: 0.8713 (mt) cc_final: 0.8335 (mp)
REVERT: A  706 TYR cc_start: 0.9117 (m-80) cc_final: 0.8694 (m-10)
REVERT: A  720 MET cc_start: 0.8968 (mmp) cc_final: 0.8728 (mmm)
REVERT: A  774 MET cc_start: 0.9070 (ptp) cc_final: 0.8825 (ppp)
REVERT: A  844 MET cc_start: 0.9270 (ttm) cc_final: 0.9022 (tpt)
REVERT: A  878 ILE cc_start: 0.9178 (tp) cc_final: 0.8968 (pt)
REVERT: A  911 MET cc_start: 0.9285 (mtm) cc_final: 0.8906 (mtm)
REVERT: A 1072 MET cc_start: 0.8042 (mtm) cc_final: 0.7715 (mtt)
REVERT: B  545 ASP cc_start: 0.8584 (m-30) cc_final: 0.8322 (p0)
REVERT: B  706 TYR cc_start: 0.9196 (m-80) cc_final: 0.8743 (m-10)
REVERT: B  711 TRP cc_start: 0.9044 (m100) cc_final: 0.8815 (m100)
REVERT: B  720 MET cc_start: 0.8849 (mmp) cc_final: 0.8514 (mmm)
REVERT: B  733 MET cc_start: 0.9308 (mmp) cc_final: 0.9041 (mmp)
REVERT: B  774 MET cc_start: 0.9019 (ptp) cc_final: 0.8694 (ppp)
REVERT: B  840 TYR cc_start: 0.9392 (t80) cc_final: 0.9049 (t80)
REVERT: B  844 MET cc_start: 0.9156 (ttp) cc_final: 0.8777 (tpt)
REVERT: B 1072 MET cc_start: 0.8188 (mtm) cc_final: 0.7818 (mtt)
REVERT: C  697 LEU cc_start: 0.8656 (mt) cc_final: 0.8194 (mp)
REVERT: C  706 TYR cc_start: 0.9134 (m-80) cc_final: 0.8704 (m-10)
REVERT: C  720 MET cc_start: 0.8967 (mmp) cc_final: 0.8734 (mmm)
REVERT: C  733 MET cc_start: 0.9223 (mmp) cc_final: 0.8948 (mmp)
REVERT: C  844 MET cc_start: 0.9272 (ttm) cc_final: 0.9049 (tpt)
REVERT: C  878 ILE cc_start: 0.9198 (tp) cc_final: 0.8993 (pt)
REVERT: C 1072 MET cc_start: 0.8187 (mtm) cc_final: 0.7816 (mtt)
  outliers start: 4
  outliers final: 4
  residues processed: 293
  average time/residue: 0.2832
  time to fit residues: 126.0168
Evaluate side-chains
  235 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 231
  time to evaluate  : 2.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 28 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9980
   chunk 100 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 27 optimal weight:    6.9990
   chunk 200 optimal weight:    2.9990
   chunk 179 optimal weight:    9.9990
   chunk 185 optimal weight:    0.0470
   chunk 69 optimal weight:    6.9990
   chunk 104 optimal weight:    8.9990
   chunk 155 optimal weight:    6.9990
   overall best weight:    3.0084

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

Flipped N/Q/H residues before XYZ refinement:
** D 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 851 GLN
** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.040275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2600 r_free = 0.2600 target = 0.031443 restraints weight = 124553.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.032454 restraints weight = 87575.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.033235 restraints weight = 66397.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.7537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  17304  Z= 0.213
  Angle     :  0.893  10.415  23488  Z= 0.466
  Chirality :  0.045   0.191   2808
  Planarity :  0.005   0.046   2888
  Dihedral  :  6.334  34.643   2356
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 20.27
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  9.45 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  2.59 %
    Favored  : 97.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 3.91 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.17), residues: 2200
  helix: -0.43 (0.13), residues: 1416
  sheet:  None (None), residues: 0
  loop : -2.93 (0.21), residues: 784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 605 
 HIS   0.010   0.002   HIS D 933 
 PHE   0.022   0.002   PHE A 877 
 TYR   0.040   0.002   TYR A 842 
 ARG   0.005   0.000   ARG B 919 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05009 (  904)
  hydrogen bonds       : angle       5.08597 ( 2712)
  covalent geometry    : bond        0.00455 (17304)
  covalent geometry    : angle       0.89276 (23488)

*********************** 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
  275 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 274
  time to evaluate  : 2.041 
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  698 LEU cc_start: 0.9196 (tp) cc_final: 0.8592 (tt)
REVERT: D  706 TYR cc_start: 0.9145 (m-80) cc_final: 0.8760 (m-10)
REVERT: D  720 MET cc_start: 0.8938 (mmp) cc_final: 0.8630 (mmm)
REVERT: D  774 MET cc_start: 0.9218 (ptp) cc_final: 0.8998 (ppp)
REVERT: D  844 MET cc_start: 0.9261 (ttm) cc_final: 0.8997 (tpt)
REVERT: D  878 ILE cc_start: 0.9272 (tp) cc_final: 0.9065 (pt)
REVERT: A  642 MET cc_start: 0.7001 (pmm) cc_final: 0.6724 (pmm)
REVERT: A  697 LEU cc_start: 0.8589 (mt) cc_final: 0.8069 (mp)
REVERT: A  706 TYR cc_start: 0.9053 (m-80) cc_final: 0.8715 (m-10)
REVERT: A  720 MET cc_start: 0.9010 (mmp) cc_final: 0.8755 (mmm)
REVERT: A  774 MET cc_start: 0.9221 (ptp) cc_final: 0.9006 (ppp)
REVERT: A  844 MET cc_start: 0.9258 (ttm) cc_final: 0.9001 (tpt)
REVERT: A  850 LEU cc_start: 0.8869 (mt) cc_final: 0.8645 (mt)
REVERT: A  877 PHE cc_start: 0.9106 (p90) cc_final: 0.8746 (p90)
REVERT: A  878 ILE cc_start: 0.9283 (tp) cc_final: 0.9064 (pt)
REVERT: A  911 MET cc_start: 0.9293 (mtm) cc_final: 0.8928 (mtm)
REVERT: A 1059 GLU cc_start: 0.9289 (pt0) cc_final: 0.9023 (pp20)
REVERT: A 1072 MET cc_start: 0.8142 (mtm) cc_final: 0.7785 (mtt)
REVERT: B  545 ASP cc_start: 0.8816 (m-30) cc_final: 0.8347 (p0)
REVERT: B  698 LEU cc_start: 0.9242 (tp) cc_final: 0.8700 (tt)
REVERT: B  706 TYR cc_start: 0.9118 (m-80) cc_final: 0.8671 (m-10)
REVERT: B  711 TRP cc_start: 0.9029 (m100) cc_final: 0.8775 (m100)
REVERT: B  720 MET cc_start: 0.8862 (mmp) cc_final: 0.8533 (mmm)
REVERT: B  733 MET cc_start: 0.9272 (mmp) cc_final: 0.8994 (mmp)
REVERT: B  840 TYR cc_start: 0.9281 (t80) cc_final: 0.9023 (t80)
REVERT: B  844 MET cc_start: 0.9156 (ttp) cc_final: 0.8952 (tpt)
REVERT: B  850 LEU cc_start: 0.8871 (mt) cc_final: 0.8578 (mt)
REVERT: B 1059 GLU cc_start: 0.9296 (pt0) cc_final: 0.9027 (pp20)
REVERT: B 1072 MET cc_start: 0.8117 (mtm) cc_final: 0.7777 (mtt)
REVERT: C  642 MET cc_start: 0.7021 (pmm) cc_final: 0.6744 (pmm)
REVERT: C  697 LEU cc_start: 0.8688 (mt) cc_final: 0.8154 (mt)
REVERT: C  706 TYR cc_start: 0.9138 (m-80) cc_final: 0.8794 (m-10)
REVERT: C  720 MET cc_start: 0.9008 (mmp) cc_final: 0.8767 (mmm)
REVERT: C  733 MET cc_start: 0.9342 (mmp) cc_final: 0.9089 (mmp)
REVERT: C  774 MET cc_start: 0.9231 (ptp) cc_final: 0.8889 (ptp)
REVERT: C  844 MET cc_start: 0.9292 (ttm) cc_final: 0.9010 (tpt)
REVERT: C  878 ILE cc_start: 0.9241 (tp) cc_final: 0.9016 (pt)
  outliers start: 1
  outliers final: 0
  residues processed: 275
  average time/residue: 0.2658
  time to fit residues: 111.7973
Evaluate side-chains
  230 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 1.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 175 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 108 optimal weight:    0.4980
   chunk 102 optimal weight:    0.8980
   chunk 158 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 216 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0770
   chunk 52 optimal weight:    0.7980
   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 851 GLN
** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 700 HIS
A 940 GLN
** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.042363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2657 r_free = 0.2657 target = 0.033063 restraints weight = 115932.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.034105 restraints weight = 83035.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.034909 restraints weight = 63289.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.7764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  17304  Z= 0.160
  Angle     :  0.872  10.913  23488  Z= 0.446
  Chirality :  0.044   0.186   2808
  Planarity :  0.005   0.052   2888
  Dihedral  :  5.810  32.685   2356
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 15.51
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  9.14 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 3.91 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.17), residues: 2200
  helix: -0.22 (0.13), residues: 1404
  sheet:  None (None), residues: 0
  loop : -2.88 (0.22), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 711 
 HIS   0.007   0.001   HIS D 933 
 PHE   0.026   0.001   PHE C 877 
 TYR   0.034   0.001   TYR C 842 
 ARG   0.003   0.000   ARG B 919 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04711 (  904)
  hydrogen bonds       : angle       4.80659 ( 2712)
  covalent geometry    : bond        0.00327 (17304)
  covalent geometry    : angle       0.87237 (23488)

*********************** 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
  304 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 304
  time to evaluate  : 2.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  545 ASP cc_start: 0.8669 (m-30) cc_final: 0.8232 (p0)
REVERT: D  642 MET cc_start: 0.6883 (pmm) cc_final: 0.6636 (pmm)
REVERT: D  706 TYR cc_start: 0.9156 (m-80) cc_final: 0.8788 (m-10)
REVERT: D  720 MET cc_start: 0.8903 (mmp) cc_final: 0.8656 (mmm)
REVERT: D  774 MET cc_start: 0.9248 (ptp) cc_final: 0.9028 (ppp)
REVERT: D  840 TYR cc_start: 0.9249 (t80) cc_final: 0.8850 (t80)
REVERT: D  844 MET cc_start: 0.9201 (ttm) cc_final: 0.8747 (mmm)
REVERT: D  877 PHE cc_start: 0.9157 (p90) cc_final: 0.8723 (p90)
REVERT: D  878 ILE cc_start: 0.9264 (tp) cc_final: 0.9053 (pt)
REVERT: D  912 MET cc_start: 0.9324 (tmm) cc_final: 0.9082 (tmm)
REVERT: A  545 ASP cc_start: 0.8686 (m-30) cc_final: 0.8252 (p0)
REVERT: A  601 ARG cc_start: 0.9212 (mtt90) cc_final: 0.8894 (mtt-85)
REVERT: A  642 MET cc_start: 0.6877 (pmm) cc_final: 0.6667 (pmm)
REVERT: A  697 LEU cc_start: 0.8511 (mt) cc_final: 0.7998 (mp)
REVERT: A  706 TYR cc_start: 0.9131 (m-80) cc_final: 0.8770 (m-10)
REVERT: A  720 MET cc_start: 0.8932 (mmp) cc_final: 0.8661 (mmm)
REVERT: A  733 MET cc_start: 0.9277 (mmp) cc_final: 0.8990 (mmp)
REVERT: A  840 TYR cc_start: 0.9133 (t80) cc_final: 0.8889 (t80)
REVERT: A  844 MET cc_start: 0.9222 (ttm) cc_final: 0.8636 (mmm)
REVERT: A  911 MET cc_start: 0.9301 (mtm) cc_final: 0.8829 (mtm)
REVERT: A  913 LEU cc_start: 0.8633 (tp) cc_final: 0.8367 (tp)
REVERT: A  918 TYR cc_start: 0.7493 (m-80) cc_final: 0.6677 (m-80)
REVERT: A 1059 GLU cc_start: 0.9254 (pt0) cc_final: 0.9036 (pt0)
REVERT: B  503 LYS cc_start: 0.9490 (ttpt) cc_final: 0.9279 (ptmt)
REVERT: B  545 ASP cc_start: 0.8661 (m-30) cc_final: 0.8176 (p0)
REVERT: B  642 MET cc_start: 0.6961 (pmm) cc_final: 0.6674 (pmm)
REVERT: B  698 LEU cc_start: 0.9213 (tp) cc_final: 0.8431 (tt)
REVERT: B  706 TYR cc_start: 0.9135 (m-80) cc_final: 0.8707 (m-10)
REVERT: B  711 TRP cc_start: 0.8990 (m100) cc_final: 0.8733 (m100)
REVERT: B  720 MET cc_start: 0.8874 (mmp) cc_final: 0.8610 (mmm)
REVERT: B  733 MET cc_start: 0.9217 (mmp) cc_final: 0.8945 (mmp)
REVERT: B  840 TYR cc_start: 0.9144 (t80) cc_final: 0.8817 (t80)
REVERT: B  844 MET cc_start: 0.9164 (ttp) cc_final: 0.8824 (tpt)
REVERT: B  877 PHE cc_start: 0.9212 (p90) cc_final: 0.8751 (p90)
REVERT: B  878 ILE cc_start: 0.9265 (tp) cc_final: 0.9051 (pt)
REVERT: B  953 MET cc_start: 0.9114 (mmm) cc_final: 0.8891 (mmm)
REVERT: C  503 LYS cc_start: 0.9498 (ttpt) cc_final: 0.9283 (ptmt)
REVERT: C  642 MET cc_start: 0.6950 (pmm) cc_final: 0.6717 (pmm)
REVERT: C  697 LEU cc_start: 0.8772 (mt) cc_final: 0.8221 (mt)
REVERT: C  706 TYR cc_start: 0.9132 (m-80) cc_final: 0.8755 (m-10)
REVERT: C  709 MET cc_start: 0.9126 (tpt) cc_final: 0.8916 (tpt)
REVERT: C  720 MET cc_start: 0.8942 (mmp) cc_final: 0.8683 (mmm)
REVERT: C  733 MET cc_start: 0.9285 (mmp) cc_final: 0.9031 (mmp)
REVERT: C  774 MET cc_start: 0.9211 (ptp) cc_final: 0.8992 (ppp)
REVERT: C  840 TYR cc_start: 0.9233 (t80) cc_final: 0.8862 (t80)
REVERT: C  844 MET cc_start: 0.9210 (ttm) cc_final: 0.8801 (mmm)
REVERT: C  878 ILE cc_start: 0.9245 (tp) cc_final: 0.9030 (pt)
REVERT: C 1059 GLU cc_start: 0.9203 (pt0) cc_final: 0.8938 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 304
  average time/residue: 0.3061
  time to fit residues: 143.0775
Evaluate side-chains
  230 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 2.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 149 optimal weight:    4.9990
   chunk 192 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 168 optimal weight:    4.9990
   chunk 157 optimal weight:    1.9990
   chunk 182 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 179 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 153 optimal weight:    2.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** D 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.041461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.032490 restraints weight = 121153.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.033469 restraints weight = 87370.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.034223 restraints weight = 67224.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.7925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  17304  Z= 0.170
  Angle     :  0.875  10.787  23488  Z= 0.452
  Chirality :  0.044   0.177   2808
  Planarity :  0.005   0.052   2888
  Dihedral  :  5.812  32.662   2356
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 16.98
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  8.91 %
    Favored  : 90.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 3.91 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.17), residues: 2200
  helix: -0.20 (0.13), residues: 1400
  sheet:  None (None), residues: 0
  loop : -2.96 (0.21), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 711 
 HIS   0.007   0.001   HIS B 700 
 PHE   0.013   0.001   PHE B 716 
 TYR   0.032   0.002   TYR C 842 
 ARG   0.004   0.001   ARG A 919 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04699 (  904)
  hydrogen bonds       : angle       4.90828 ( 2712)
  covalent geometry    : bond        0.00358 (17304)
  covalent geometry    : angle       0.87505 (23488)

*********************** 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
  289 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 289
  time to evaluate  : 2.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  545 ASP cc_start: 0.8655 (m-30) cc_final: 0.8186 (p0)
REVERT: D  642 MET cc_start: 0.6723 (pmm) cc_final: 0.6418 (pmm)
REVERT: D  697 LEU cc_start: 0.8680 (mt) cc_final: 0.8364 (mt)
REVERT: D  706 TYR cc_start: 0.9093 (m-80) cc_final: 0.8708 (m-80)
REVERT: D  720 MET cc_start: 0.8924 (mmp) cc_final: 0.8673 (mmm)
REVERT: D  774 MET cc_start: 0.9227 (ptp) cc_final: 0.8986 (ppp)
REVERT: D  840 TYR cc_start: 0.9278 (t80) cc_final: 0.8892 (t80)
REVERT: D  844 MET cc_start: 0.9190 (ttm) cc_final: 0.8790 (mmm)
REVERT: D  878 ILE cc_start: 0.9233 (tp) cc_final: 0.9004 (pt)
REVERT: D 1059 GLU cc_start: 0.9102 (pt0) cc_final: 0.8612 (pp20)
REVERT: A  545 ASP cc_start: 0.8640 (m-30) cc_final: 0.8187 (p0)
REVERT: A  601 ARG cc_start: 0.9181 (mtt90) cc_final: 0.8901 (mtt-85)
REVERT: A  642 MET cc_start: 0.6970 (pmm) cc_final: 0.6708 (pmm)
REVERT: A  697 LEU cc_start: 0.8557 (mt) cc_final: 0.8049 (mp)
REVERT: A  706 TYR cc_start: 0.9135 (m-80) cc_final: 0.8797 (m-10)
REVERT: A  711 TRP cc_start: 0.8872 (m100) cc_final: 0.8498 (m-90)
REVERT: A  720 MET cc_start: 0.8969 (mmp) cc_final: 0.8708 (mmp)
REVERT: A  733 MET cc_start: 0.9296 (mmp) cc_final: 0.9027 (mmp)
REVERT: A  840 TYR cc_start: 0.9127 (t80) cc_final: 0.8796 (t80)
REVERT: A  844 MET cc_start: 0.9193 (ttm) cc_final: 0.8640 (mmm)
REVERT: A  911 MET cc_start: 0.9316 (mtm) cc_final: 0.8927 (mtm)
REVERT: A  913 LEU cc_start: 0.8614 (tp) cc_final: 0.8361 (tp)
REVERT: A 1068 ILE cc_start: 0.9343 (mm) cc_final: 0.9082 (mm)
REVERT: B  545 ASP cc_start: 0.8618 (m-30) cc_final: 0.8105 (p0)
REVERT: B  642 MET cc_start: 0.6764 (pmm) cc_final: 0.6455 (pmm)
REVERT: B  697 LEU cc_start: 0.8879 (mt) cc_final: 0.8438 (mt)
REVERT: B  698 LEU cc_start: 0.9033 (tp) cc_final: 0.8800 (tt)
REVERT: B  706 TYR cc_start: 0.9132 (m-80) cc_final: 0.8706 (m-10)
REVERT: B  711 TRP cc_start: 0.9008 (m100) cc_final: 0.8745 (m100)
REVERT: B  720 MET cc_start: 0.8937 (mmp) cc_final: 0.8610 (mmm)
REVERT: B  733 MET cc_start: 0.9256 (mmp) cc_final: 0.8973 (mmp)
REVERT: B  844 MET cc_start: 0.9172 (ttp) cc_final: 0.8838 (tpt)
REVERT: B  878 ILE cc_start: 0.9234 (tp) cc_final: 0.9018 (pt)
REVERT: B  953 MET cc_start: 0.9051 (mmm) cc_final: 0.8838 (mmm)
REVERT: B 1059 GLU cc_start: 0.9093 (pt0) cc_final: 0.8724 (pp20)
REVERT: B 1068 ILE cc_start: 0.9404 (mm) cc_final: 0.9151 (mm)
REVERT: C  642 MET cc_start: 0.6981 (pmm) cc_final: 0.6727 (pmm)
REVERT: C  706 TYR cc_start: 0.9135 (m-80) cc_final: 0.8720 (m-10)
REVERT: C  720 MET cc_start: 0.8958 (mmp) cc_final: 0.8695 (mmm)
REVERT: C  733 MET cc_start: 0.9336 (mmp) cc_final: 0.9092 (mmp)
REVERT: C  840 TYR cc_start: 0.9292 (t80) cc_final: 0.8945 (t80)
REVERT: C  844 MET cc_start: 0.9278 (ttm) cc_final: 0.8836 (mmm)
REVERT: C  912 MET cc_start: 0.9220 (tmm) cc_final: 0.8937 (tmm)
REVERT: C  913 LEU cc_start: 0.8774 (tp) cc_final: 0.8432 (tp)
REVERT: C 1059 GLU cc_start: 0.9157 (pt0) cc_final: 0.8908 (pp20)
REVERT: C 1068 ILE cc_start: 0.9333 (mm) cc_final: 0.8975 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 289
  average time/residue: 0.3235
  time to fit residues: 147.3402
Evaluate side-chains
  226 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 2.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 215 optimal weight:    0.0870
   chunk 162 optimal weight:    5.9990
   chunk 117 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 136 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 119 optimal weight:    3.9990
   chunk 165 optimal weight:    1.9990
   chunk 175 optimal weight:    8.9990
   chunk 150 optimal weight:    1.9990
   chunk 142 optimal weight:    0.3980
   overall best weight:    1.2964

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

Flipped N/Q/H residues before XYZ refinement:
** D 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 691 GLN
** B 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.042015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2642 r_free = 0.2642 target = 0.032985 restraints weight = 118591.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.034009 restraints weight = 83391.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.034778 restraints weight = 63644.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.8076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  17304  Z= 0.158
  Angle     :  0.859  10.841  23488  Z= 0.441
  Chirality :  0.044   0.182   2808
  Planarity :  0.005   0.056   2888
  Dihedral  :  5.612  32.440   2356
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 16.20
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  8.41 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.78 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 3.91 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.17), residues: 2200
  helix: -0.17 (0.13), residues: 1400
  sheet:  None (None), residues: 0
  loop : -2.92 (0.21), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 711 
 HIS   0.006   0.001   HIS A 512 
 PHE   0.047   0.002   PHE D 877 
 TYR   0.028   0.002   TYR A 842 
 ARG   0.003   0.000   ARG A 919 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04573 (  904)
  hydrogen bonds       : angle       4.81938 ( 2712)
  covalent geometry    : bond        0.00330 (17304)
  covalent geometry    : angle       0.85870 (23488)

*********************** 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
  286 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 285
  time to evaluate  : 2.051 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  545 ASP cc_start: 0.8697 (m-30) cc_final: 0.8065 (p0)
REVERT: D  642 MET cc_start: 0.6654 (pmm) cc_final: 0.6371 (pmm)
REVERT: D  697 LEU cc_start: 0.8669 (mt) cc_final: 0.8355 (mt)
REVERT: D  706 TYR cc_start: 0.9065 (m-80) cc_final: 0.8642 (m-80)
REVERT: D  720 MET cc_start: 0.8897 (mmp) cc_final: 0.8643 (mmm)
REVERT: D  774 MET cc_start: 0.9229 (ptp) cc_final: 0.8970 (ppp)
REVERT: D  840 TYR cc_start: 0.9261 (t80) cc_final: 0.8909 (t80)
REVERT: D  844 MET cc_start: 0.9248 (ttm) cc_final: 0.8824 (mmm)
REVERT: A  545 ASP cc_start: 0.8705 (m-30) cc_final: 0.8108 (p0)
REVERT: A  642 MET cc_start: 0.6918 (pmm) cc_final: 0.6646 (pmm)
REVERT: A  691 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8333 (pp30)
REVERT: A  697 LEU cc_start: 0.8642 (mt) cc_final: 0.7766 (mp)
REVERT: A  706 TYR cc_start: 0.9151 (m-80) cc_final: 0.8784 (m-10)
REVERT: A  720 MET cc_start: 0.8952 (mmp) cc_final: 0.8676 (mmp)
REVERT: A  733 MET cc_start: 0.9271 (mmp) cc_final: 0.8996 (mmp)
REVERT: A  840 TYR cc_start: 0.9139 (t80) cc_final: 0.8743 (t80)
REVERT: A  844 MET cc_start: 0.9112 (ttm) cc_final: 0.8698 (mmm)
REVERT: A  911 MET cc_start: 0.9304 (mtm) cc_final: 0.8873 (mtm)
REVERT: A  913 LEU cc_start: 0.8645 (tp) cc_final: 0.8377 (tp)
REVERT: A  918 TYR cc_start: 0.7502 (m-80) cc_final: 0.6590 (m-80)
REVERT: A 1059 GLU cc_start: 0.9073 (pt0) cc_final: 0.8565 (pp20)
REVERT: A 1063 GLU cc_start: 0.9302 (mm-30) cc_final: 0.9078 (mm-30)
REVERT: A 1068 ILE cc_start: 0.9318 (mm) cc_final: 0.9116 (mm)
REVERT: B  545 ASP cc_start: 0.8680 (m-30) cc_final: 0.8095 (p0)
REVERT: B  642 MET cc_start: 0.6942 (pmm) cc_final: 0.6676 (pmm)
REVERT: B  698 LEU cc_start: 0.9141 (tp) cc_final: 0.8920 (tt)
REVERT: B  706 TYR cc_start: 0.9219 (m-80) cc_final: 0.8742 (m-10)
REVERT: B  711 TRP cc_start: 0.8962 (m100) cc_final: 0.8737 (m100)
REVERT: B  720 MET cc_start: 0.8933 (mmp) cc_final: 0.8679 (mmm)
REVERT: B  733 MET cc_start: 0.9255 (mmp) cc_final: 0.8980 (mmp)
REVERT: B  840 TYR cc_start: 0.9201 (t80) cc_final: 0.8488 (t80)
REVERT: B  878 ILE cc_start: 0.9258 (tp) cc_final: 0.9024 (pt)
REVERT: B  953 MET cc_start: 0.9026 (mmm) cc_final: 0.8787 (mmm)
REVERT: B 1059 GLU cc_start: 0.9058 (pt0) cc_final: 0.8468 (pp20)
REVERT: C  503 LYS cc_start: 0.9531 (ttpt) cc_final: 0.9319 (ptmt)
REVERT: C  642 MET cc_start: 0.6935 (pmm) cc_final: 0.6679 (pmm)
REVERT: C  706 TYR cc_start: 0.9141 (m-80) cc_final: 0.8717 (m-10)
REVERT: C  720 MET cc_start: 0.8948 (mmp) cc_final: 0.8671 (mmp)
REVERT: C  733 MET cc_start: 0.9328 (mmp) cc_final: 0.9098 (mmp)
REVERT: C  774 MET cc_start: 0.9206 (ptp) cc_final: 0.8910 (ppp)
REVERT: C  840 TYR cc_start: 0.9295 (t80) cc_final: 0.8969 (t80)
REVERT: C  844 MET cc_start: 0.9212 (ttm) cc_final: 0.8848 (mmm)
REVERT: C  878 ILE cc_start: 0.9272 (tp) cc_final: 0.9051 (pt)
REVERT: C 1059 GLU cc_start: 0.9118 (pt0) cc_final: 0.8846 (pp20)
REVERT: C 1068 ILE cc_start: 0.9176 (mm) cc_final: 0.8969 (mm)
REVERT: C 1072 MET cc_start: 0.8316 (mtm) cc_final: 0.8015 (mtt)
  outliers start: 1
  outliers final: 0
  residues processed: 286
  average time/residue: 0.2529
  time to fit residues: 115.9631
Evaluate side-chains
  227 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 226
  time to evaluate  : 1.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 132 optimal weight:    5.9990
   chunk 150 optimal weight:    1.9990
   chunk 166 optimal weight:    0.9990
   chunk 112 optimal weight:    0.0370
   chunk 98 optimal weight:    2.9990
   chunk 159 optimal weight:    1.9990
   chunk 74 optimal weight:    9.9990
   chunk 137 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 59 optimal weight:   10.0000
   chunk 170 optimal weight:    4.9990
   overall best weight:    1.2066

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

Flipped N/Q/H residues before XYZ refinement:
B 691 GLN
** B 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 845 ASN
C 691 GLN
C 940 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.042387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.033264 restraints weight = 118445.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.034312 restraints weight = 84068.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.035113 restraints weight = 63907.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.8235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  17304  Z= 0.157
  Angle     :  0.867  10.888  23488  Z= 0.443
  Chirality :  0.044   0.179   2808
  Planarity :  0.005   0.057   2888
  Dihedral  :  5.532  32.116   2356
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 16.65
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  8.68 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.36 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 3.91 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.17), residues: 2200
  helix: -0.21 (0.13), residues: 1396
  sheet:  None (None), residues: 0
  loop : -2.95 (0.21), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 711 
 HIS   0.006   0.001   HIS D 512 
 PHE   0.042   0.001   PHE B 877 
 TYR   0.029   0.002   TYR C 842 
 ARG   0.003   0.000   ARG A 919 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04536 (  904)
  hydrogen bonds       : angle       4.84346 ( 2712)
  covalent geometry    : bond        0.00326 (17304)
  covalent geometry    : angle       0.86742 (23488)

********************** 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
  289 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 287
  time to evaluate  : 2.964 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  545 ASP cc_start: 0.8699 (m-30) cc_final: 0.8063 (p0)
REVERT: D  642 MET cc_start: 0.6682 (pmm) cc_final: 0.6389 (pmm)
REVERT: D  697 LEU cc_start: 0.8735 (mt) cc_final: 0.8504 (mt)
REVERT: D  706 TYR cc_start: 0.9077 (m-80) cc_final: 0.8642 (m-80)
REVERT: D  720 MET cc_start: 0.8892 (mmp) cc_final: 0.8633 (mmm)
REVERT: D  733 MET cc_start: 0.9291 (mmp) cc_final: 0.8901 (mmp)
REVERT: D  817 ILE cc_start: 0.9294 (tp) cc_final: 0.9007 (pt)
REVERT: D  840 TYR cc_start: 0.9310 (t80) cc_final: 0.9063 (t80)
REVERT: D  844 MET cc_start: 0.9198 (ttm) cc_final: 0.8948 (mmm)
REVERT: A  503 LYS cc_start: 0.9251 (ptmt) cc_final: 0.9006 (ptpt)
REVERT: A  545 ASP cc_start: 0.8685 (m-30) cc_final: 0.8066 (p0)
REVERT: A  642 MET cc_start: 0.6916 (pmm) cc_final: 0.6639 (pmm)
REVERT: A  697 LEU cc_start: 0.8751 (mt) cc_final: 0.7935 (mt)
REVERT: A  706 TYR cc_start: 0.9158 (m-80) cc_final: 0.8802 (m-10)
REVERT: A  720 MET cc_start: 0.8923 (mmp) cc_final: 0.8659 (mmp)
REVERT: A  733 MET cc_start: 0.9289 (mmp) cc_final: 0.9021 (mmp)
REVERT: A  840 TYR cc_start: 0.9167 (t80) cc_final: 0.8808 (t80)
REVERT: A  844 MET cc_start: 0.9116 (ttm) cc_final: 0.8615 (mmm)
REVERT: A  911 MET cc_start: 0.9328 (mtm) cc_final: 0.8866 (mtm)
REVERT: A  913 LEU cc_start: 0.8538 (tp) cc_final: 0.8293 (tp)
REVERT: A  918 TYR cc_start: 0.7633 (m-80) cc_final: 0.6813 (m-80)
REVERT: A 1059 GLU cc_start: 0.9100 (pt0) cc_final: 0.8566 (pp20)
REVERT: A 1063 GLU cc_start: 0.9291 (mm-30) cc_final: 0.9073 (mm-30)
REVERT: A 1068 ILE cc_start: 0.9285 (mm) cc_final: 0.9005 (mm)
REVERT: B  545 ASP cc_start: 0.8667 (m-30) cc_final: 0.8071 (p0)
REVERT: B  642 MET cc_start: 0.6817 (pmm) cc_final: 0.6474 (pmm)
REVERT: B  691 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8278 (pp30)
REVERT: B  698 LEU cc_start: 0.9107 (tp) cc_final: 0.8861 (tt)
REVERT: B  706 TYR cc_start: 0.9236 (m-80) cc_final: 0.8756 (m-10)
REVERT: B  711 TRP cc_start: 0.8947 (m100) cc_final: 0.8729 (m100)
REVERT: B  720 MET cc_start: 0.8935 (mmp) cc_final: 0.8678 (mmm)
REVERT: B  733 MET cc_start: 0.9271 (mmp) cc_final: 0.9005 (mmp)
REVERT: B  878 ILE cc_start: 0.9239 (tp) cc_final: 0.9010 (pt)
REVERT: B  953 MET cc_start: 0.9044 (mmm) cc_final: 0.8788 (mmm)
REVERT: B 1068 ILE cc_start: 0.9428 (mm) cc_final: 0.9194 (mm)
REVERT: C  642 MET cc_start: 0.6862 (pmm) cc_final: 0.6603 (pmm)
REVERT: C  691 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8321 (pp30)
REVERT: C  706 TYR cc_start: 0.9143 (m-80) cc_final: 0.8646 (m-10)
REVERT: C  720 MET cc_start: 0.8981 (mmp) cc_final: 0.8715 (mmm)
REVERT: C  733 MET cc_start: 0.9345 (mmp) cc_final: 0.9115 (mmp)
REVERT: C  774 MET cc_start: 0.9200 (ptp) cc_final: 0.8898 (ppp)
REVERT: C  817 ILE cc_start: 0.9287 (tp) cc_final: 0.9015 (pt)
REVERT: C  840 TYR cc_start: 0.9358 (t80) cc_final: 0.9036 (t80)
REVERT: C  844 MET cc_start: 0.9132 (ttm) cc_final: 0.8789 (mmm)
REVERT: C  878 ILE cc_start: 0.9231 (tp) cc_final: 0.8996 (pt)
REVERT: C 1059 GLU cc_start: 0.9113 (pt0) cc_final: 0.8827 (pp20)
REVERT: C 1068 ILE cc_start: 0.9315 (mm) cc_final: 0.8997 (mm)
REVERT: C 1072 MET cc_start: 0.8364 (mtm) cc_final: 0.8048 (mtt)
  outliers start: 2
  outliers final: 0
  residues processed: 289
  average time/residue: 0.3489
  time to fit residues: 158.8151
Evaluate side-chains
  236 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 234
  time to evaluate  : 2.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 77 optimal weight:    7.9990
   chunk 55 optimal weight:    0.1980
   chunk 178 optimal weight:    9.9990
   chunk 24 optimal weight:    0.7980
   chunk 88 optimal weight:    6.9990
   chunk 85 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 112 optimal weight:    0.0370
   chunk 223 optimal weight:    0.0970
   chunk 172 optimal weight:    0.9990
   chunk 62 optimal weight:    0.3980
   overall best weight:    0.3056

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

Flipped N/Q/H residues before XYZ refinement:
** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 700 HIS
B 940 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.044093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.034792 restraints weight = 115847.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.035855 restraints weight = 82196.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.036648 restraints weight = 63040.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.8405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  17304  Z= 0.156
  Angle     :  0.869  11.142  23488  Z= 0.437
  Chirality :  0.043   0.201   2808
  Planarity :  0.005   0.056   2888
  Dihedral  :  5.325  31.693   2356
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 14.88
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  8.05 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 3.91 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.17), residues: 2200
  helix: -0.18 (0.13), residues: 1396
  sheet:  None (None), residues: 0
  loop : -2.95 (0.21), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 711 
 HIS   0.006   0.001   HIS A 512 
 PHE   0.044   0.001   PHE D 877 
 TYR   0.023   0.002   TYR D 629 
 ARG   0.003   0.000   ARG A 919 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04409 (  904)
  hydrogen bonds       : angle       4.71810 ( 2712)
  covalent geometry    : bond        0.00311 (17304)
  covalent geometry    : angle       0.86939 (23488)

===============================================================================
Job complete
usr+sys time: 4972.63 seconds
wall clock time: 89 minutes 9.78 seconds (5349.78 seconds total)