Starting phenix.real_space_refine
on Thu Sep 18 16:00:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6v9x_21129/09_2025/6v9x_21129.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6v9x_21129/09_2025/6v9x_21129.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6v9x_21129/09_2025/6v9x_21129.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6v9x_21129/09_2025/6v9x_21129.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6v9x_21129/09_2025/6v9x_21129.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6v9x_21129/09_2025/6v9x_21129.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   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     128      5.16       5
     C   11856      2.51       5
     N    3000      2.21       5
     O    3100      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 68 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 18084
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4521
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 571, 4521
          Classifications: {'peptide': 571}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 20, 'TRANS': 550}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 94
          Unresolved non-hydrogen angles: 117
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 3, 'ASN:plan1': 2, 'YCM:plan-2': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 50
  Restraints were copied for chains:
    B, D, C
  Time building chain proxies: 3.87, per 1000 atoms: 0.21
  Number of scatterers: 18084
  At special positions: 0
  Unit cell: (117.913, 117.913, 141.01, 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     128     16.00
     O    3100      8.00
     N    3000      7.00
     C   11856      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.29
  Conformation dependent library (CDL) restraints added in 581.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  4480 Ramachandran restraints generated.
    2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4376

  Finding SS restraints...
    Secondary structure from input PDB file:
      132 helices and 4 sheets defined
      75.0% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 447 through 456
    Processing helix  chain 'A' and resid 458 through 466
    Processing helix  chain 'A' and resid 484 through 492
    Processing helix  chain 'A' and resid 494 through 503
    Processing helix  chain 'A' and resid 511 through 515
      removed outlier: 4.232A  pdb=" N   TRP A 515 " --> pdb=" O   HIS A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 523
      removed outlier: 3.558A  pdb=" N   MET A 523 " --> pdb=" O   HIS A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 535
    Processing helix  chain 'A' and resid 539 through 543
      removed outlier: 3.513A  pdb=" N   ASP A 542 " --> pdb=" O   LYS A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 558
      removed outlier: 4.034A  pdb=" N   PHE A 554 " --> pdb=" O   THR A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 570
    Processing helix  chain 'A' and resid 582 through 590
      removed outlier: 3.717A  pdb=" N   ALA A 587 " --> pdb=" O   PHE A 583 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ASN A 590 " --> pdb=" O   LEU A 586 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 601
    Processing helix  chain 'A' and resid 604 through 610
    Processing helix  chain 'A' and resid 621 through 630
    Processing helix  chain 'A' and resid 630 through 642
      removed outlier: 3.522A  pdb=" N   MET A 634 " --> pdb=" O   LEU A 630 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   MET A 642 " --> pdb=" O   LEU A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 670
    Processing helix  chain 'A' and resid 683 through 692
    Processing helix  chain 'A' and resid 694 through 699
    Processing helix  chain 'A' and resid 700 through 714
    Processing helix  chain 'A' and resid 714 through 740
      removed outlier: 3.586A  pdb=" N   GLY A 729 " --> pdb=" O   SER A 725 " (cutoff:3.500A)
      Proline residue:  A 732  - end of helix
      removed outlier: 3.542A  pdb=" N   ILE A 740 " --> pdb=" O   LEU A 736 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 790
    Processing helix  chain 'A' and resid 803 through 820
      removed outlier: 4.059A  pdb=" N   ILE A 816 " --> pdb=" O   TYR A 812 " (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 827 through 852
      removed outlier: 3.685A  pdb=" N   TRP A 843 " --> pdb=" O   VAL A 839 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 857 through 892
      removed outlier: 3.677A  pdb=" N   GLU A 864 " --> pdb=" O   ILE A 860 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   VAL A 865 " --> pdb=" O   VAL A 861 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LYS A 868 " --> pdb=" O   GLU A 864 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   VAL A 875 " --> pdb=" O   LEU A 871 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE A 878 " --> pdb=" O   THR A 874 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 900 through 914
    Processing helix  chain 'A' and resid 917 through 922
    Processing helix  chain 'A' and resid 922 through 928
    Processing helix  chain 'A' and resid 933 through 946
    Processing helix  chain 'A' and resid 946 through 969
      removed outlier: 3.753A  pdb=" N   LEU A 952 " --> pdb=" O   VAL A 948 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU A 955 " --> pdb=" O   VAL A 951 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 990
      removed outlier: 3.729A  pdb=" N   ILE A 976 " --> pdb=" O   SER A 972 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LYS A 989 " --> pdb=" O   SER A 985 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 991 through 999
      removed outlier: 3.521A  pdb=" N   LEU A 995 " --> pdb=" O   PRO A 991 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   LYS A 997 " --> pdb=" O   TRP A 993 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1040 through 1069
      removed outlier: 3.597A  pdb=" N   LEU A1064 " --> pdb=" O   LYS A1060 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 456
    Processing helix  chain 'B' and resid 458 through 466
    Processing helix  chain 'B' and resid 484 through 492
    Processing helix  chain 'B' and resid 494 through 503
    Processing helix  chain 'B' and resid 511 through 515
      removed outlier: 4.233A  pdb=" N   TRP B 515 " --> pdb=" O   HIS B 512 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 516 through 523
      removed outlier: 3.559A  pdb=" N   MET B 523 " --> pdb=" O   HIS B 519 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 526 through 535
    Processing helix  chain 'B' and resid 539 through 543
      removed outlier: 3.513A  pdb=" N   ASP B 542 " --> pdb=" O   LYS B 539 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 550 through 558
      removed outlier: 4.034A  pdb=" N   PHE B 554 " --> pdb=" O   THR B 550 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 570
    Processing helix  chain 'B' and resid 582 through 590
      removed outlier: 3.717A  pdb=" N   ALA B 587 " --> pdb=" O   PHE B 583 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ASN B 590 " --> pdb=" O   LEU B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 592 through 601
    Processing helix  chain 'B' and resid 604 through 610
    Processing helix  chain 'B' and resid 621 through 630
    Processing helix  chain 'B' and resid 630 through 642
      removed outlier: 3.522A  pdb=" N   MET B 634 " --> pdb=" O   LEU B 630 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   MET B 642 " --> pdb=" O   LEU B 638 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 666 through 670
    Processing helix  chain 'B' and resid 683 through 692
    Processing helix  chain 'B' and resid 694 through 699
    Processing helix  chain 'B' and resid 700 through 714
    Processing helix  chain 'B' and resid 714 through 740
      removed outlier: 3.586A  pdb=" N   GLY B 729 " --> pdb=" O   SER B 725 " (cutoff:3.500A)
      Proline residue:  B 732  - end of helix
      removed outlier: 3.542A  pdb=" N   ILE B 740 " --> pdb=" O   LEU B 736 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 769 through 790
    Processing helix  chain 'B' and resid 803 through 820
      removed outlier: 4.059A  pdb=" N   ILE B 816 " --> pdb=" O   TYR B 812 " (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 827 through 852
      removed outlier: 3.685A  pdb=" N   TRP B 843 " --> pdb=" O   VAL B 839 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 857 through 892
      removed outlier: 3.676A  pdb=" N   GLU B 864 " --> pdb=" O   ILE B 860 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   VAL B 865 " --> pdb=" O   VAL B 861 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LYS B 868 " --> pdb=" O   GLU B 864 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   VAL B 875 " --> pdb=" O   LEU B 871 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE B 878 " --> pdb=" O   THR B 874 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 900 through 914
    Processing helix  chain 'B' and resid 917 through 922
    Processing helix  chain 'B' and resid 922 through 928
    Processing helix  chain 'B' and resid 933 through 946
    Processing helix  chain 'B' and resid 946 through 969
      removed outlier: 3.753A  pdb=" N   LEU B 952 " --> pdb=" O   VAL B 948 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU B 955 " --> pdb=" O   VAL B 951 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 970 through 990
      removed outlier: 3.729A  pdb=" N   ILE B 976 " --> pdb=" O   SER B 972 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LYS B 989 " --> pdb=" O   SER B 985 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 991 through 999
      removed outlier: 3.522A  pdb=" N   LEU B 995 " --> pdb=" O   PRO B 991 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   LYS B 997 " --> pdb=" O   TRP B 993 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1040 through 1069
      removed outlier: 3.596A  pdb=" N   LEU B1064 " --> pdb=" O   LYS B1060 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 448 through 456
    Processing helix  chain 'D' and resid 458 through 466
    Processing helix  chain 'D' and resid 484 through 492
    Processing helix  chain 'D' and resid 494 through 503
    Processing helix  chain 'D' and resid 511 through 515
      removed outlier: 4.232A  pdb=" N   TRP D 515 " --> pdb=" O   HIS D 512 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 516 through 523
      removed outlier: 3.558A  pdb=" N   MET D 523 " --> pdb=" O   HIS D 519 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 526 through 535
    Processing helix  chain 'D' and resid 539 through 543
      removed outlier: 3.512A  pdb=" N   ASP D 542 " --> pdb=" O   LYS D 539 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 550 through 558
      removed outlier: 4.034A  pdb=" N   PHE D 554 " --> pdb=" O   THR D 550 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 560 through 570
    Processing helix  chain 'D' and resid 582 through 590
      removed outlier: 3.717A  pdb=" N   ALA D 587 " --> pdb=" O   PHE D 583 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ASN D 590 " --> pdb=" O   LEU D 586 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 592 through 601
    Processing helix  chain 'D' and resid 604 through 610
    Processing helix  chain 'D' and resid 621 through 630
    Processing helix  chain 'D' and resid 630 through 642
      removed outlier: 3.522A  pdb=" N   MET D 634 " --> pdb=" O   LEU D 630 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   MET D 642 " --> pdb=" O   LEU D 638 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 666 through 670
    Processing helix  chain 'D' and resid 683 through 692
    Processing helix  chain 'D' and resid 694 through 699
    Processing helix  chain 'D' and resid 700 through 714
    Processing helix  chain 'D' and resid 714 through 740
      removed outlier: 3.585A  pdb=" N   GLY D 729 " --> pdb=" O   SER D 725 " (cutoff:3.500A)
      Proline residue:  D 732  - end of helix
      removed outlier: 3.542A  pdb=" N   ILE D 740 " --> pdb=" O   LEU D 736 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 769 through 790
    Processing helix  chain 'D' and resid 803 through 820
      removed outlier: 4.059A  pdb=" N   ILE D 816 " --> pdb=" O   TYR D 812 " (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 827 through 852
      removed outlier: 3.684A  pdb=" N   TRP D 843 " --> pdb=" O   VAL D 839 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 857 through 892
      removed outlier: 3.677A  pdb=" N   GLU D 864 " --> pdb=" O   ILE D 860 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   VAL D 865 " --> pdb=" O   VAL D 861 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LYS D 868 " --> pdb=" O   GLU D 864 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   VAL D 875 " --> pdb=" O   LEU D 871 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE D 878 " --> pdb=" O   THR D 874 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 900 through 914
    Processing helix  chain 'D' and resid 917 through 922
    Processing helix  chain 'D' and resid 922 through 928
    Processing helix  chain 'D' and resid 933 through 946
    Processing helix  chain 'D' and resid 946 through 969
      removed outlier: 3.753A  pdb=" N   LEU D 952 " --> pdb=" O   VAL D 948 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU D 955 " --> pdb=" O   VAL D 951 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 970 through 990
      removed outlier: 3.729A  pdb=" N   ILE D 976 " --> pdb=" O   SER D 972 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LYS D 989 " --> pdb=" O   SER D 985 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 991 through 999
      removed outlier: 3.521A  pdb=" N   LEU D 995 " --> pdb=" O   PRO D 991 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   LYS D 997 " --> pdb=" O   TRP D 993 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1040 through 1069
      removed outlier: 3.597A  pdb=" N   LEU D1064 " --> pdb=" O   LYS D1060 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 448 through 456
    Processing helix  chain 'C' and resid 458 through 466
    Processing helix  chain 'C' and resid 484 through 492
    Processing helix  chain 'C' and resid 494 through 503
    Processing helix  chain 'C' and resid 511 through 515
      removed outlier: 4.232A  pdb=" N   TRP C 515 " --> pdb=" O   HIS C 512 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 516 through 523
      removed outlier: 3.558A  pdb=" N   MET C 523 " --> pdb=" O   HIS C 519 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 526 through 535
    Processing helix  chain 'C' and resid 539 through 543
      removed outlier: 3.514A  pdb=" N   ASP C 542 " --> pdb=" O   LYS C 539 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 550 through 558
      removed outlier: 4.033A  pdb=" N   PHE C 554 " --> pdb=" O   THR C 550 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 560 through 570
    Processing helix  chain 'C' and resid 582 through 590
      removed outlier: 3.717A  pdb=" N   ALA C 587 " --> pdb=" O   PHE C 583 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ASN C 590 " --> pdb=" O   LEU C 586 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 592 through 601
    Processing helix  chain 'C' and resid 604 through 610
    Processing helix  chain 'C' and resid 621 through 630
    Processing helix  chain 'C' and resid 630 through 642
      removed outlier: 3.521A  pdb=" N   MET C 634 " --> pdb=" O   LEU C 630 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   MET C 642 " --> pdb=" O   LEU C 638 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 666 through 670
    Processing helix  chain 'C' and resid 683 through 692
    Processing helix  chain 'C' and resid 694 through 699
    Processing helix  chain 'C' and resid 700 through 714
    Processing helix  chain 'C' and resid 714 through 740
      removed outlier: 3.586A  pdb=" N   GLY C 729 " --> pdb=" O   SER C 725 " (cutoff:3.500A)
      Proline residue:  C 732  - end of helix
      removed outlier: 3.543A  pdb=" N   ILE C 740 " --> pdb=" O   LEU C 736 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 769 through 790
    Processing helix  chain 'C' and resid 803 through 820
      removed outlier: 4.058A  pdb=" N   ILE C 816 " --> pdb=" O   TYR C 812 " (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 827 through 852
      removed outlier: 3.684A  pdb=" N   TRP C 843 " --> pdb=" O   VAL C 839 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 857 through 892
      removed outlier: 3.677A  pdb=" N   GLU C 864 " --> pdb=" O   ILE C 860 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   VAL C 865 " --> pdb=" O   VAL C 861 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LYS C 868 " --> pdb=" O   GLU C 864 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   VAL C 875 " --> pdb=" O   LEU C 871 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE C 878 " --> pdb=" O   THR C 874 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 900 through 914
    Processing helix  chain 'C' and resid 917 through 922
    Processing helix  chain 'C' and resid 922 through 928
    Processing helix  chain 'C' and resid 933 through 946
    Processing helix  chain 'C' and resid 946 through 969
      removed outlier: 3.753A  pdb=" N   LEU C 952 " --> pdb=" O   VAL C 948 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LEU C 955 " --> pdb=" O   VAL C 951 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 970 through 990
      removed outlier: 3.729A  pdb=" N   ILE C 976 " --> pdb=" O   SER C 972 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LYS C 989 " --> pdb=" O   SER C 985 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 991 through 999
      removed outlier: 3.521A  pdb=" N   LEU C 995 " --> pdb=" O   PRO C 991 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   LYS C 997 " --> pdb=" O   TRP C 993 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1040 through 1069
      removed outlier: 3.597A  pdb=" N   LEU C1064 " --> pdb=" O   LYS C1060 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 656 through 657
    Processing sheet with id=AA2, first strand: chain 'B' and resid 656 through 657
    Processing sheet with id=AA3, first strand: chain 'D' and resid 656 through 657
    Processing sheet with id=AA4, first strand: chain 'C' and resid 656 through 657

    1101 hydrogen bonds defined for protein.
    3243 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.77

  Time building geometry restraints manager: 1.78 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 2816
        1.31 -     1.44: 4836
        1.44 -     1.56: 10616
        1.56 -     1.69: 8
        1.69 -     1.82: 212
  Bond restraints: 18488
  Sorted by residual:
  bond pdb=" CE  YCM C 621 "
       pdb=" NZ2 YCM C 621 "
    ideal  model  delta    sigma   weight residual
    1.369  1.451 -0.082 2.00e-02 2.50e+03 1.70e+01
  bond pdb=" CE  YCM B 621 "
       pdb=" NZ2 YCM B 621 "
    ideal  model  delta    sigma   weight residual
    1.369  1.451 -0.082 2.00e-02 2.50e+03 1.69e+01
  bond pdb=" CE  YCM D 621 "
       pdb=" NZ2 YCM D 621 "
    ideal  model  delta    sigma   weight residual
    1.369  1.451 -0.082 2.00e-02 2.50e+03 1.69e+01
  bond pdb=" CE  YCM A 621 "
       pdb=" NZ2 YCM A 621 "
    ideal  model  delta    sigma   weight residual
    1.369  1.451 -0.082 2.00e-02 2.50e+03 1.68e+01
  bond pdb=" CE  YCM D 621 "
       pdb=" OZ1 YCM D 621 "
    ideal  model  delta    sigma   weight residual
    1.251  1.184  0.067 2.00e-02 2.50e+03 1.11e+01
  ... (remaining 18483 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 24001
        1.95 -     3.91: 828
        3.91 -     5.86: 128
        5.86 -     7.81: 81
        7.81 -     9.76: 18
  Bond angle restraints: 25056
  Sorted by residual:
  angle pdb=" N   ILE C 803 "
        pdb=" CA  ILE C 803 "
        pdb=" C   ILE C 803 "
      ideal   model   delta    sigma   weight residual
     113.53  107.12    6.41 9.80e-01 1.04e+00 4.28e+01
  angle pdb=" N   ILE D 803 "
        pdb=" CA  ILE D 803 "
        pdb=" C   ILE D 803 "
      ideal   model   delta    sigma   weight residual
     113.53  107.14    6.39 9.80e-01 1.04e+00 4.25e+01
  angle pdb=" N   ILE B 803 "
        pdb=" CA  ILE B 803 "
        pdb=" C   ILE B 803 "
      ideal   model   delta    sigma   weight residual
     113.53  107.16    6.37 9.80e-01 1.04e+00 4.23e+01
  angle pdb=" N   ILE A 803 "
        pdb=" CA  ILE A 803 "
        pdb=" C   ILE A 803 "
      ideal   model   delta    sigma   weight residual
     113.53  107.16    6.37 9.80e-01 1.04e+00 4.23e+01
  angle pdb=" CB  GLU A 788 "
        pdb=" CG  GLU A 788 "
        pdb=" CD  GLU A 788 "
      ideal   model   delta    sigma   weight residual
     112.60  119.46   -6.86 1.70e+00 3.46e-01 1.63e+01
  ... (remaining 25051 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.77: 9684
       16.77 -    33.53: 1057
       33.53 -    50.30: 239
       50.30 -    67.07: 56
       67.07 -    83.83: 16
  Dihedral angle restraints: 11052
    sinusoidal: 4324
      harmonic: 6728
  Sorted by residual:
  dihedral pdb=" CA  VAL C 948 "
           pdb=" C   VAL C 948 "
           pdb=" N   PRO C 949 "
           pdb=" CA  PRO C 949 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.20   26.80     0      5.00e+00 4.00e-02 2.87e+01
  dihedral pdb=" CA  VAL D 948 "
           pdb=" C   VAL D 948 "
           pdb=" N   PRO D 949 "
           pdb=" CA  PRO D 949 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.21   26.79     0      5.00e+00 4.00e-02 2.87e+01
  dihedral pdb=" CA  VAL A 948 "
           pdb=" C   VAL A 948 "
           pdb=" N   PRO A 949 "
           pdb=" CA  PRO A 949 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.23   26.77     0      5.00e+00 4.00e-02 2.87e+01
  ... (remaining 11049 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 2309
       0.055 -    0.110: 496
       0.110 -    0.165: 107
       0.165 -    0.220: 24
       0.220 -    0.276: 4
  Chirality restraints: 2940
  Sorted by residual:
  chirality pdb=" CB  ILE B 811 "
            pdb=" CA  ILE B 811 "
            pdb=" CG1 ILE B 811 "
            pdb=" CG2 ILE B 811 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.28 2.00e-01 2.50e+01 1.90e+00
  chirality pdb=" CB  ILE A 811 "
            pdb=" CA  ILE A 811 "
            pdb=" CG1 ILE A 811 "
            pdb=" CG2 ILE A 811 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" CB  ILE C 811 "
            pdb=" CA  ILE C 811 "
            pdb=" CG1 ILE C 811 "
            pdb=" CG2 ILE C 811 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.83e+00
  ... (remaining 2937 not shown)

  Planarity restraints: 3084
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 820 "    0.051 5.00e-02 4.00e+02   7.74e-02 9.60e+00
        pdb=" N   PRO C 821 "   -0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO C 821 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO C 821 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 820 "    0.051 5.00e-02 4.00e+02   7.74e-02 9.59e+00
        pdb=" N   PRO B 821 "   -0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO B 821 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B 821 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 820 "   -0.051 5.00e-02 4.00e+02   7.73e-02 9.56e+00
        pdb=" N   PRO A 821 "    0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO A 821 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 821 "   -0.044 5.00e-02 4.00e+02
  ... (remaining 3081 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 4968
        2.80 -     3.33: 16084
        3.33 -     3.85: 28980
        3.85 -     4.38: 35610
        4.38 -     4.90: 58836
  Nonbonded interactions: 144478
  Sorted by model distance:
  nonbonded pdb=" O   ILE C 810 "
            pdb=" OG1 THR C 814 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   ILE B 810 "
            pdb=" OG1 THR B 814 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   ILE A 810 "
            pdb=" OG1 THR A 814 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   ILE D 810 "
            pdb=" OG1 THR D 814 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   VAL B 980 "
            pdb=" OG1 THR B 984 "
     model   vdw
     2.353 3.040
  ... (remaining 144473 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'D'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     15.750
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
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      :  0.005   0.082  18488  Z= 0.213
  Angle     :  0.901   9.763  25056  Z= 0.472
  Chirality :  0.051   0.276   2940
  Planarity :  0.008   0.077   3084
  Dihedral  : 15.215  83.833   6676
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  7.94 %
    Favored  : 90.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.84 (0.11), residues: 2240
  helix: -4.14 (0.06), residues: 1552
  sheet: -0.83 (0.71), residues: 40
  loop : -2.65 (0.20), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 852 
 TYR   0.018   0.002   TYR C 842 
 PHE   0.016   0.002   PHE D 612 
 TRP   0.005   0.001   TRP B 711 
 HIS   0.005   0.001   HIS D 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (18488)
  covalent geometry    : angle       0.90143 (25056)
  hydrogen bonds       : bond        0.30724 ( 1101)
  hydrogen bonds       : angle       9.74045 ( 3243)

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

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

  4480 Ramachandran restraints generated.
    2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4480 Ramachandran restraints generated.
    2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  532 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 508
  time to evaluate  : 0.694 
Fit side-chains
   revert: symmetry clash
REVERT: A  481 HIS cc_start: 0.7945 (m90) cc_final: 0.7700 (m170)
REVERT: A  483 MET cc_start: 0.8417 (mtt) cc_final: 0.8169 (mtt)
REVERT: A  509 LEU cc_start: 0.8614 (mm) cc_final: 0.8332 (mt)
REVERT: A  708 LEU cc_start: 0.8506 (tt) cc_final: 0.8203 (tp)
REVERT: A  833 GLN cc_start: 0.7963 (mt0) cc_final: 0.7719 (tt0)
REVERT: A  868 LYS cc_start: 0.6429 (tptt) cc_final: 0.6136 (tptt)
REVERT: A  952 LEU cc_start: 0.8601 (tp) cc_final: 0.8383 (mt)
REVERT: B  509 LEU cc_start: 0.8441 (mm) cc_final: 0.8212 (mt)
REVERT: B  597 LEU cc_start: 0.8943 (mt) cc_final: 0.8717 (mt)
REVERT: B  634 MET cc_start: 0.8492 (tpt) cc_final: 0.7848 (tpt)
REVERT: B  720 MET cc_start: 0.7569 (tpp) cc_final: 0.7249 (mmm)
REVERT: B  833 GLN cc_start: 0.7892 (mt0) cc_final: 0.7500 (tt0)
REVERT: B  878 ILE cc_start: 0.8760 (tp) cc_final: 0.8553 (tp)
REVERT: B  963 ASP cc_start: 0.7260 (m-30) cc_final: 0.7055 (m-30)
REVERT: D  483 MET cc_start: 0.8231 (mtt) cc_final: 0.8008 (mtt)
REVERT: D  808 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7396 (mt-10)
REVERT: D  830 LEU cc_start: 0.8785 (tp) cc_final: 0.8135 (tp)
REVERT: D  834 CYS cc_start: 0.8137 (m) cc_final: 0.7612 (m)
REVERT: D  966 ASP cc_start: 0.8245 (m-30) cc_final: 0.7911 (m-30)
REVERT: D  978 MET cc_start: 0.6949 (ptm) cc_final: 0.6623 (ptm)
REVERT: D  987 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6700 (mt-10)
REVERT: C  480 LEU cc_start: 0.8374 (pt) cc_final: 0.8142 (pt)
REVERT: C  612 PHE cc_start: 0.7513 (p90) cc_final: 0.7247 (p90)
REVERT: C  775 ILE cc_start: 0.9078 (pt) cc_final: 0.8754 (pt)
REVERT: C  779 LEU cc_start: 0.8223 (tt) cc_final: 0.7780 (mm)
REVERT: C  786 CYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7717 (m)
REVERT: C  830 LEU cc_start: 0.8784 (tp) cc_final: 0.8068 (tp)
REVERT: C  834 CYS cc_start: 0.8127 (m) cc_final: 0.7613 (m)
REVERT: C  905 ILE cc_start: 0.8734 (tt) cc_final: 0.8507 (mt)
REVERT: C  908 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8396 (m)
REVERT: C  959 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7497 (mt)
REVERT: C  966 ASP cc_start: 0.8263 (m-30) cc_final: 0.7914 (m-30)
REVERT: C  974 LYS cc_start: 0.8217 (tptp) cc_final: 0.7722 (mtpp)
REVERT: C  987 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6749 (mt-10)
REVERT: C 1059 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7315 (mt-10)
  outliers start: 24
  outliers final: 7
  residues processed: 519
  average time/residue: 0.1207
  time to fit residues: 97.6500
Evaluate side-chains
  358 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 348
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  786 CYS
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain B residue  786 CYS
Chi-restraints excluded: chain B residue  788 GLU
Chi-restraints excluded: chain D residue  786 CYS
Chi-restraints excluded: chain D residue  788 GLU
Chi-restraints excluded: chain C residue  786 CYS
Chi-restraints excluded: chain C residue  788 GLU
Chi-restraints excluded: chain C residue  908 THR
Chi-restraints excluded: chain C residue  959 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 216 optimal weight:    0.9980
   chunk 98 optimal weight:    1.9990
   chunk 194 optimal weight:    0.9980
   chunk 227 optimal weight:    0.4980
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    0.3980
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.7980
   chunk 200 optimal weight:    0.0030
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
A 460 ASN
A 492 ASN
A 579 GLN
A 614 HIS
A 700 HIS
A 805 ASN
A 855 ASN
B 460 ASN
B 492 ASN
B 614 HIS
B 700 HIS
B 805 ASN
B 855 ASN
B 968 GLN
B1047 GLN
D 460 ASN
D 492 ASN
D 619 ASN
D 700 HIS
D 805 ASN
D 855 ASN
C 460 ASN
C 492 ASN
C 614 HIS
C 700 HIS
C 739 ASN
C 805 ASN
C 855 ASN
C1047 GLN

Total number of N/Q/H flips: 29

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.169905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.139811 restraints weight = 26616.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 2.32
r_work: 0.3443 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  18488  Z= 0.148
  Angle     :  0.636  10.570  25056  Z= 0.333
  Chirality :  0.040   0.176   2940
  Planarity :  0.007   0.062   3084
  Dihedral  :  5.783  57.185   2447
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 12.03 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.35 (0.15), residues: 2240
  helix: -1.20 (0.11), residues: 1568
  sheet: -1.28 (0.68), residues: 48
  loop : -2.12 (0.24), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 928 
 TYR   0.017   0.001   TYR C 812 
 PHE   0.017   0.001   PHE A 612 
 TRP   0.023   0.002   TRP D 993 
 HIS   0.004   0.001   HIS A 970 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (18488)
  covalent geometry    : angle       0.63606 (25056)
  hydrogen bonds       : bond        0.05355 ( 1101)
  hydrogen bonds       : angle       4.50153 ( 3243)

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

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

  4480 Ramachandran restraints generated.
    2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4480 Ramachandran restraints generated.
    2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  454 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 405
  time to evaluate  : 0.673 
Fit side-chains
   revert: symmetry clash
REVERT: A  483 MET cc_start: 0.8444 (mtt) cc_final: 0.8144 (mtt)
REVERT: A  509 LEU cc_start: 0.8671 (mm) cc_final: 0.8434 (mt)
REVERT: A  612 PHE cc_start: 0.8262 (p90) cc_final: 0.7611 (p90)
REVERT: A  634 MET cc_start: 0.8563 (tpt) cc_final: 0.8226 (tpp)
REVERT: A  695 ILE cc_start: 0.8841 (tp) cc_final: 0.8602 (tp)
REVERT: A  699 ASN cc_start: 0.8930 (m110) cc_final: 0.8608 (m-40)
REVERT: A  708 LEU cc_start: 0.8408 (tt) cc_final: 0.8191 (tp)
REVERT: A  717 ARG cc_start: 0.8045 (mtt-85) cc_final: 0.7437 (tmm-80)
REVERT: A  774 MET cc_start: 0.8359 (mtp) cc_final: 0.8095 (mtp)
REVERT: A  785 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.6756 (t80)
REVERT: A  833 GLN cc_start: 0.8199 (mt0) cc_final: 0.7653 (tt0)
REVERT: A  868 LYS cc_start: 0.6440 (tptt) cc_final: 0.5929 (tppt)
REVERT: A  905 ILE cc_start: 0.8648 (tt) cc_final: 0.8430 (mt)
REVERT: A  978 MET cc_start: 0.8262 (ptp) cc_final: 0.7967 (ptp)
REVERT: B  597 LEU cc_start: 0.9058 (mt) cc_final: 0.8800 (mt)
REVERT: B  720 MET cc_start: 0.8289 (tpp) cc_final: 0.7826 (tpp)
REVERT: B  726 TYR cc_start: 0.8380 (t80) cc_final: 0.8034 (t80)
REVERT: B  774 MET cc_start: 0.8445 (ttm) cc_final: 0.7736 (mtp)
REVERT: B  868 LYS cc_start: 0.6232 (tptt) cc_final: 0.5669 (tppt)
REVERT: D  486 LEU cc_start: 0.9108 (tp) cc_final: 0.8803 (tp)
REVERT: D  528 GLN cc_start: 0.8208 (tp40) cc_final: 0.7994 (mp10)
REVERT: D  774 MET cc_start: 0.7813 (mtp) cc_final: 0.7503 (mtp)
REVERT: D  779 LEU cc_start: 0.8512 (tt) cc_final: 0.7799 (mt)
REVERT: D  785 TYR cc_start: 0.7066 (OUTLIER) cc_final: 0.6557 (t80)
REVERT: D  830 LEU cc_start: 0.8621 (tp) cc_final: 0.8237 (tp)
REVERT: D  834 CYS cc_start: 0.8562 (m) cc_final: 0.8089 (m)
REVERT: D  867 LEU cc_start: 0.8044 (tp) cc_final: 0.7836 (tp)
REVERT: D  978 MET cc_start: 0.7645 (ptm) cc_final: 0.7330 (ptm)
REVERT: D  987 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7576 (mt-10)
REVERT: D 1042 MET cc_start: 0.7605 (tpt) cc_final: 0.7404 (tpt)
REVERT: C  480 LEU cc_start: 0.8845 (pt) cc_final: 0.8633 (pt)
REVERT: C  486 LEU cc_start: 0.9078 (tp) cc_final: 0.8732 (tp)
REVERT: C  612 PHE cc_start: 0.7868 (p90) cc_final: 0.7276 (p90)
REVERT: C  779 LEU cc_start: 0.8421 (tt) cc_final: 0.7893 (mm)
REVERT: C  867 LEU cc_start: 0.8032 (tp) cc_final: 0.7691 (tp)
REVERT: C  868 LYS cc_start: 0.5987 (tptt) cc_final: 0.5656 (tppt)
REVERT: C  987 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7556 (mt-10)
  outliers start: 49
  outliers final: 20
  residues processed: 432
  average time/residue: 0.1132
  time to fit residues: 78.2719
Evaluate side-chains
  365 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 343
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  680 TYR
Chi-restraints excluded: chain A residue  785 TYR
Chi-restraints excluded: chain A residue  786 CYS
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain B residue  480 LEU
Chi-restraints excluded: chain B residue  583 PHE
Chi-restraints excluded: chain B residue  935 VAL
Chi-restraints excluded: chain B residue  961 VAL
Chi-restraints excluded: chain B residue  981 GLU
Chi-restraints excluded: chain B residue 1047 GLN
Chi-restraints excluded: chain D residue  583 PHE
Chi-restraints excluded: chain D residue  680 TYR
Chi-restraints excluded: chain D residue  785 TYR
Chi-restraints excluded: chain D residue  786 CYS
Chi-restraints excluded: chain D residue  869 THR
Chi-restraints excluded: chain D residue  986 LEU
Chi-restraints excluded: chain D residue 1005 VAL
Chi-restraints excluded: chain C residue  583 PHE
Chi-restraints excluded: chain C residue  956 LEU
Chi-restraints excluded: chain C residue  986 LEU
Chi-restraints excluded: chain C residue 1005 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 52 optimal weight:    7.9990
   chunk 23 optimal weight:    0.0970
   chunk 101 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 95 optimal weight:    1.9990
   chunk 174 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   chunk 225 optimal weight:    0.5980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A 968 GLN
B 907 GLN
B1047 GLN
** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 719 HIS
D 968 GLN
** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 968 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.164116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.137428 restraints weight = 26436.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 2.08
r_work: 0.3476 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.2924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  18488  Z= 0.136
  Angle     :  0.593   8.318  25056  Z= 0.305
  Chirality :  0.040   0.218   2940
  Planarity :  0.005   0.060   3084
  Dihedral  :  4.824  52.175   2430
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 13.49 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.78 (0.17), residues: 2240
  helix:  0.09 (0.13), residues: 1600
  sheet: -0.39 (0.74), residues: 48
  loop : -2.01 (0.25), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 464 
 TYR   0.027   0.001   TYR D 812 
 PHE   0.019   0.001   PHE C 922 
 TRP   0.028   0.002   TRP D 993 
 HIS   0.006   0.001   HIS B 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (18488)
  covalent geometry    : angle       0.59335 (25056)
  hydrogen bonds       : bond        0.04772 ( 1101)
  hydrogen bonds       : angle       4.08403 ( 3243)

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

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

  4480 Ramachandran restraints generated.
    2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4480 Ramachandran restraints generated.
    2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  425 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 369
  time to evaluate  : 0.718 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  483 MET cc_start: 0.8415 (mtt) cc_final: 0.8147 (mtt)
REVERT: A  509 LEU cc_start: 0.8748 (mm) cc_final: 0.8526 (mt)
REVERT: A  612 PHE cc_start: 0.8309 (p90) cc_final: 0.7621 (p90)
REVERT: A  695 ILE cc_start: 0.8829 (tp) cc_final: 0.8587 (tp)
REVERT: A  699 ASN cc_start: 0.8892 (m110) cc_final: 0.8603 (m-40)
REVERT: A  720 MET cc_start: 0.8290 (tpp) cc_final: 0.8056 (tpp)
REVERT: A  726 TYR cc_start: 0.8510 (t80) cc_final: 0.8022 (t80)
REVERT: A  774 MET cc_start: 0.8323 (mtp) cc_final: 0.8113 (mtp)
REVERT: A  785 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.6932 (t80)
REVERT: A  833 GLN cc_start: 0.8178 (mt0) cc_final: 0.7773 (tt0)
REVERT: A  842 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.6872 (t80)
REVERT: A  867 LEU cc_start: 0.8152 (tp) cc_final: 0.7890 (tp)
REVERT: A  868 LYS cc_start: 0.6352 (tptt) cc_final: 0.5843 (tppt)
REVERT: A  970 HIS cc_start: 0.6937 (p-80) cc_final: 0.6646 (p-80)
REVERT: B  597 LEU cc_start: 0.9074 (mt) cc_final: 0.8839 (mt)
REVERT: B  693 ASN cc_start: 0.8774 (p0) cc_final: 0.8303 (p0)
REVERT: B  720 MET cc_start: 0.8096 (tpp) cc_final: 0.7742 (tpp)
REVERT: B  726 TYR cc_start: 0.8383 (t80) cc_final: 0.8154 (t80)
REVERT: B  774 MET cc_start: 0.8223 (ttm) cc_final: 0.7622 (mtp)
REVERT: B  851 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8356 (tm-30)
REVERT: B  868 LYS cc_start: 0.6153 (tptt) cc_final: 0.5629 (tppt)
REVERT: B 1042 MET cc_start: 0.6864 (tpt) cc_final: 0.6602 (mmt)
REVERT: D  486 LEU cc_start: 0.9065 (tp) cc_final: 0.8754 (tp)
REVERT: D  509 LEU cc_start: 0.8874 (mm) cc_final: 0.8663 (mt)
REVERT: D  717 ARG cc_start: 0.7959 (mtt-85) cc_final: 0.7489 (tmm-80)
REVERT: D  726 TYR cc_start: 0.8555 (t80) cc_final: 0.8296 (t80)
REVERT: D  774 MET cc_start: 0.7724 (mtp) cc_final: 0.7394 (mtp)
REVERT: D  779 LEU cc_start: 0.8629 (tt) cc_final: 0.7941 (mp)
REVERT: D  785 TYR cc_start: 0.6897 (OUTLIER) cc_final: 0.6560 (t80)
REVERT: D  808 GLU cc_start: 0.7903 (mp0) cc_final: 0.7599 (mp0)
REVERT: D  812 TYR cc_start: 0.8369 (m-80) cc_final: 0.8032 (m-80)
REVERT: D  833 GLN cc_start: 0.8191 (mt0) cc_final: 0.7665 (tt0)
REVERT: D  978 MET cc_start: 0.7604 (ptm) cc_final: 0.6975 (ptm)
REVERT: D 1042 MET cc_start: 0.7354 (tpt) cc_final: 0.7151 (mmt)
REVERT: C  486 LEU cc_start: 0.9017 (tp) cc_final: 0.8652 (tp)
REVERT: C  612 PHE cc_start: 0.7950 (p90) cc_final: 0.7448 (p90)
REVERT: C  779 LEU cc_start: 0.8480 (tt) cc_final: 0.7983 (mp)
REVERT: C  808 GLU cc_start: 0.7865 (mp0) cc_final: 0.7560 (mp0)
REVERT: C  833 GLN cc_start: 0.8329 (mt0) cc_final: 0.7749 (tt0)
REVERT: C  867 LEU cc_start: 0.7944 (tp) cc_final: 0.7669 (tp)
REVERT: C 1042 MET cc_start: 0.6888 (tpt) cc_final: 0.6619 (mmt)
  outliers start: 56
  outliers final: 30
  residues processed: 402
  average time/residue: 0.1110
  time to fit residues: 72.7414
Evaluate side-chains
  376 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 343
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  680 TYR
Chi-restraints excluded: chain A residue  773 CYS
Chi-restraints excluded: chain A residue  785 TYR
Chi-restraints excluded: chain A residue  842 TYR
Chi-restraints excluded: chain A residue  869 THR
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain A residue 1043 GLU
Chi-restraints excluded: chain B residue  583 PHE
Chi-restraints excluded: chain B residue  625 GLU
Chi-restraints excluded: chain B residue  684 THR
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  769 LEU
Chi-restraints excluded: chain B residue  842 TYR
Chi-restraints excluded: chain B residue  894 LEU
Chi-restraints excluded: chain B residue  935 VAL
Chi-restraints excluded: chain B residue  981 GLU
Chi-restraints excluded: chain B residue  986 LEU
Chi-restraints excluded: chain D residue  583 PHE
Chi-restraints excluded: chain D residue  680 TYR
Chi-restraints excluded: chain D residue  709 MET
Chi-restraints excluded: chain D residue  769 LEU
Chi-restraints excluded: chain D residue  785 TYR
Chi-restraints excluded: chain D residue  866 ILE
Chi-restraints excluded: chain D residue  952 LEU
Chi-restraints excluded: chain D residue  986 LEU
Chi-restraints excluded: chain D residue 1005 VAL
Chi-restraints excluded: chain C residue  583 PHE
Chi-restraints excluded: chain C residue  869 THR
Chi-restraints excluded: chain C residue  957 ILE
Chi-restraints excluded: chain C residue  986 LEU
Chi-restraints excluded: chain C residue 1005 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 201 optimal weight:    0.4980
   chunk 189 optimal weight:    2.9990
   chunk 193 optimal weight:    6.9990
   chunk 17 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 167 optimal weight:    3.9990
   chunk 218 optimal weight:    0.9990
   chunk 208 optimal weight:    2.9990
   chunk 169 optimal weight:    0.3980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 494 HIS
** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 494 HIS
B 954 ASN
** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 494 HIS
D 719 HIS
** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 494 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.161169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.133825 restraints weight = 26155.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 2.08
r_work: 0.3424 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.3315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  18488  Z= 0.177
  Angle     :  0.609   8.020  25056  Z= 0.314
  Chirality :  0.042   0.302   2940
  Planarity :  0.005   0.059   3084
  Dihedral  :  4.635  51.427   2428
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 14.37 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.10 (0.18), residues: 2240
  helix:  0.61 (0.13), residues: 1612
  sheet:  0.16 (0.80), residues: 48
  loop : -1.86 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 852 
 TYR   0.023   0.002   TYR A 714 
 PHE   0.022   0.002   PHE C 922 
 TRP   0.030   0.002   TRP D 993 
 HIS   0.005   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (18488)
  covalent geometry    : angle       0.60860 (25056)
  hydrogen bonds       : bond        0.04670 ( 1101)
  hydrogen bonds       : angle       4.01222 ( 3243)

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

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

  4480 Ramachandran restraints generated.
    2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4480 Ramachandran restraints generated.
    2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  420 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 351
  time to evaluate  : 0.618 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  612 PHE cc_start: 0.8385 (p90) cc_final: 0.7671 (p90)
REVERT: A  695 ILE cc_start: 0.8907 (tp) cc_final: 0.8629 (tp)
REVERT: A  699 ASN cc_start: 0.8947 (m110) cc_final: 0.8597 (m-40)
REVERT: A  717 ARG cc_start: 0.7927 (mtt-85) cc_final: 0.7556 (tmm-80)
REVERT: A  833 GLN cc_start: 0.8193 (mt0) cc_final: 0.7815 (tt0)
REVERT: A  842 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.6885 (t80)
REVERT: A  867 LEU cc_start: 0.8157 (tp) cc_final: 0.7939 (tp)
REVERT: A  954 ASN cc_start: 0.8256 (m-40) cc_final: 0.8048 (m-40)
REVERT: A  987 GLU cc_start: 0.8241 (tp30) cc_final: 0.7927 (tp30)
REVERT: B  509 LEU cc_start: 0.8849 (mm) cc_final: 0.8628 (mt)
REVERT: B  693 ASN cc_start: 0.8718 (p0) cc_final: 0.8260 (p0)
REVERT: B  720 MET cc_start: 0.8129 (tpp) cc_final: 0.7769 (tpp)
REVERT: B  726 TYR cc_start: 0.8366 (t80) cc_final: 0.8155 (t80)
REVERT: B  774 MET cc_start: 0.8146 (mtm) cc_final: 0.7843 (mtp)
REVERT: B  851 GLN cc_start: 0.8796 (tm-30) cc_final: 0.8537 (tm-30)
REVERT: B  868 LYS cc_start: 0.6293 (tptt) cc_final: 0.5772 (tppt)
REVERT: D  486 LEU cc_start: 0.9082 (tp) cc_final: 0.8782 (tp)
REVERT: D  717 ARG cc_start: 0.7972 (mtt-85) cc_final: 0.7565 (tmm-80)
REVERT: D  726 TYR cc_start: 0.8536 (t80) cc_final: 0.8103 (t80)
REVERT: D  774 MET cc_start: 0.7918 (mtp) cc_final: 0.7631 (mtp)
REVERT: D  779 LEU cc_start: 0.8647 (tt) cc_final: 0.8077 (mp)
REVERT: D  808 GLU cc_start: 0.7878 (mp0) cc_final: 0.7528 (mp0)
REVERT: D  833 GLN cc_start: 0.8240 (mt0) cc_final: 0.7698 (tt0)
REVERT: D  842 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.7487 (t80)
REVERT: D  966 ASP cc_start: 0.8528 (m-30) cc_final: 0.8125 (m-30)
REVERT: D  978 MET cc_start: 0.7389 (ptm) cc_final: 0.6941 (ptm)
REVERT: C  486 LEU cc_start: 0.9016 (tp) cc_final: 0.8705 (tp)
REVERT: C  720 MET cc_start: 0.8379 (tpp) cc_final: 0.8134 (tpp)
REVERT: C  726 TYR cc_start: 0.8450 (t80) cc_final: 0.7893 (t80)
REVERT: C  779 LEU cc_start: 0.8548 (tt) cc_final: 0.8134 (mp)
REVERT: C  808 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7748 (mp0)
REVERT: C  833 GLN cc_start: 0.8328 (mt0) cc_final: 0.7771 (tt0)
REVERT: C  842 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7277 (t80)
REVERT: C  867 LEU cc_start: 0.8000 (tp) cc_final: 0.7723 (tp)
REVERT: C  868 LYS cc_start: 0.6033 (tptt) cc_final: 0.5701 (tppt)
REVERT: C  953 MET cc_start: 0.7679 (mmm) cc_final: 0.7342 (tpp)
  outliers start: 69
  outliers final: 38
  residues processed: 395
  average time/residue: 0.1159
  time to fit residues: 73.8937
Evaluate side-chains
  366 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 325
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  772 THR
Chi-restraints excluded: chain A residue  773 CYS
Chi-restraints excluded: chain A residue  842 TYR
Chi-restraints excluded: chain A residue  869 THR
Chi-restraints excluded: chain A residue  957 ILE
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue  999 ASP
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain A residue 1043 GLU
Chi-restraints excluded: chain B residue  480 LEU
Chi-restraints excluded: chain B residue  583 PHE
Chi-restraints excluded: chain B residue  684 THR
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  772 THR
Chi-restraints excluded: chain B residue  842 TYR
Chi-restraints excluded: chain B residue  869 THR
Chi-restraints excluded: chain B residue  894 LEU
Chi-restraints excluded: chain B residue  935 VAL
Chi-restraints excluded: chain B residue  981 GLU
Chi-restraints excluded: chain B residue  986 LEU
Chi-restraints excluded: chain D residue  583 PHE
Chi-restraints excluded: chain D residue  680 TYR
Chi-restraints excluded: chain D residue  842 TYR
Chi-restraints excluded: chain D residue  866 ILE
Chi-restraints excluded: chain D residue  869 THR
Chi-restraints excluded: chain D residue  952 LEU
Chi-restraints excluded: chain D residue  957 ILE
Chi-restraints excluded: chain D residue  986 LEU
Chi-restraints excluded: chain D residue 1005 VAL
Chi-restraints excluded: chain C residue  583 PHE
Chi-restraints excluded: chain C residue  769 LEU
Chi-restraints excluded: chain C residue  816 ILE
Chi-restraints excluded: chain C residue  842 TYR
Chi-restraints excluded: chain C residue  866 ILE
Chi-restraints excluded: chain C residue  869 THR
Chi-restraints excluded: chain C residue  951 VAL
Chi-restraints excluded: chain C residue  952 LEU
Chi-restraints excluded: chain C residue  957 ILE
Chi-restraints excluded: chain C residue  986 LEU
Chi-restraints excluded: chain C residue 1005 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 119 optimal weight:    0.3980
   chunk 123 optimal weight:    5.9990
   chunk 127 optimal weight:    0.9980
   chunk 180 optimal weight:    3.9990
   chunk 132 optimal weight:    0.9980
   chunk 209 optimal weight:    2.9990
   chunk 176 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 141 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B1047 GLN
** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 619 ASN
D 719 HIS
** D1061 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 = 0.4022 r_free = 0.4022 target = 0.162081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.134887 restraints weight = 26128.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 2.05
r_work: 0.3449 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.3528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  18488  Z= 0.146
  Angle     :  0.585   9.607  25056  Z= 0.299
  Chirality :  0.041   0.288   2940
  Planarity :  0.005   0.059   3084
  Dihedral  :  4.533  51.033   2428
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 15.82 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.18), residues: 2240
  helix:  0.94 (0.13), residues: 1616
  sheet:  0.34 (0.81), residues: 48
  loop : -1.69 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 464 
 TYR   0.020   0.001   TYR A 714 
 PHE   0.019   0.001   PHE C 922 
 TRP   0.032   0.002   TRP D 993 
 HIS   0.008   0.001   HIS A 970 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (18488)
  covalent geometry    : angle       0.58522 (25056)
  hydrogen bonds       : bond        0.04343 ( 1101)
  hydrogen bonds       : angle       3.90171 ( 3243)

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

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

  4480 Ramachandran restraints generated.
    2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4480 Ramachandran restraints generated.
    2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  397 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 340
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  612 PHE cc_start: 0.8382 (p90) cc_final: 0.7778 (p90)
REVERT: A  693 ASN cc_start: 0.8945 (p0) cc_final: 0.8430 (p0)
REVERT: A  695 ILE cc_start: 0.8898 (tp) cc_final: 0.8610 (tp)
REVERT: A  699 ASN cc_start: 0.8934 (m110) cc_final: 0.8556 (m-40)
REVERT: A  720 MET cc_start: 0.8335 (tpp) cc_final: 0.8130 (tpp)
REVERT: A  842 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.6736 (t80)
REVERT: A  953 MET cc_start: 0.7512 (mmt) cc_final: 0.7001 (tpp)
REVERT: A 1043 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7170 (tt0)
REVERT: B  693 ASN cc_start: 0.8726 (p0) cc_final: 0.8246 (p0)
REVERT: B  720 MET cc_start: 0.8089 (tpp) cc_final: 0.7742 (tpp)
REVERT: B  851 GLN cc_start: 0.8800 (tm-30) cc_final: 0.8474 (tm-30)
REVERT: B  868 LYS cc_start: 0.6126 (tptt) cc_final: 0.5572 (tppt)
REVERT: B  953 MET cc_start: 0.7637 (mmm) cc_final: 0.7393 (tpp)
REVERT: B  997 LYS cc_start: 0.8993 (mtmt) cc_final: 0.8788 (mtmm)
REVERT: D  486 LEU cc_start: 0.9046 (tp) cc_final: 0.8724 (tp)
REVERT: D  717 ARG cc_start: 0.7983 (mtt-85) cc_final: 0.7555 (tmm-80)
REVERT: D  720 MET cc_start: 0.8287 (tpp) cc_final: 0.8052 (tpp)
REVERT: D  779 LEU cc_start: 0.8673 (tt) cc_final: 0.8139 (mp)
REVERT: D  783 PHE cc_start: 0.8365 (t80) cc_final: 0.8153 (t80)
REVERT: D  808 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7675 (mp0)
REVERT: D  833 GLN cc_start: 0.8194 (mt0) cc_final: 0.7769 (tt0)
REVERT: D  842 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.7464 (t80)
REVERT: D  966 ASP cc_start: 0.8399 (m-30) cc_final: 0.8039 (m-30)
REVERT: D  978 MET cc_start: 0.7326 (ptm) cc_final: 0.6965 (ptm)
REVERT: D 1042 MET cc_start: 0.7204 (tpt) cc_final: 0.6973 (mmt)
REVERT: C  726 TYR cc_start: 0.8406 (t80) cc_final: 0.7927 (t80)
REVERT: C  774 MET cc_start: 0.8009 (mtp) cc_final: 0.7550 (mtp)
REVERT: C  779 LEU cc_start: 0.8643 (tt) cc_final: 0.8159 (mp)
REVERT: C  808 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7769 (mp0)
REVERT: C  833 GLN cc_start: 0.8268 (mt0) cc_final: 0.7831 (tt0)
REVERT: C  842 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7461 (t80)
REVERT: C  867 LEU cc_start: 0.8079 (tp) cc_final: 0.7839 (tp)
REVERT: C  868 LYS cc_start: 0.6010 (tptt) cc_final: 0.5641 (tppt)
REVERT: C  953 MET cc_start: 0.7618 (mmm) cc_final: 0.7250 (tpp)
  outliers start: 57
  outliers final: 34
  residues processed: 378
  average time/residue: 0.1126
  time to fit residues: 69.4316
Evaluate side-chains
  360 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 322
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  773 CYS
Chi-restraints excluded: chain A residue  842 TYR
Chi-restraints excluded: chain A residue  894 LEU
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue  999 ASP
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain A residue 1043 GLU
Chi-restraints excluded: chain B residue  480 LEU
Chi-restraints excluded: chain B residue  583 PHE
Chi-restraints excluded: chain B residue  684 THR
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  842 TYR
Chi-restraints excluded: chain B residue  866 ILE
Chi-restraints excluded: chain B residue  869 THR
Chi-restraints excluded: chain B residue  894 LEU
Chi-restraints excluded: chain B residue  986 LEU
Chi-restraints excluded: chain B residue 1047 GLN
Chi-restraints excluded: chain D residue  583 PHE
Chi-restraints excluded: chain D residue  816 ILE
Chi-restraints excluded: chain D residue  842 TYR
Chi-restraints excluded: chain D residue  866 ILE
Chi-restraints excluded: chain D residue  869 THR
Chi-restraints excluded: chain D residue  952 LEU
Chi-restraints excluded: chain D residue  957 ILE
Chi-restraints excluded: chain D residue  986 LEU
Chi-restraints excluded: chain D residue 1005 VAL
Chi-restraints excluded: chain C residue  583 PHE
Chi-restraints excluded: chain C residue  816 ILE
Chi-restraints excluded: chain C residue  842 TYR
Chi-restraints excluded: chain C residue  866 ILE
Chi-restraints excluded: chain C residue  869 THR
Chi-restraints excluded: chain C residue  951 VAL
Chi-restraints excluded: chain C residue  952 LEU
Chi-restraints excluded: chain C residue  957 ILE
Chi-restraints excluded: chain C residue  986 LEU
Chi-restraints excluded: chain C residue 1005 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 163 optimal weight:    0.9980
   chunk 189 optimal weight:    1.9990
   chunk 90 optimal weight:    0.6980
   chunk 138 optimal weight:    0.7980
   chunk 204 optimal weight:    0.8980
   chunk 179 optimal weight:    0.7980
   chunk 217 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 218 optimal weight:    1.9990
   chunk 212 optimal weight:    0.0770
   chunk 197 optimal weight:    0.5980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
B1047 GLN
** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 719 HIS
** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 719 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.163074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.136224 restraints weight = 25928.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 2.00
r_work: 0.3471 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.3676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  18488  Z= 0.132
  Angle     :  0.572   9.102  25056  Z= 0.292
  Chirality :  0.041   0.270   2940
  Planarity :  0.004   0.058   3084
  Dihedral  :  4.455  50.624   2428
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 16.55 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.18), residues: 2240
  helix:  1.08 (0.13), residues: 1636
  sheet:  0.50 (0.81), residues: 48
  loop : -1.54 (0.27), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 464 
 TYR   0.028   0.001   TYR D 714 
 PHE   0.019   0.001   PHE B 612 
 TRP   0.034   0.002   TRP D 993 
 HIS   0.006   0.001   HIS C 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (18488)
  covalent geometry    : angle       0.57223 (25056)
  hydrogen bonds       : bond        0.04169 ( 1101)
  hydrogen bonds       : angle       3.84824 ( 3243)

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

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

  4480 Ramachandran restraints generated.
    2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4480 Ramachandran restraints generated.
    2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  386 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 330
  time to evaluate  : 0.737 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  693 ASN cc_start: 0.8901 (p0) cc_final: 0.8379 (p0)
REVERT: A  695 ILE cc_start: 0.8889 (tp) cc_final: 0.8593 (tp)
REVERT: A  699 ASN cc_start: 0.8914 (m110) cc_final: 0.8537 (m-40)
REVERT: A  842 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.6688 (t80)
REVERT: A  868 LYS cc_start: 0.6304 (tptt) cc_final: 0.5807 (tppt)
REVERT: A  953 MET cc_start: 0.7511 (mmt) cc_final: 0.7012 (tpp)
REVERT: A 1043 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7138 (tt0)
REVERT: B  693 ASN cc_start: 0.8688 (p0) cc_final: 0.8225 (p0)
REVERT: B  720 MET cc_start: 0.8074 (tpp) cc_final: 0.7764 (tpp)
REVERT: B  721 MET cc_start: 0.8241 (tpp) cc_final: 0.7997 (tpp)
REVERT: B  774 MET cc_start: 0.8278 (mtp) cc_final: 0.8077 (mtp)
REVERT: B  851 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8481 (tm-30)
REVERT: B  953 MET cc_start: 0.7603 (mmm) cc_final: 0.7332 (tpp)
REVERT: D  717 ARG cc_start: 0.8078 (mtt-85) cc_final: 0.7577 (tmm-80)
REVERT: D  720 MET cc_start: 0.8300 (tpp) cc_final: 0.8056 (tpp)
REVERT: D  779 LEU cc_start: 0.8657 (tt) cc_final: 0.8137 (mp)
REVERT: D  783 PHE cc_start: 0.8383 (t80) cc_final: 0.8170 (t80)
REVERT: D  842 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.7581 (t80)
REVERT: D  868 LYS cc_start: 0.6112 (tptt) cc_final: 0.5658 (tppt)
REVERT: D  882 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8309 (mm)
REVERT: D  953 MET cc_start: 0.7333 (mmt) cc_final: 0.6863 (tpp)
REVERT: D  966 ASP cc_start: 0.8388 (m-30) cc_final: 0.8027 (m-30)
REVERT: D  978 MET cc_start: 0.7283 (ptm) cc_final: 0.6919 (ptm)
REVERT: D 1042 MET cc_start: 0.7156 (tpt) cc_final: 0.6928 (mmt)
REVERT: C  612 PHE cc_start: 0.8236 (p90) cc_final: 0.8024 (p90)
REVERT: C  720 MET cc_start: 0.8359 (tpp) cc_final: 0.8107 (tpp)
REVERT: C  726 TYR cc_start: 0.8411 (t80) cc_final: 0.7875 (t80)
REVERT: C  774 MET cc_start: 0.7967 (mtp) cc_final: 0.7590 (mtp)
REVERT: C  779 LEU cc_start: 0.8630 (tt) cc_final: 0.8184 (mp)
REVERT: C  783 PHE cc_start: 0.8430 (t80) cc_final: 0.8227 (t80)
REVERT: C  842 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7147 (t80)
REVERT: C  867 LEU cc_start: 0.7882 (tp) cc_final: 0.7680 (tp)
REVERT: C  868 LYS cc_start: 0.5992 (tptt) cc_final: 0.5581 (tppt)
REVERT: C  953 MET cc_start: 0.7546 (mmm) cc_final: 0.7176 (tpp)
  outliers start: 56
  outliers final: 40
  residues processed: 367
  average time/residue: 0.1109
  time to fit residues: 66.4214
Evaluate side-chains
  362 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 317
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  772 THR
Chi-restraints excluded: chain A residue  773 CYS
Chi-restraints excluded: chain A residue  842 TYR
Chi-restraints excluded: chain A residue  869 THR
Chi-restraints excluded: chain A residue  894 LEU
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  957 ILE
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue  999 ASP
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain A residue 1043 GLU
Chi-restraints excluded: chain B residue  480 LEU
Chi-restraints excluded: chain B residue  583 PHE
Chi-restraints excluded: chain B residue  625 GLU
Chi-restraints excluded: chain B residue  684 THR
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  842 TYR
Chi-restraints excluded: chain B residue  866 ILE
Chi-restraints excluded: chain B residue  869 THR
Chi-restraints excluded: chain B residue  894 LEU
Chi-restraints excluded: chain B residue  981 GLU
Chi-restraints excluded: chain B residue  986 LEU
Chi-restraints excluded: chain B residue 1047 GLN
Chi-restraints excluded: chain B residue 1075 ILE
Chi-restraints excluded: chain D residue  564 VAL
Chi-restraints excluded: chain D residue  583 PHE
Chi-restraints excluded: chain D residue  816 ILE
Chi-restraints excluded: chain D residue  842 TYR
Chi-restraints excluded: chain D residue  866 ILE
Chi-restraints excluded: chain D residue  882 LEU
Chi-restraints excluded: chain D residue  952 LEU
Chi-restraints excluded: chain D residue  957 ILE
Chi-restraints excluded: chain D residue  986 LEU
Chi-restraints excluded: chain D residue 1005 VAL
Chi-restraints excluded: chain C residue  583 PHE
Chi-restraints excluded: chain C residue  655 TYR
Chi-restraints excluded: chain C residue  816 ILE
Chi-restraints excluded: chain C residue  842 TYR
Chi-restraints excluded: chain C residue  866 ILE
Chi-restraints excluded: chain C residue  952 LEU
Chi-restraints excluded: chain C residue  956 LEU
Chi-restraints excluded: chain C residue  957 ILE
Chi-restraints excluded: chain C residue  986 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 104 optimal weight:    1.9990
   chunk 221 optimal weight:    0.6980
   chunk 112 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 183 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 199 optimal weight:    0.5980
   chunk 79 optimal weight:    5.9990
   chunk 132 optimal weight:    1.9990
   chunk 176 optimal weight:    0.8980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 719 HIS
** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1047 GLN
** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 719 HIS
** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 719 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.161353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.134243 restraints weight = 26072.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 2.02
r_work: 0.3444 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.3765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  18488  Z= 0.164
  Angle     :  0.597   9.064  25056  Z= 0.306
  Chirality :  0.042   0.274   2940
  Planarity :  0.005   0.057   3084
  Dihedral  :  4.440  46.919   2428
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 16.60 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.18), residues: 2240
  helix:  1.13 (0.13), residues: 1636
  sheet:  0.50 (0.80), residues: 48
  loop : -1.42 (0.28), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 464 
 TYR   0.022   0.002   TYR D 714 
 PHE   0.016   0.001   PHE C 922 
 TRP   0.038   0.002   TRP D 993 
 HIS   0.005   0.001   HIS C 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (18488)
  covalent geometry    : angle       0.59688 (25056)
  hydrogen bonds       : bond        0.04362 ( 1101)
  hydrogen bonds       : angle       3.90179 ( 3243)

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

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

  4480 Ramachandran restraints generated.
    2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4480 Ramachandran restraints generated.
    2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  390 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 323
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  693 ASN cc_start: 0.8898 (p0) cc_final: 0.8349 (p0)
REVERT: A  695 ILE cc_start: 0.8893 (tp) cc_final: 0.8586 (tp)
REVERT: A  699 ASN cc_start: 0.8927 (m110) cc_final: 0.8526 (m-40)
REVERT: A  842 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.6866 (t80)
REVERT: A  868 LYS cc_start: 0.6334 (tptt) cc_final: 0.5819 (tppt)
REVERT: A  953 MET cc_start: 0.7525 (mmt) cc_final: 0.6969 (tpp)
REVERT: B  693 ASN cc_start: 0.8711 (p0) cc_final: 0.8252 (p0)
REVERT: B  720 MET cc_start: 0.8099 (tpp) cc_final: 0.7731 (mmm)
REVERT: B  851 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8493 (tm-30)
REVERT: B  953 MET cc_start: 0.7655 (mmm) cc_final: 0.7399 (tpp)
REVERT: B  997 LYS cc_start: 0.8920 (mtmt) cc_final: 0.8704 (mtmm)
REVERT: D  509 LEU cc_start: 0.9042 (mm) cc_final: 0.8808 (mt)
REVERT: D  779 LEU cc_start: 0.8703 (tt) cc_final: 0.8176 (mp)
REVERT: D  783 PHE cc_start: 0.8415 (t80) cc_final: 0.8181 (t80)
REVERT: D  833 GLN cc_start: 0.8174 (mt0) cc_final: 0.7769 (tt0)
REVERT: D  842 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7467 (t80)
REVERT: D  868 LYS cc_start: 0.6028 (tptt) cc_final: 0.5615 (tppt)
REVERT: D  882 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8360 (mm)
REVERT: D  953 MET cc_start: 0.7310 (mmt) cc_final: 0.6922 (tpp)
REVERT: D  966 ASP cc_start: 0.8389 (m-30) cc_final: 0.8016 (m-30)
REVERT: D  978 MET cc_start: 0.7375 (ptm) cc_final: 0.7093 (ptm)
REVERT: C  612 PHE cc_start: 0.8300 (p90) cc_final: 0.8080 (p90)
REVERT: C  720 MET cc_start: 0.8388 (tpp) cc_final: 0.8124 (tpp)
REVERT: C  726 TYR cc_start: 0.8455 (t80) cc_final: 0.7768 (t80)
REVERT: C  779 LEU cc_start: 0.8632 (tt) cc_final: 0.8182 (mp)
REVERT: C  783 PHE cc_start: 0.8445 (t80) cc_final: 0.8215 (t80)
REVERT: C  842 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7011 (t80)
REVERT: C  868 LYS cc_start: 0.6000 (tptt) cc_final: 0.5585 (tppt)
REVERT: C  882 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8451 (mm)
  outliers start: 67
  outliers final: 44
  residues processed: 369
  average time/residue: 0.1093
  time to fit residues: 66.2162
Evaluate side-chains
  368 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 319
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  772 THR
Chi-restraints excluded: chain A residue  773 CYS
Chi-restraints excluded: chain A residue  842 TYR
Chi-restraints excluded: chain A residue  869 THR
Chi-restraints excluded: chain A residue  894 LEU
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  957 ILE
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue  999 ASP
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain B residue  480 LEU
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  583 PHE
Chi-restraints excluded: chain B residue  684 THR
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  772 THR
Chi-restraints excluded: chain B residue  842 TYR
Chi-restraints excluded: chain B residue  869 THR
Chi-restraints excluded: chain B residue  894 LEU
Chi-restraints excluded: chain B residue  981 GLU
Chi-restraints excluded: chain B residue  986 LEU
Chi-restraints excluded: chain B residue 1047 GLN
Chi-restraints excluded: chain D residue  564 VAL
Chi-restraints excluded: chain D residue  583 PHE
Chi-restraints excluded: chain D residue  719 HIS
Chi-restraints excluded: chain D residue  842 TYR
Chi-restraints excluded: chain D residue  854 GLU
Chi-restraints excluded: chain D residue  866 ILE
Chi-restraints excluded: chain D residue  869 THR
Chi-restraints excluded: chain D residue  882 LEU
Chi-restraints excluded: chain D residue  952 LEU
Chi-restraints excluded: chain D residue  957 ILE
Chi-restraints excluded: chain D residue  986 LEU
Chi-restraints excluded: chain D residue 1005 VAL
Chi-restraints excluded: chain C residue  564 VAL
Chi-restraints excluded: chain C residue  583 PHE
Chi-restraints excluded: chain C residue  655 TYR
Chi-restraints excluded: chain C residue  816 ILE
Chi-restraints excluded: chain C residue  842 TYR
Chi-restraints excluded: chain C residue  866 ILE
Chi-restraints excluded: chain C residue  869 THR
Chi-restraints excluded: chain C residue  882 LEU
Chi-restraints excluded: chain C residue  951 VAL
Chi-restraints excluded: chain C residue  952 LEU
Chi-restraints excluded: chain C residue  956 LEU
Chi-restraints excluded: chain C residue  957 ILE
Chi-restraints excluded: chain C residue  986 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 137 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 129 optimal weight:    0.1980
   chunk 30 optimal weight:    3.9990
   chunk 97 optimal weight:    0.5980
   chunk 203 optimal weight:    5.9990
   chunk 93 optimal weight:    0.5980
   chunk 64 optimal weight:    3.9990
   chunk 118 optimal weight:    0.3980
   chunk 193 optimal weight:   10.0000
   chunk 177 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1047 GLN
** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 719 HIS
** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 719 HIS
C1047 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.161256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.134342 restraints weight = 26044.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 2.01
r_work: 0.3443 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.3854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  18488  Z= 0.159
  Angle     :  0.605  10.657  25056  Z= 0.309
  Chirality :  0.042   0.263   2940
  Planarity :  0.004   0.058   3084
  Dihedral  :  4.406  44.712   2428
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 17.38 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.18), residues: 2240
  helix:  1.25 (0.13), residues: 1612
  sheet:  0.64 (0.81), residues: 48
  loop : -1.27 (0.27), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 464 
 TYR   0.023   0.002   TYR A 726 
 PHE   0.019   0.001   PHE B 612 
 TRP   0.040   0.002   TRP D 993 
 HIS   0.005   0.001   HIS B 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (18488)
  covalent geometry    : angle       0.60461 (25056)
  hydrogen bonds       : bond        0.04309 ( 1101)
  hydrogen bonds       : angle       3.89508 ( 3243)

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

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

  4480 Ramachandran restraints generated.
    2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4480 Ramachandran restraints generated.
    2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  382 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 322
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  693 ASN cc_start: 0.8881 (p0) cc_final: 0.8357 (p0)
REVERT: A  695 ILE cc_start: 0.8893 (tp) cc_final: 0.8583 (tp)
REVERT: A  699 ASN cc_start: 0.8928 (m110) cc_final: 0.8527 (m-40)
REVERT: A  842 TYR cc_start: 0.8194 (OUTLIER) cc_final: 0.6813 (t80)
REVERT: A  868 LYS cc_start: 0.6323 (tptt) cc_final: 0.5819 (tppt)
REVERT: A  924 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7475 (tp30)
REVERT: A  953 MET cc_start: 0.7590 (mmt) cc_final: 0.7029 (tpp)
REVERT: B  693 ASN cc_start: 0.8711 (p0) cc_final: 0.8250 (p0)
REVERT: B  726 TYR cc_start: 0.8339 (t80) cc_final: 0.7784 (t80)
REVERT: B  851 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8488 (tm-30)
REVERT: B  953 MET cc_start: 0.7704 (mmm) cc_final: 0.7428 (tpp)
REVERT: B  987 GLU cc_start: 0.8381 (tp30) cc_final: 0.8146 (tp30)
REVERT: D  509 LEU cc_start: 0.9062 (mm) cc_final: 0.8801 (mt)
REVERT: D  717 ARG cc_start: 0.8130 (mtt-85) cc_final: 0.7624 (tmm-80)
REVERT: D  720 MET cc_start: 0.8254 (tpp) cc_final: 0.8006 (tpp)
REVERT: D  779 LEU cc_start: 0.8730 (tt) cc_final: 0.8223 (mp)
REVERT: D  783 PHE cc_start: 0.8405 (t80) cc_final: 0.8162 (t80)
REVERT: D  842 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.7574 (t80)
REVERT: D  866 ILE cc_start: 0.6921 (OUTLIER) cc_final: 0.6687 (mm)
REVERT: D  868 LYS cc_start: 0.6123 (tptt) cc_final: 0.5676 (tppt)
REVERT: D  882 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8474 (mm)
REVERT: D  953 MET cc_start: 0.7284 (mmt) cc_final: 0.6880 (tpp)
REVERT: D  966 ASP cc_start: 0.8387 (m-30) cc_final: 0.8024 (m-30)
REVERT: C  612 PHE cc_start: 0.8310 (p90) cc_final: 0.8092 (p90)
REVERT: C  720 MET cc_start: 0.8407 (tpp) cc_final: 0.8167 (tpp)
REVERT: C  726 TYR cc_start: 0.8458 (t80) cc_final: 0.7778 (t80)
REVERT: C  779 LEU cc_start: 0.8654 (tt) cc_final: 0.8192 (mp)
REVERT: C  842 TYR cc_start: 0.8244 (OUTLIER) cc_final: 0.7023 (t80)
REVERT: C  868 LYS cc_start: 0.5965 (tptt) cc_final: 0.5532 (tppt)
REVERT: C  882 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8456 (mm)
  outliers start: 60
  outliers final: 45
  residues processed: 362
  average time/residue: 0.1144
  time to fit residues: 67.5907
Evaluate side-chains
  359 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 307
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  655 TYR
Chi-restraints excluded: chain A residue  772 THR
Chi-restraints excluded: chain A residue  773 CYS
Chi-restraints excluded: chain A residue  824 VAL
Chi-restraints excluded: chain A residue  842 TYR
Chi-restraints excluded: chain A residue  850 LEU
Chi-restraints excluded: chain A residue  869 THR
Chi-restraints excluded: chain A residue  894 LEU
Chi-restraints excluded: chain A residue  924 GLU
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  957 ILE
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue 1043 GLU
Chi-restraints excluded: chain B residue  480 LEU
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  583 PHE
Chi-restraints excluded: chain B residue  684 THR
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  772 THR
Chi-restraints excluded: chain B residue  842 TYR
Chi-restraints excluded: chain B residue  866 ILE
Chi-restraints excluded: chain B residue  869 THR
Chi-restraints excluded: chain B residue  894 LEU
Chi-restraints excluded: chain B residue  981 GLU
Chi-restraints excluded: chain B residue  986 LEU
Chi-restraints excluded: chain B residue 1047 GLN
Chi-restraints excluded: chain D residue  564 VAL
Chi-restraints excluded: chain D residue  583 PHE
Chi-restraints excluded: chain D residue  842 TYR
Chi-restraints excluded: chain D residue  854 GLU
Chi-restraints excluded: chain D residue  866 ILE
Chi-restraints excluded: chain D residue  869 THR
Chi-restraints excluded: chain D residue  882 LEU
Chi-restraints excluded: chain D residue  952 LEU
Chi-restraints excluded: chain D residue  957 ILE
Chi-restraints excluded: chain D residue  986 LEU
Chi-restraints excluded: chain D residue 1005 VAL
Chi-restraints excluded: chain C residue  564 VAL
Chi-restraints excluded: chain C residue  583 PHE
Chi-restraints excluded: chain C residue  642 MET
Chi-restraints excluded: chain C residue  655 TYR
Chi-restraints excluded: chain C residue  816 ILE
Chi-restraints excluded: chain C residue  842 TYR
Chi-restraints excluded: chain C residue  866 ILE
Chi-restraints excluded: chain C residue  869 THR
Chi-restraints excluded: chain C residue  882 LEU
Chi-restraints excluded: chain C residue  952 LEU
Chi-restraints excluded: chain C residue  956 LEU
Chi-restraints excluded: chain C residue  957 ILE
Chi-restraints excluded: chain C residue  986 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 119 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 99 optimal weight:    0.6980
   chunk 60 optimal weight:    0.7980
   chunk 165 optimal weight:    1.9990
   chunk 136 optimal weight:    2.9990
   chunk 104 optimal weight:    0.6980
   chunk 82 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 5 optimal weight:    0.3980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1047 GLN
B 719 HIS
B1047 GLN
** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 719 HIS
** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 719 HIS
C1047 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.162529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.135244 restraints weight = 25815.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 1.98
r_work: 0.3456 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.3933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  18488  Z= 0.138
  Angle     :  0.601  12.014  25056  Z= 0.304
  Chirality :  0.041   0.240   2940
  Planarity :  0.004   0.058   3084
  Dihedral  :  4.348  43.252   2428
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 18.21 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.18), residues: 2240
  helix:  1.35 (0.13), residues: 1608
  sheet:  0.80 (0.81), residues: 48
  loop : -1.03 (0.28), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 464 
 TYR   0.029   0.002   TYR D 714 
 PHE   0.018   0.001   PHE C 922 
 TRP   0.043   0.002   TRP D 993 
 HIS   0.006   0.001   HIS B 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (18488)
  covalent geometry    : angle       0.60078 (25056)
  hydrogen bonds       : bond        0.04144 ( 1101)
  hydrogen bonds       : angle       3.85319 ( 3243)

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

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

  4480 Ramachandran restraints generated.
    2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4480 Ramachandran restraints generated.
    2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  377 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 323
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
REVERT: A  612 PHE cc_start: 0.8336 (p90) cc_final: 0.7860 (p90)
REVERT: A  693 ASN cc_start: 0.8865 (p0) cc_final: 0.8348 (p0)
REVERT: A  695 ILE cc_start: 0.8904 (tp) cc_final: 0.8586 (tp)
REVERT: A  699 ASN cc_start: 0.8923 (m110) cc_final: 0.8500 (m-40)
REVERT: A  842 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.6798 (t80)
REVERT: A  868 LYS cc_start: 0.6164 (tptt) cc_final: 0.5670 (tppt)
REVERT: A  924 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7454 (tp30)
REVERT: A  953 MET cc_start: 0.7620 (mmt) cc_final: 0.7074 (tpp)
REVERT: B  693 ASN cc_start: 0.8691 (p0) cc_final: 0.8173 (p0)
REVERT: B  726 TYR cc_start: 0.8259 (t80) cc_final: 0.7754 (t80)
REVERT: B  851 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8438 (tm-30)
REVERT: B  953 MET cc_start: 0.7737 (mmm) cc_final: 0.7494 (tpp)
REVERT: D  509 LEU cc_start: 0.8865 (mm) cc_final: 0.8572 (mt)
REVERT: D  720 MET cc_start: 0.8376 (tpp) cc_final: 0.8091 (tpp)
REVERT: D  779 LEU cc_start: 0.8724 (tt) cc_final: 0.8276 (mp)
REVERT: D  783 PHE cc_start: 0.8363 (t80) cc_final: 0.8133 (t80)
REVERT: D  842 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.7396 (t80)
REVERT: D  866 ILE cc_start: 0.6909 (OUTLIER) cc_final: 0.6674 (mm)
REVERT: D  868 LYS cc_start: 0.6090 (tptt) cc_final: 0.5641 (tppt)
REVERT: D  882 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8425 (mm)
REVERT: D  953 MET cc_start: 0.7319 (mmt) cc_final: 0.6932 (tpp)
REVERT: D  966 ASP cc_start: 0.8413 (m-30) cc_final: 0.8057 (m-30)
REVERT: D 1042 MET cc_start: 0.7205 (tpt) cc_final: 0.6992 (mmt)
REVERT: D 1047 GLN cc_start: 0.8385 (tt0) cc_final: 0.8145 (tt0)
REVERT: C  612 PHE cc_start: 0.8310 (p90) cc_final: 0.8108 (p90)
REVERT: C  720 MET cc_start: 0.8377 (tpp) cc_final: 0.8165 (tpp)
REVERT: C  726 TYR cc_start: 0.8412 (t80) cc_final: 0.7831 (t80)
REVERT: C  774 MET cc_start: 0.7747 (mtp) cc_final: 0.7291 (mtp)
REVERT: C  779 LEU cc_start: 0.8631 (tt) cc_final: 0.8162 (mp)
REVERT: C  842 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.6921 (t80)
REVERT: C  868 LYS cc_start: 0.5931 (tptt) cc_final: 0.5501 (tppt)
REVERT: C  882 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8388 (mm)
  outliers start: 54
  outliers final: 42
  residues processed: 357
  average time/residue: 0.1089
  time to fit residues: 63.6908
Evaluate side-chains
  361 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 312
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  655 TYR
Chi-restraints excluded: chain A residue  772 THR
Chi-restraints excluded: chain A residue  773 CYS
Chi-restraints excluded: chain A residue  824 VAL
Chi-restraints excluded: chain A residue  842 TYR
Chi-restraints excluded: chain A residue  850 LEU
Chi-restraints excluded: chain A residue  869 THR
Chi-restraints excluded: chain A residue  894 LEU
Chi-restraints excluded: chain A residue  924 GLU
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  957 ILE
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue 1043 GLU
Chi-restraints excluded: chain B residue  480 LEU
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  583 PHE
Chi-restraints excluded: chain B residue  684 THR
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  772 THR
Chi-restraints excluded: chain B residue  842 TYR
Chi-restraints excluded: chain B residue  866 ILE
Chi-restraints excluded: chain B residue  869 THR
Chi-restraints excluded: chain B residue  894 LEU
Chi-restraints excluded: chain B residue  981 GLU
Chi-restraints excluded: chain B residue  986 LEU
Chi-restraints excluded: chain B residue 1047 GLN
Chi-restraints excluded: chain B residue 1075 ILE
Chi-restraints excluded: chain D residue  564 VAL
Chi-restraints excluded: chain D residue  583 PHE
Chi-restraints excluded: chain D residue  719 HIS
Chi-restraints excluded: chain D residue  842 TYR
Chi-restraints excluded: chain D residue  866 ILE
Chi-restraints excluded: chain D residue  869 THR
Chi-restraints excluded: chain D residue  882 LEU
Chi-restraints excluded: chain D residue  952 LEU
Chi-restraints excluded: chain D residue  957 ILE
Chi-restraints excluded: chain D residue  986 LEU
Chi-restraints excluded: chain C residue  583 PHE
Chi-restraints excluded: chain C residue  655 TYR
Chi-restraints excluded: chain C residue  816 ILE
Chi-restraints excluded: chain C residue  842 TYR
Chi-restraints excluded: chain C residue  866 ILE
Chi-restraints excluded: chain C residue  882 LEU
Chi-restraints excluded: chain C residue  952 LEU
Chi-restraints excluded: chain C residue  956 LEU
Chi-restraints excluded: chain C residue  957 ILE
Chi-restraints excluded: chain C residue  986 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 204 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   chunk 207 optimal weight:    0.5980
   chunk 116 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   chunk 217 optimal weight:    0.6980
   chunk 195 optimal weight:    0.2980
   chunk 151 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 719 HIS
B1047 GLN
** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 719 HIS
** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 719 HIS
C1047 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.162806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.135679 restraints weight = 25818.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3697 rms_B_bonded: 1.99
r_work: 0.3467 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.4003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  18488  Z= 0.137
  Angle     :  0.608  13.300  25056  Z= 0.308
  Chirality :  0.041   0.229   2940
  Planarity :  0.004   0.059   3084
  Dihedral  :  4.320  42.553   2428
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 18.26 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.18), residues: 2240
  helix:  1.38 (0.13), residues: 1612
  sheet:  0.94 (0.82), residues: 48
  loop : -0.96 (0.28), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 464 
 TYR   0.026   0.001   TYR D 714 
 PHE   0.020   0.001   PHE B 612 
 TRP   0.043   0.002   TRP D 993 
 HIS   0.006   0.001   HIS B 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (18488)
  covalent geometry    : angle       0.60842 (25056)
  hydrogen bonds       : bond        0.04141 ( 1101)
  hydrogen bonds       : angle       3.85142 ( 3243)

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

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

  4480 Ramachandran restraints generated.
    2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4480 Ramachandran restraints generated.
    2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  374 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 317
  time to evaluate  : 0.720 
Fit side-chains
   revert: symmetry clash
REVERT: A  612 PHE cc_start: 0.8327 (p90) cc_final: 0.7854 (p90)
REVERT: A  680 TYR cc_start: 0.7512 (m-10) cc_final: 0.6975 (m-10)
REVERT: A  693 ASN cc_start: 0.8852 (p0) cc_final: 0.8341 (p0)
REVERT: A  695 ILE cc_start: 0.8910 (tp) cc_final: 0.8585 (tp)
REVERT: A  699 ASN cc_start: 0.8911 (m110) cc_final: 0.8491 (m-40)
REVERT: A  723 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8544 (tt)
REVERT: A  842 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.6741 (t80)
REVERT: A  868 LYS cc_start: 0.6164 (tptt) cc_final: 0.5671 (tppt)
REVERT: A  924 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7451 (tp30)
REVERT: A  953 MET cc_start: 0.7610 (mmt) cc_final: 0.7052 (tpp)
REVERT: B  612 PHE cc_start: 0.8295 (p90) cc_final: 0.7641 (p90)
REVERT: B  693 ASN cc_start: 0.8671 (p0) cc_final: 0.8151 (p0)
REVERT: B  721 MET cc_start: 0.8348 (tpp) cc_final: 0.8136 (tpp)
REVERT: B  726 TYR cc_start: 0.8255 (t80) cc_final: 0.7692 (t80)
REVERT: B  953 MET cc_start: 0.7717 (mmm) cc_final: 0.7462 (tpp)
REVERT: D  509 LEU cc_start: 0.9008 (mm) cc_final: 0.8724 (mt)
REVERT: D  720 MET cc_start: 0.8390 (tpp) cc_final: 0.8101 (tpp)
REVERT: D  779 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8325 (mp)
REVERT: D  842 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7374 (t80)
REVERT: D  868 LYS cc_start: 0.6076 (tptt) cc_final: 0.5609 (tppt)
REVERT: D  882 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8270 (mm)
REVERT: D  953 MET cc_start: 0.7345 (mmt) cc_final: 0.6957 (tpp)
REVERT: D  966 ASP cc_start: 0.8387 (m-30) cc_final: 0.8047 (m-30)
REVERT: D 1042 MET cc_start: 0.7143 (tpt) cc_final: 0.6935 (mmt)
REVERT: C  612 PHE cc_start: 0.8310 (p90) cc_final: 0.8108 (p90)
REVERT: C  726 TYR cc_start: 0.8390 (t80) cc_final: 0.7847 (t80)
REVERT: C  774 MET cc_start: 0.7623 (mtp) cc_final: 0.7245 (mtp)
REVERT: C  779 LEU cc_start: 0.8629 (tt) cc_final: 0.8165 (mp)
REVERT: C  842 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.6974 (t80)
REVERT: C  868 LYS cc_start: 0.6060 (tptt) cc_final: 0.5584 (tppt)
REVERT: C  882 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8326 (mm)
  outliers start: 57
  outliers final: 40
  residues processed: 354
  average time/residue: 0.1036
  time to fit residues: 59.9660
Evaluate side-chains
  351 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 303
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  655 TYR
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  772 THR
Chi-restraints excluded: chain A residue  773 CYS
Chi-restraints excluded: chain A residue  824 VAL
Chi-restraints excluded: chain A residue  842 TYR
Chi-restraints excluded: chain A residue  850 LEU
Chi-restraints excluded: chain A residue  869 THR
Chi-restraints excluded: chain A residue  894 LEU
Chi-restraints excluded: chain A residue  924 GLU
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  957 ILE
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue 1043 GLU
Chi-restraints excluded: chain B residue  480 LEU
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  583 PHE
Chi-restraints excluded: chain B residue  684 THR
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  772 THR
Chi-restraints excluded: chain B residue  866 ILE
Chi-restraints excluded: chain B residue  869 THR
Chi-restraints excluded: chain B residue  894 LEU
Chi-restraints excluded: chain B residue  981 GLU
Chi-restraints excluded: chain B residue 1047 GLN
Chi-restraints excluded: chain B residue 1075 ILE
Chi-restraints excluded: chain D residue  564 VAL
Chi-restraints excluded: chain D residue  583 PHE
Chi-restraints excluded: chain D residue  719 HIS
Chi-restraints excluded: chain D residue  779 LEU
Chi-restraints excluded: chain D residue  842 TYR
Chi-restraints excluded: chain D residue  869 THR
Chi-restraints excluded: chain D residue  882 LEU
Chi-restraints excluded: chain D residue  952 LEU
Chi-restraints excluded: chain D residue  957 ILE
Chi-restraints excluded: chain D residue  986 LEU
Chi-restraints excluded: chain C residue  583 PHE
Chi-restraints excluded: chain C residue  655 TYR
Chi-restraints excluded: chain C residue  816 ILE
Chi-restraints excluded: chain C residue  842 TYR
Chi-restraints excluded: chain C residue  866 ILE
Chi-restraints excluded: chain C residue  882 LEU
Chi-restraints excluded: chain C residue  952 LEU
Chi-restraints excluded: chain C residue  956 LEU
Chi-restraints excluded: chain C residue  957 ILE
Chi-restraints excluded: chain C residue  986 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 228
   random chunks:
   chunk 144 optimal weight:    0.0980
   chunk 12 optimal weight:    0.6980
   chunk 138 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 142 optimal weight:    0.8980
   chunk 126 optimal weight:    0.8980
   chunk 197 optimal weight:    0.9990
   chunk 100 optimal weight:    0.0570
   chunk 143 optimal weight:    0.3980
   overall best weight:    0.3898

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

Flipped N/Q/H residues before XYZ refinement:
B 719 HIS
B1047 GLN
** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 719 HIS
** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 719 HIS
C1047 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.164356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.136595 restraints weight = 25866.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3731 rms_B_bonded: 1.98
r_work: 0.3510 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.4086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  18488  Z= 0.126
  Angle     :  0.607  13.027  25056  Z= 0.307
  Chirality :  0.041   0.223   2940
  Planarity :  0.004   0.059   3084
  Dihedral  :  4.271  42.690   2428
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.78 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.18), residues: 2240
  helix:  1.49 (0.13), residues: 1612
  sheet:  1.05 (0.83), residues: 48
  loop : -0.93 (0.28), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 464 
 TYR   0.025   0.001   TYR A 726 
 PHE   0.019   0.001   PHE B 612 
 TRP   0.049   0.002   TRP B 993 
 HIS   0.009   0.001   HIS D 719 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (18488)
  covalent geometry    : angle       0.60715 (25056)
  hydrogen bonds       : bond        0.03991 ( 1101)
  hydrogen bonds       : angle       3.82444 ( 3243)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3770.06 seconds
wall clock time: 65 minutes 40.61 seconds (3940.61 seconds total)