Starting phenix.real_space_refine
on Thu Sep 18 22:47:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pqq_20451/09_2025/6pqq_20451.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pqq_20451/09_2025/6pqq_20451.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6pqq_20451/09_2025/6pqq_20451.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pqq_20451/09_2025/6pqq_20451.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pqq_20451/09_2025/6pqq_20451.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pqq_20451/09_2025/6pqq_20451.cif"
  }
  resolution = 2.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      28      5.49       5
     S     136      5.16       5
     C   13200      2.51       5
     N    3148      2.21       5
     O    3504      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s

  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: 20016
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 604, 4740
          Classifications: {'peptide': 604}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 20, 'TRANS': 583}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 160
          Unresolved non-hydrogen angles: 195
          Unresolved non-hydrogen dihedrals: 135
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 4, 'GLU:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 2, 'PHE:plan': 4, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 100
    Chain: "A"
      Number of atoms: 264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 264
          Unusual residues: {'6OU': 5, 'LBN': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 85
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 89
          Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 3}
          Unresolved non-hydrogen planarities: 10
  Restraints were copied for chains:
    B, D, C
  Time building chain proxies: 4.76, per 1000 atoms: 0.24
  Number of scatterers: 20016
  At special positions: 0
  Unit cell: (113.4, 113.4, 147.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S     136     16.00
     P      28     15.00
     O    3504      8.00
     N    3148      7.00
     C   13200      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: 1.79
  Conformation dependent library (CDL) restraints added in 688.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4632

  Finding SS restraints...
    Secondary structure from input PDB file:
      136 helices and 8 sheets defined
      73.2% alpha, 1.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 446 through 456
      removed outlier: 3.575A  pdb=" N   LEU A 450 " --> pdb=" O   LYS A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 466
    Processing helix  chain 'A' and resid 484 through 492
      removed outlier: 3.623A  pdb=" N   ASN A 492 " --> pdb=" O   LEU A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 504
    Processing helix  chain 'A' and resid 516 through 525
    Processing helix  chain 'A' and resid 526 through 535
    Processing helix  chain 'A' and resid 537 through 541
      removed outlier: 3.709A  pdb=" N   CYS A 540 " --> pdb=" O   ASN A 537 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   THR A 541 " --> pdb=" O   LEU A 538 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 537 through 541'
    Processing helix  chain 'A' and resid 550 through 558
      removed outlier: 3.536A  pdb=" N   PHE A 554 " --> pdb=" O   THR A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 570
      removed outlier: 3.524A  pdb=" N   HIS A 570 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 589
    Processing helix  chain 'A' and resid 592 through 601
      removed outlier: 3.644A  pdb=" N   VAL A 596 " --> pdb=" O   ARG A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 611
      removed outlier: 3.670A  pdb=" N   LYS A 610 " --> pdb=" O   ASP A 606 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   ILE A 611 " --> pdb=" O   GLU A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 629
    Processing helix  chain 'A' and resid 630 through 640
      removed outlier: 3.647A  pdb=" N   PHE A 640 " --> pdb=" O   VAL A 636 " (cutoff:3.500A)
    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 740
      removed outlier: 3.760A  pdb=" N   TYR A 714 " --> pdb=" O   LYS A 710 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   PHE A 716 " --> pdb=" O   LEU A 712 " (cutoff:3.500A)
      removed outlier: 6.005A  pdb=" N   ARG A 717 " --> pdb=" O   ALA A 713 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   TYR A 726 " --> pdb=" O   ASN A 722 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   GLY A 729 " --> pdb=" O   SER A 725 " (cutoff:3.500A)
      Proline residue:  A 732  - end of helix
    Processing helix  chain 'A' and resid 766 through 796
      removed outlier: 3.765A  pdb=" N   PHE A 793 " --> pdb=" O   ALA A 789 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 820
      removed outlier: 3.883A  pdb=" N   VAL A 806 " --> pdb=" O   ASP A 802 " (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 850
      removed outlier: 3.718A  pdb=" N   ILE A 837 " --> pdb=" O   GLN A 833 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   LEU A 847 " --> pdb=" O   TRP A 843 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   LEU A 848 " --> pdb=" O   MET A 844 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   TYR A 849 " --> pdb=" O   ASN A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 851 through 853
      No H-bonds generated for 'chain 'A' and resid 851 through 853'
    Processing helix  chain 'A' and resid 856 through 892
      removed outlier: 3.729A  pdb=" N   ILE A 860 " --> pdb=" O   CYS A 856 " (cutoff:3.500A)
      removed outlier: 5.095A  pdb=" N   VAL A 875 " --> pdb=" O   LEU A 871 " (cutoff:3.500A)
      removed outlier: 5.719A  pdb=" N   VAL A 876 " --> pdb=" O   ARG A 872 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 895 through 899
    Processing helix  chain 'A' and resid 900 through 912
    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 948
    Processing helix  chain 'A' and resid 950 through 969
    Processing helix  chain 'A' and resid 970 through 987
      removed outlier: 3.552A  pdb=" N   LYS A 974 " --> pdb=" O   HIS A 970 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ILE A 976 " --> pdb=" O   SER A 972 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 991 through 999
      removed outlier: 3.544A  pdb=" N   ASP A 999 " --> pdb=" O   LEU A 995 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1012 through 1012
      No H-bonds generated for 'chain 'A' and resid 1012 through 1012'
    Processing helix  chain 'A' and resid 1016 through 1025
    Processing helix  chain 'A' and resid 1040 through 1072
    Processing helix  chain 'B' and resid 447 through 456
    Processing helix  chain 'B' and resid 458 through 466
    Processing helix  chain 'B' and resid 484 through 492
      removed outlier: 3.623A  pdb=" N   ASN B 492 " --> pdb=" O   LEU B 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 494 through 504
    Processing helix  chain 'B' and resid 516 through 525
    Processing helix  chain 'B' and resid 526 through 535
    Processing helix  chain 'B' and resid 537 through 541
      removed outlier: 3.709A  pdb=" N   CYS B 540 " --> pdb=" O   ASN B 537 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   THR B 541 " --> pdb=" O   LEU B 538 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 537 through 541'
    Processing helix  chain 'B' and resid 550 through 558
      removed outlier: 3.536A  pdb=" N   PHE B 554 " --> pdb=" O   THR B 550 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 570
      removed outlier: 3.524A  pdb=" N   HIS B 570 " --> pdb=" O   LEU B 566 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 582 through 589
    Processing helix  chain 'B' and resid 592 through 601
      removed outlier: 3.645A  pdb=" N   VAL B 596 " --> pdb=" O   ARG B 592 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 604 through 611
      removed outlier: 3.669A  pdb=" N   LYS B 610 " --> pdb=" O   ASP B 606 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   ILE B 611 " --> pdb=" O   GLU B 607 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 621 through 629
    Processing helix  chain 'B' and resid 630 through 640
      removed outlier: 3.647A  pdb=" N   PHE B 640 " --> pdb=" O   VAL B 636 " (cutoff:3.500A)
    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 740
      removed outlier: 3.759A  pdb=" N   TYR B 714 " --> pdb=" O   LYS B 710 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   PHE B 716 " --> pdb=" O   LEU B 712 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   ARG B 717 " --> pdb=" O   ALA B 713 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   TYR B 726 " --> pdb=" O   ASN B 722 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   GLY B 729 " --> pdb=" O   SER B 725 " (cutoff:3.500A)
      Proline residue:  B 732  - end of helix
    Processing helix  chain 'B' and resid 766 through 796
      removed outlier: 3.765A  pdb=" N   PHE B 793 " --> pdb=" O   ALA B 789 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 802 through 820
      removed outlier: 3.882A  pdb=" N   VAL B 806 " --> pdb=" O   ASP B 802 " (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 850
      removed outlier: 3.718A  pdb=" N   ILE B 837 " --> pdb=" O   GLN B 833 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   LEU B 847 " --> pdb=" O   TRP B 843 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   LEU B 848 " --> pdb=" O   MET B 844 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   TYR B 849 " --> pdb=" O   ASN B 845 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 851 through 853
      No H-bonds generated for 'chain 'B' and resid 851 through 853'
    Processing helix  chain 'B' and resid 856 through 892
      removed outlier: 3.729A  pdb=" N   ILE B 860 " --> pdb=" O   CYS B 856 " (cutoff:3.500A)
      removed outlier: 5.096A  pdb=" N   VAL B 875 " --> pdb=" O   LEU B 871 " (cutoff:3.500A)
      removed outlier: 5.719A  pdb=" N   VAL B 876 " --> pdb=" O   ARG B 872 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 895 through 899
    Processing helix  chain 'B' and resid 900 through 912
    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 948
    Processing helix  chain 'B' and resid 950 through 969
    Processing helix  chain 'B' and resid 970 through 987
      removed outlier: 3.551A  pdb=" N   LYS B 974 " --> pdb=" O   HIS B 970 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ILE B 976 " --> pdb=" O   SER B 972 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 991 through 999
      removed outlier: 3.544A  pdb=" N   ASP B 999 " --> pdb=" O   LEU B 995 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1012 through 1012
      No H-bonds generated for 'chain 'B' and resid 1012 through 1012'
    Processing helix  chain 'B' and resid 1016 through 1025
    Processing helix  chain 'B' and resid 1040 through 1072
    Processing helix  chain 'D' and resid 447 through 456
    Processing helix  chain 'D' and resid 458 through 466
    Processing helix  chain 'D' and resid 484 through 492
      removed outlier: 3.623A  pdb=" N   ASN D 492 " --> pdb=" O   LEU D 488 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 494 through 504
    Processing helix  chain 'D' and resid 516 through 525
    Processing helix  chain 'D' and resid 526 through 535
    Processing helix  chain 'D' and resid 537 through 541
      removed outlier: 3.709A  pdb=" N   CYS D 540 " --> pdb=" O   ASN D 537 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   THR D 541 " --> pdb=" O   LEU D 538 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 537 through 541'
    Processing helix  chain 'D' and resid 550 through 558
      removed outlier: 3.536A  pdb=" N   PHE D 554 " --> pdb=" O   THR D 550 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 560 through 570
      removed outlier: 3.524A  pdb=" N   HIS D 570 " --> pdb=" O   LEU D 566 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 582 through 589
    Processing helix  chain 'D' and resid 592 through 601
      removed outlier: 3.645A  pdb=" N   VAL D 596 " --> pdb=" O   ARG D 592 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 604 through 611
      removed outlier: 3.670A  pdb=" N   LYS D 610 " --> pdb=" O   ASP D 606 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   ILE D 611 " --> pdb=" O   GLU D 607 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 621 through 629
    Processing helix  chain 'D' and resid 630 through 640
      removed outlier: 3.648A  pdb=" N   PHE D 640 " --> pdb=" O   VAL D 636 " (cutoff:3.500A)
    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 740
      removed outlier: 3.760A  pdb=" N   TYR D 714 " --> pdb=" O   LYS D 710 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   PHE D 716 " --> pdb=" O   LEU D 712 " (cutoff:3.500A)
      removed outlier: 6.005A  pdb=" N   ARG D 717 " --> pdb=" O   ALA D 713 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   TYR D 726 " --> pdb=" O   ASN D 722 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   GLY D 729 " --> pdb=" O   SER D 725 " (cutoff:3.500A)
      Proline residue:  D 732  - end of helix
    Processing helix  chain 'D' and resid 766 through 796
      removed outlier: 3.765A  pdb=" N   PHE D 793 " --> pdb=" O   ALA D 789 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 802 through 820
      removed outlier: 3.883A  pdb=" N   VAL D 806 " --> pdb=" O   ASP D 802 " (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 850
      removed outlier: 3.718A  pdb=" N   ILE D 837 " --> pdb=" O   GLN D 833 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   LEU D 847 " --> pdb=" O   TRP D 843 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   LEU D 848 " --> pdb=" O   MET D 844 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   TYR D 849 " --> pdb=" O   ASN D 845 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 851 through 853
      No H-bonds generated for 'chain 'D' and resid 851 through 853'
    Processing helix  chain 'D' and resid 856 through 892
      removed outlier: 3.730A  pdb=" N   ILE D 860 " --> pdb=" O   CYS D 856 " (cutoff:3.500A)
      removed outlier: 5.095A  pdb=" N   VAL D 875 " --> pdb=" O   LEU D 871 " (cutoff:3.500A)
      removed outlier: 5.719A  pdb=" N   VAL D 876 " --> pdb=" O   ARG D 872 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 895 through 899
    Processing helix  chain 'D' and resid 900 through 912
    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 948
    Processing helix  chain 'D' and resid 950 through 969
    Processing helix  chain 'D' and resid 970 through 987
      removed outlier: 3.552A  pdb=" N   LYS D 974 " --> pdb=" O   HIS D 970 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ILE D 976 " --> pdb=" O   SER D 972 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 991 through 999
      removed outlier: 3.544A  pdb=" N   ASP D 999 " --> pdb=" O   LEU D 995 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1012 through 1012
      No H-bonds generated for 'chain 'D' and resid 1012 through 1012'
    Processing helix  chain 'D' and resid 1016 through 1025
    Processing helix  chain 'D' and resid 1040 through 1072
    Processing helix  chain 'C' and resid 447 through 456
    Processing helix  chain 'C' and resid 458 through 466
    Processing helix  chain 'C' and resid 484 through 492
      removed outlier: 3.622A  pdb=" N   ASN C 492 " --> pdb=" O   LEU C 488 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 494 through 504
    Processing helix  chain 'C' and resid 516 through 525
    Processing helix  chain 'C' and resid 526 through 535
    Processing helix  chain 'C' and resid 537 through 541
      removed outlier: 3.708A  pdb=" N   CYS C 540 " --> pdb=" O   ASN C 537 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   THR C 541 " --> pdb=" O   LEU C 538 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 537 through 541'
    Processing helix  chain 'C' and resid 550 through 558
      removed outlier: 3.536A  pdb=" N   PHE C 554 " --> pdb=" O   THR C 550 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 560 through 570
      removed outlier: 3.524A  pdb=" N   HIS C 570 " --> pdb=" O   LEU C 566 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 582 through 589
    Processing helix  chain 'C' and resid 592 through 601
      removed outlier: 3.644A  pdb=" N   VAL C 596 " --> pdb=" O   ARG C 592 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 604 through 611
      removed outlier: 3.669A  pdb=" N   LYS C 610 " --> pdb=" O   ASP C 606 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   ILE C 611 " --> pdb=" O   GLU C 607 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 621 through 629
    Processing helix  chain 'C' and resid 630 through 640
      removed outlier: 3.647A  pdb=" N   PHE C 640 " --> pdb=" O   VAL C 636 " (cutoff:3.500A)
    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 740
      removed outlier: 3.760A  pdb=" N   TYR C 714 " --> pdb=" O   LYS C 710 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   PHE C 716 " --> pdb=" O   LEU C 712 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   ARG C 717 " --> pdb=" O   ALA C 713 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   TYR C 726 " --> pdb=" O   ASN C 722 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   GLY C 729 " --> pdb=" O   SER C 725 " (cutoff:3.500A)
      Proline residue:  C 732  - end of helix
    Processing helix  chain 'C' and resid 766 through 796
      removed outlier: 3.765A  pdb=" N   PHE C 793 " --> pdb=" O   ALA C 789 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 802 through 820
      removed outlier: 3.882A  pdb=" N   VAL C 806 " --> pdb=" O   ASP C 802 " (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 850
      removed outlier: 3.718A  pdb=" N   ILE C 837 " --> pdb=" O   GLN C 833 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   LEU C 847 " --> pdb=" O   TRP C 843 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   LEU C 848 " --> pdb=" O   MET C 844 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   TYR C 849 " --> pdb=" O   ASN C 845 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 851 through 853
      No H-bonds generated for 'chain 'C' and resid 851 through 853'
    Processing helix  chain 'C' and resid 856 through 892
      removed outlier: 3.729A  pdb=" N   ILE C 860 " --> pdb=" O   CYS C 856 " (cutoff:3.500A)
      removed outlier: 5.096A  pdb=" N   VAL C 875 " --> pdb=" O   LEU C 871 " (cutoff:3.500A)
      removed outlier: 5.720A  pdb=" N   VAL C 876 " --> pdb=" O   ARG C 872 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 895 through 899
    Processing helix  chain 'C' and resid 900 through 912
    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 948
    Processing helix  chain 'C' and resid 950 through 969
    Processing helix  chain 'C' and resid 970 through 987
      removed outlier: 3.553A  pdb=" N   LYS C 974 " --> pdb=" O   HIS C 970 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ILE C 976 " --> pdb=" O   SER C 972 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 991 through 999
      removed outlier: 3.544A  pdb=" N   ASP C 999 " --> pdb=" O   LEU C 995 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1012 through 1012
      No H-bonds generated for 'chain 'C' and resid 1012 through 1012'
    Processing helix  chain 'C' and resid 1016 through 1025
    Processing helix  chain 'C' and resid 1040 through 1072
    Processing sheet with id=AA1, first strand: chain 'A' and resid 642 through 644
    Processing sheet with id=AA2, first strand: chain 'A' and resid 745 through 746
      removed outlier: 4.022A  pdb=" N   ALA A 745 " --> pdb=" O   ILE A 752 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 642 through 644
    Processing sheet with id=AA4, first strand: chain 'B' and resid 745 through 746
      removed outlier: 4.021A  pdb=" N   ALA B 745 " --> pdb=" O   ILE B 752 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 642 through 644
    Processing sheet with id=AA6, first strand: chain 'D' and resid 745 through 746
      removed outlier: 4.022A  pdb=" N   ALA D 745 " --> pdb=" O   ILE D 752 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 642 through 644
    Processing sheet with id=AA8, first strand: chain 'C' and resid 745 through 746
      removed outlier: 4.021A  pdb=" N   ALA C 745 " --> pdb=" O   ILE C 752 " (cutoff:3.500A)

    1164 hydrogen bonds defined for protein.
    3456 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: 3.29

  Time building geometry restraints manager: 2.34 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 3012
        1.30 -     1.43: 5112
        1.43 -     1.56: 11738
        1.56 -     1.69: 274
        1.69 -     1.81: 268
  Bond restraints: 20404
  Sorted by residual:
  bond pdb=" O2  LBN D1202 "
       pdb=" P1  LBN D1202 "
    ideal  model  delta    sigma   weight residual
    1.650  1.791 -0.141 2.00e-02 2.50e+03 4.98e+01
  bond pdb=" O2  LBN B1202 "
       pdb=" P1  LBN B1202 "
    ideal  model  delta    sigma   weight residual
    1.650  1.791 -0.141 2.00e-02 2.50e+03 4.94e+01
  bond pdb=" O2  LBN A1202 "
       pdb=" P1  LBN A1202 "
    ideal  model  delta    sigma   weight residual
    1.650  1.791 -0.141 2.00e-02 2.50e+03 4.94e+01
  bond pdb=" O2  LBN C1202 "
       pdb=" P1  LBN C1202 "
    ideal  model  delta    sigma   weight residual
    1.650  1.790 -0.140 2.00e-02 2.50e+03 4.91e+01
  bond pdb=" O2  LBN B1201 "
       pdb=" P1  LBN B1201 "
    ideal  model  delta    sigma   weight residual
    1.650  1.783 -0.133 2.00e-02 2.50e+03 4.41e+01
  ... (remaining 20399 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.96: 26430
        2.96 -     5.92: 862
        5.92 -     8.88: 108
        8.88 -    11.84: 40
       11.84 -    14.80: 32
  Bond angle restraints: 27472
  Sorted by residual:
  angle pdb=" N   ILE A 611 "
        pdb=" CA  ILE A 611 "
        pdb=" C   ILE A 611 "
      ideal   model   delta    sigma   weight residual
     108.12  122.55  -14.43 1.34e+00 5.57e-01 1.16e+02
  angle pdb=" N   ILE C 611 "
        pdb=" CA  ILE C 611 "
        pdb=" C   ILE C 611 "
      ideal   model   delta    sigma   weight residual
     108.12  122.54  -14.42 1.34e+00 5.57e-01 1.16e+02
  angle pdb=" N   ILE B 611 "
        pdb=" CA  ILE B 611 "
        pdb=" C   ILE B 611 "
      ideal   model   delta    sigma   weight residual
     108.12  122.53  -14.41 1.34e+00 5.57e-01 1.16e+02
  angle pdb=" N   ILE D 611 "
        pdb=" CA  ILE D 611 "
        pdb=" C   ILE D 611 "
      ideal   model   delta    sigma   weight residual
     108.12  122.52  -14.40 1.34e+00 5.57e-01 1.15e+02
  angle pdb=" C   ILE D 611 "
        pdb=" CA  ILE D 611 "
        pdb=" CB  ILE D 611 "
      ideal   model   delta    sigma   weight residual
     111.35  105.60    5.75 1.09e+00 8.42e-01 2.79e+01
  ... (remaining 27467 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.71: 11992
       35.71 -    71.42: 360
       71.42 -   107.12: 64
      107.12 -   142.83: 28
      142.83 -   178.54: 32
  Dihedral angle restraints: 12476
    sinusoidal: 5356
      harmonic: 7120
  Sorted by residual:
  dihedral pdb=" C19 6OU D1205 "
           pdb=" C20 6OU D1205 "
           pdb=" C21 6OU D1205 "
           pdb=" O22 6OU D1205 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -59.00  119.54 -178.54     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C19 6OU C1205 "
           pdb=" C20 6OU C1205 "
           pdb=" C21 6OU C1205 "
           pdb=" O22 6OU C1205 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -59.00  119.54 -178.54     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C19 6OU A1205 "
           pdb=" C20 6OU A1205 "
           pdb=" C21 6OU A1205 "
           pdb=" O22 6OU A1205 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -59.00  119.53 -178.53     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 12473 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.134: 3042
       0.134 -    0.269: 70
       0.269 -    0.403: 0
       0.403 -    0.538: 8
       0.538 -    0.672: 12
  Chirality restraints: 3132
  Sorted by residual:
  chirality pdb=" C20 6OU D1205 "
            pdb=" C19 6OU D1205 "
            pdb=" C21 6OU D1205 "
            pdb=" O30 6OU D1205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    3.02   -0.67 2.00e-01 2.50e+01 1.13e+01
  chirality pdb=" C20 6OU C1205 "
            pdb=" C19 6OU C1205 "
            pdb=" C21 6OU C1205 "
            pdb=" O30 6OU C1205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    3.02   -0.67 2.00e-01 2.50e+01 1.13e+01
  chirality pdb=" C20 6OU A1205 "
            pdb=" C19 6OU A1205 "
            pdb=" C21 6OU A1205 "
            pdb=" O30 6OU A1205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    3.02   -0.67 2.00e-01 2.50e+01 1.13e+01
  ... (remaining 3129 not shown)

  Planarity restraints: 3304
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 820 "    0.045 5.00e-02 4.00e+02   6.80e-02 7.40e+00
        pdb=" N   PRO C 821 "   -0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO C 821 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO C 821 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 820 "    0.045 5.00e-02 4.00e+02   6.79e-02 7.37e+00
        pdb=" N   PRO B 821 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO B 821 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 821 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 820 "   -0.045 5.00e-02 4.00e+02   6.77e-02 7.34e+00
        pdb=" N   PRO A 821 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A 821 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 821 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 3301 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 5760
        2.83 -     3.35: 17625
        3.35 -     3.87: 31401
        3.87 -     4.38: 35950
        4.38 -     4.90: 61651
  Nonbonded interactions: 152387
  Sorted by model distance:
  nonbonded pdb=" O   ILE D 810 "
            pdb=" OG1 THR D 814 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" O   ILE A 810 "
            pdb=" OG1 THR A 814 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" O   ILE C 810 "
            pdb=" OG1 THR C 814 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" O   ILE B 810 "
            pdb=" OG1 THR B 814 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" O   MET B 744 "
            pdb=" NE1 TRP B 832 "
     model   vdw
     2.392 3.120
  ... (remaining 152382 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: 0.06
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:             1.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     18.520
  Find NCS groups from input model:        0.180
  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:6.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
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      :  0.011   0.141  20404  Z= 0.517
  Angle     :  1.262  14.804  27472  Z= 0.561
  Chirality :  0.070   0.672   3132
  Planarity :  0.007   0.068   3304
  Dihedral  : 21.090 178.540   7844
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  3.77 %
    Favored  : 96.03 %
  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: -3.37 (0.14), residues: 2376
  helix: -2.18 (0.09), residues: 1720
  sheet: -0.88 (0.68), residues: 68
  loop : -1.79 (0.23), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 919 
 TYR   0.033   0.003   TYR C 842 
 PHE   0.019   0.002   PHE D 888 
 TRP   0.013   0.002   TRP D 832 
 HIS   0.010   0.002   HIS A 589 

Details of bonding type rmsd
  covalent geometry    : bond        0.01062 (20404)
  covalent geometry    : angle       1.26156 (27472)
  hydrogen bonds       : bond        0.13953 ( 1164)
  hydrogen bonds       : angle       5.59426 ( 3456)

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

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

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  491 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 487
  time to evaluate  : 0.797 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  509 LEU cc_start: 0.9313 (mt) cc_final: 0.9078 (mp)
REVERT: A  544 LEU cc_start: 0.9158 (mt) cc_final: 0.8816 (mm)
REVERT: A  873 SER cc_start: 0.8434 (t) cc_final: 0.8176 (p)
REVERT: A  986 LEU cc_start: 0.9074 (tt) cc_final: 0.8817 (tp)
REVERT: A  992 LEU cc_start: 0.9160 (tt) cc_final: 0.8845 (tm)
REVERT: B  580 GLN cc_start: 0.8506 (mp10) cc_final: 0.8119 (mp10)
REVERT: B  717 ARG cc_start: 0.8170 (ttt180) cc_final: 0.7893 (ttt90)
REVERT: B  912 MET cc_start: 0.8371 (ttm) cc_final: 0.8169 (ttp)
REVERT: B 1075 ILE cc_start: 0.8707 (mt) cc_final: 0.7406 (mm)
REVERT: D  693 ASN cc_start: 0.8755 (m-40) cc_final: 0.8269 (t0)
REVERT: D  783 PHE cc_start: 0.7805 (m-10) cc_final: 0.7510 (m-10)
REVERT: D  981 GLU cc_start: 0.8049 (tp30) cc_final: 0.7848 (tp30)
REVERT: D  992 LEU cc_start: 0.9092 (tt) cc_final: 0.8576 (tm)
REVERT: D 1059 GLU cc_start: 0.8219 (tp30) cc_final: 0.7857 (tp30)
REVERT: D 1075 ILE cc_start: 0.8795 (mt) cc_final: 0.8326 (mp)
REVERT: C  475 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7946 (tp)
REVERT: C  634 MET cc_start: 0.8512 (tpt) cc_final: 0.7956 (tpt)
REVERT: C  635 LYS cc_start: 0.8212 (ttpt) cc_final: 0.7986 (tptp)
REVERT: C  720 MET cc_start: 0.7594 (mmm) cc_final: 0.7229 (mmt)
REVERT: C  854 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7761 (mp0)
REVERT: C  873 SER cc_start: 0.7711 (t) cc_final: 0.7457 (p)
REVERT: C 1042 MET cc_start: 0.7921 (ppp) cc_final: 0.7720 (pp-130)
REVERT: C 1059 GLU cc_start: 0.8325 (tp30) cc_final: 0.7999 (tp30)
  outliers start: 4
  outliers final: 1
  residues processed: 491
  average time/residue: 0.6936
  time to fit residues: 379.7477
Evaluate side-chains
  242 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 240
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain C residue  475 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 216 optimal weight:    3.9990
   chunk 98 optimal weight:    0.6980
   chunk 194 optimal weight:    1.9990
   chunk 227 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.0870
   chunk 235 optimal weight:   30.0000
   overall best weight:    0.9564

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

Flipped N/Q/H residues before XYZ refinement:
A 451 HIS
A 460 ASN
A 476 ASN
A 512 HIS
A 519 HIS
A 644 HIS
A 700 HIS
A 805 ASN
A 907 GLN
A 983 HIS
B 451 HIS
B 476 ASN
B 512 HIS
B 519 HIS
B 549 ASN
B 644 HIS
B 700 HIS
B 722 ASN
B 805 ASN
B 907 GLN
B 983 HIS
** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 476 ASN
D 512 HIS
D 519 HIS
D 644 HIS
D 700 HIS
D 805 ASN
D 907 GLN
D 983 HIS
C 451 HIS
C 460 ASN
C 476 ASN
C 512 HIS
C 519 HIS
C 644 HIS
C 700 HIS
C 747 ASN
C 805 ASN
C 983 HIS
** C1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 39

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.124151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.090301 restraints weight = 32142.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 2.53
r_work: 0.3041 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  20404  Z= 0.130
  Angle     :  0.600   7.929  27472  Z= 0.290
  Chirality :  0.040   0.154   3132
  Planarity :  0.005   0.063   3304
  Dihedral  : 23.924 176.656   3476
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 14.34 %
    Favored  : 82.79 %
  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: -0.81 (0.16), residues: 2376
  helix: -0.20 (0.11), residues: 1740
  sheet: -0.22 (0.73), residues: 68
  loop : -1.20 (0.25), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D 975 
 TYR   0.011   0.001   TYR C 842 
 PHE   0.010   0.001   PHE B 823 
 TRP   0.012   0.001   TRP C 832 
 HIS   0.004   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (20404)
  covalent geometry    : angle       0.60031 (27472)
  hydrogen bonds       : bond        0.04943 ( 1164)
  hydrogen bonds       : angle       3.87976 ( 3456)

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

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

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 247
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  509 LEU cc_start: 0.9315 (mt) cc_final: 0.9110 (mp)
REVERT: A  544 LEU cc_start: 0.9186 (mt) cc_final: 0.8911 (mm)
REVERT: A  634 MET cc_start: 0.8821 (tpt) cc_final: 0.8499 (tpp)
REVERT: A  661 LYS cc_start: 0.8853 (pttt) cc_final: 0.8643 (ptpt)
REVERT: A  744 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7377 (mmp)
REVERT: A  826 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8321 (pt)
REVERT: A  877 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7996 (t80)
REVERT: A  986 LEU cc_start: 0.9044 (tt) cc_final: 0.8798 (tp)
REVERT: B  580 GLN cc_start: 0.8433 (mp10) cc_final: 0.8044 (mp10)
REVERT: B  693 ASN cc_start: 0.8982 (m-40) cc_final: 0.8603 (t0)
REVERT: B  717 ARG cc_start: 0.8547 (ttt180) cc_final: 0.8301 (ttt90)
REVERT: B  826 ILE cc_start: 0.8606 (tp) cc_final: 0.8226 (pt)
REVERT: B  877 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8049 (t80)
REVERT: B 1075 ILE cc_start: 0.8756 (mt) cc_final: 0.8542 (mp)
REVERT: D  634 MET cc_start: 0.8828 (tpt) cc_final: 0.8590 (tpp)
REVERT: D  693 ASN cc_start: 0.8859 (m-40) cc_final: 0.8493 (t0)
REVERT: D  783 PHE cc_start: 0.7881 (m-10) cc_final: 0.7612 (m-10)
REVERT: D  852 ARG cc_start: 0.8101 (mmt90) cc_final: 0.7698 (mpt-90)
REVERT: D  877 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7690 (t80)
REVERT: D  981 GLU cc_start: 0.8506 (tp30) cc_final: 0.8250 (tp30)
REVERT: D 1047 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6867 (tt0)
REVERT: D 1059 GLU cc_start: 0.8761 (tp30) cc_final: 0.8408 (tp30)
REVERT: C  634 MET cc_start: 0.8630 (tpt) cc_final: 0.8252 (tpt)
REVERT: C  635 LYS cc_start: 0.8307 (ttpt) cc_final: 0.8000 (tptp)
REVERT: C  689 MET cc_start: 0.8784 (mtp) cc_final: 0.8454 (mtt)
REVERT: C  854 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7869 (mp0)
REVERT: C  872 ARG cc_start: 0.8267 (mtm-85) cc_final: 0.8065 (mtm-85)
REVERT: C  873 SER cc_start: 0.7945 (t) cc_final: 0.7687 (p)
REVERT: C  981 GLU cc_start: 0.8532 (tp30) cc_final: 0.8324 (tp30)
REVERT: C 1042 MET cc_start: 0.8082 (ppp) cc_final: 0.7817 (pp-130)
REVERT: C 1059 GLU cc_start: 0.8861 (tp30) cc_final: 0.8507 (tp30)
  outliers start: 58
  outliers final: 18
  residues processed: 285
  average time/residue: 0.6162
  time to fit residues: 197.8431
Evaluate side-chains
  226 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 202
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  635 LYS
Chi-restraints excluded: chain A residue  693 ASN
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  744 MET
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain A residue  826 ILE
Chi-restraints excluded: chain A residue  877 PHE
Chi-restraints excluded: chain B residue  466 LEU
Chi-restraints excluded: chain B residue  510 SER
Chi-restraints excluded: chain B residue  748 SER
Chi-restraints excluded: chain B residue  873 SER
Chi-restraints excluded: chain B residue  877 PHE
Chi-restraints excluded: chain D residue  507 LEU
Chi-restraints excluded: chain D residue  635 LYS
Chi-restraints excluded: chain D residue  748 SER
Chi-restraints excluded: chain D residue  779 LEU
Chi-restraints excluded: chain D residue  877 PHE
Chi-restraints excluded: chain D residue  998 VAL
Chi-restraints excluded: chain D residue 1047 GLN
Chi-restraints excluded: chain C residue  502 LEU
Chi-restraints excluded: chain C residue  504 LYS
Chi-restraints excluded: chain C residue  698 LEU
Chi-restraints excluded: chain C residue  855 ASN
Chi-restraints excluded: chain C residue  894 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 109 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0570
   chunk 85 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 119 optimal weight:    1.9990
   chunk 173 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 142 optimal weight:    8.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.9300

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

Flipped N/Q/H residues before XYZ refinement:
A 747 ASN
B 460 ASN
B 570 HIS
B 590 ASN
B 722 ASN
B 747 ASN
** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 451 HIS
D 460 ASN
D 549 ASN
D 570 HIS
D 747 ASN
** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 549 ASN
C 570 HIS
C 590 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.122600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.088630 restraints weight = 32191.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 2.51
r_work: 0.2997 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  20404  Z= 0.120
  Angle     :  0.556   8.321  27472  Z= 0.267
  Chirality :  0.040   0.147   3132
  Planarity :  0.004   0.060   3304
  Dihedral  : 22.068 169.074   3472
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 13.49 %
    Favored  : 82.44 %
  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:  0.58 (0.17), residues: 2376
  helix:  0.87 (0.12), residues: 1748
  sheet:  0.43 (0.76), residues: 68
  loop : -0.94 (0.27), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 975 
 TYR   0.014   0.001   TYR D 714 
 PHE   0.011   0.001   PHE D 888 
 TRP   0.013   0.001   TRP C 605 
 HIS   0.004   0.001   HIS B 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (20404)
  covalent geometry    : angle       0.55606 (27472)
  hydrogen bonds       : bond        0.04478 ( 1164)
  hydrogen bonds       : angle       3.53851 ( 3456)

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

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

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 228
  time to evaluate  : 0.624 
Fit side-chains
REVERT: A  544 LEU cc_start: 0.9189 (mt) cc_final: 0.8913 (mm)
REVERT: A  634 MET cc_start: 0.8878 (tpt) cc_final: 0.8581 (tpp)
REVERT: A  877 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.8125 (t80)
REVERT: A  974 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.7925 (tmtt)
REVERT: A  986 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8726 (tp)
REVERT: B  580 GLN cc_start: 0.8646 (mp10) cc_final: 0.8227 (mp10)
REVERT: B  681 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7684 (pp20)
REVERT: B  717 ARG cc_start: 0.8604 (ttt180) cc_final: 0.8386 (ttt90)
REVERT: B  826 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8041 (pp)
REVERT: B  877 PHE cc_start: 0.8481 (m-80) cc_final: 0.8241 (t80)
REVERT: D  516 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8334 (p)
REVERT: D  634 MET cc_start: 0.8919 (tpt) cc_final: 0.8698 (tpp)
REVERT: D  693 ASN cc_start: 0.8991 (m-40) cc_final: 0.8579 (t0)
REVERT: D  744 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7748 (mmp)
REVERT: D  783 PHE cc_start: 0.7737 (m-10) cc_final: 0.7522 (m-10)
REVERT: D  852 ARG cc_start: 0.8147 (mmt90) cc_final: 0.7580 (mtp180)
REVERT: D  877 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7868 (t80)
REVERT: D  912 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8937 (ttm)
REVERT: D  941 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8646 (tp)
REVERT: D 1059 GLU cc_start: 0.8810 (tp30) cc_final: 0.8456 (tp30)
REVERT: C  483 MET cc_start: 0.8821 (mtm) cc_final: 0.8318 (mtp)
REVERT: C  626 MET cc_start: 0.8443 (mtp) cc_final: 0.8101 (ttm)
REVERT: C  634 MET cc_start: 0.8869 (tpt) cc_final: 0.8286 (tpt)
REVERT: C  873 SER cc_start: 0.8112 (t) cc_final: 0.7874 (p)
REVERT: C  941 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8517 (tp)
REVERT: C  981 GLU cc_start: 0.8535 (tp30) cc_final: 0.8239 (tp30)
REVERT: C 1042 MET cc_start: 0.7996 (ppp) cc_final: 0.7791 (ppp)
REVERT: C 1059 GLU cc_start: 0.8816 (tp30) cc_final: 0.8439 (tp30)
  outliers start: 82
  outliers final: 21
  residues processed: 280
  average time/residue: 0.5208
  time to fit residues: 167.8233
Evaluate side-chains
  222 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 190
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  709 MET
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain A residue  877 PHE
Chi-restraints excluded: chain A residue  974 LYS
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  681 GLU
Chi-restraints excluded: chain B residue  748 SER
Chi-restraints excluded: chain B residue  779 LEU
Chi-restraints excluded: chain B residue  819 VAL
Chi-restraints excluded: chain B residue  826 ILE
Chi-restraints excluded: chain D residue  484 THR
Chi-restraints excluded: chain D residue  507 LEU
Chi-restraints excluded: chain D residue  516 THR
Chi-restraints excluded: chain D residue  744 MET
Chi-restraints excluded: chain D residue  748 SER
Chi-restraints excluded: chain D residue  779 LEU
Chi-restraints excluded: chain D residue  782 ILE
Chi-restraints excluded: chain D residue  819 VAL
Chi-restraints excluded: chain D residue  873 SER
Chi-restraints excluded: chain D residue  877 PHE
Chi-restraints excluded: chain D residue  912 MET
Chi-restraints excluded: chain D residue  941 LEU
Chi-restraints excluded: chain D residue  998 VAL
Chi-restraints excluded: chain C residue  502 LEU
Chi-restraints excluded: chain C residue  504 LYS
Chi-restraints excluded: chain C residue  627 ILE
Chi-restraints excluded: chain C residue  698 LEU
Chi-restraints excluded: chain C residue  721 MET
Chi-restraints excluded: chain C residue  855 ASN
Chi-restraints excluded: chain C residue  941 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 193 optimal weight:   10.0000
   chunk 116 optimal weight:   10.0000
   chunk 121 optimal weight:    4.9990
   chunk 224 optimal weight:    0.9990
   chunk 221 optimal weight:    3.9990
   chunk 216 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 108 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 570 HIS
** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 494 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.118648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.083842 restraints weight = 32077.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 2.50
r_work: 0.2892 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  20404  Z= 0.163
  Angle     :  0.588   7.890  27472  Z= 0.281
  Chirality :  0.042   0.198   3132
  Planarity :  0.004   0.058   3304
  Dihedral  : 21.585 176.558   3472
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 15.38 %
    Favored  : 81.10 %
  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:  1.02 (0.17), residues: 2376
  helix:  1.19 (0.12), residues: 1752
  sheet:  0.63 (0.77), residues: 68
  loop : -0.84 (0.27), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 996 
 TYR   0.011   0.001   TYR C 706 
 PHE   0.012   0.001   PHE B 888 
 TRP   0.010   0.001   TRP B 515 
 HIS   0.005   0.001   HIS D 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (20404)
  covalent geometry    : angle       0.58832 (27472)
  hydrogen bonds       : bond        0.05039 ( 1164)
  hydrogen bonds       : angle       3.58799 ( 3456)

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

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

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 204
  time to evaluate  : 0.725 
Fit side-chains
REVERT: A  544 LEU cc_start: 0.9206 (mt) cc_final: 0.8930 (mm)
REVERT: A  634 MET cc_start: 0.8925 (tpt) cc_final: 0.8705 (tpp)
REVERT: A  720 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.7820 (mpt)
REVERT: A  986 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8842 (tp)
REVERT: A 1059 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8079 (tm-30)
REVERT: B  681 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7690 (pp20)
REVERT: B  717 ARG cc_start: 0.8543 (ttt180) cc_final: 0.8319 (ttt90)
REVERT: B  808 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8157 (mm-30)
REVERT: B  822 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8287 (pt)
REVERT: B  852 ARG cc_start: 0.8598 (mpt-90) cc_final: 0.7820 (mtp180)
REVERT: B  877 PHE cc_start: 0.8540 (m-80) cc_final: 0.8289 (t80)
REVERT: D  488 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8035 (mm)
REVERT: D  634 MET cc_start: 0.8971 (tpt) cc_final: 0.8760 (tpp)
REVERT: D  693 ASN cc_start: 0.9020 (m-40) cc_final: 0.8561 (t0)
REVERT: D  720 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7350 (mpt)
REVERT: D  744 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7807 (mmp)
REVERT: D  852 ARG cc_start: 0.8162 (mmt90) cc_final: 0.7642 (mtp180)
REVERT: D  873 SER cc_start: 0.8434 (OUTLIER) cc_final: 0.8212 (p)
REVERT: D  941 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8674 (tp)
REVERT: C  483 MET cc_start: 0.8852 (mtm) cc_final: 0.8325 (mtp)
REVERT: C  626 MET cc_start: 0.8474 (mtp) cc_final: 0.8033 (ttm)
REVERT: C  733 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8189 (tpp)
REVERT: C  744 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7878 (mmm)
REVERT: C  873 SER cc_start: 0.8184 (t) cc_final: 0.7898 (p)
REVERT: C  981 GLU cc_start: 0.8498 (tp30) cc_final: 0.8218 (tp30)
REVERT: C 1059 GLU cc_start: 0.8821 (tp30) cc_final: 0.8406 (tp30)
  outliers start: 71
  outliers final: 30
  residues processed: 246
  average time/residue: 0.5380
  time to fit residues: 151.3836
Evaluate side-chains
  221 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 180
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  709 MET
Chi-restraints excluded: chain A residue  720 MET
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  822 LEU
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain B residue  466 LEU
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  510 SER
Chi-restraints excluded: chain B residue  681 GLU
Chi-restraints excluded: chain B residue  748 SER
Chi-restraints excluded: chain B residue  819 VAL
Chi-restraints excluded: chain B residue  822 LEU
Chi-restraints excluded: chain B residue  995 LEU
Chi-restraints excluded: chain B residue  998 VAL
Chi-restraints excluded: chain D residue  488 LEU
Chi-restraints excluded: chain D residue  507 LEU
Chi-restraints excluded: chain D residue  709 MET
Chi-restraints excluded: chain D residue  720 MET
Chi-restraints excluded: chain D residue  744 MET
Chi-restraints excluded: chain D residue  748 SER
Chi-restraints excluded: chain D residue  779 LEU
Chi-restraints excluded: chain D residue  782 ILE
Chi-restraints excluded: chain D residue  819 VAL
Chi-restraints excluded: chain D residue  873 SER
Chi-restraints excluded: chain D residue  941 LEU
Chi-restraints excluded: chain D residue  998 VAL
Chi-restraints excluded: chain C residue  502 LEU
Chi-restraints excluded: chain C residue  504 LYS
Chi-restraints excluded: chain C residue  510 SER
Chi-restraints excluded: chain C residue  627 ILE
Chi-restraints excluded: chain C residue  698 LEU
Chi-restraints excluded: chain C residue  719 HIS
Chi-restraints excluded: chain C residue  721 MET
Chi-restraints excluded: chain C residue  733 MET
Chi-restraints excluded: chain C residue  744 MET
Chi-restraints excluded: chain C residue  941 LEU
Chi-restraints excluded: chain C residue 1047 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 6 optimal weight:    0.6980
   chunk 171 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 112 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 220 optimal weight:    0.9990
   chunk 76 optimal weight:    7.9990
   chunk 11 optimal weight:    7.9990
   chunk 77 optimal weight:    1.9990
   chunk 113 optimal weight:    8.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.118275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.083577 restraints weight = 31746.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 2.49
r_work: 0.2892 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.3656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  20404  Z= 0.146
  Angle     :  0.577   9.177  27472  Z= 0.275
  Chirality :  0.041   0.190   3132
  Planarity :  0.004   0.059   3304
  Dihedral  : 20.975 165.226   3472
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 15.33 %
    Favored  : 80.85 %
  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:  1.32 (0.18), residues: 2376
  helix:  1.42 (0.12), residues: 1752
  sheet:  0.89 (0.77), residues: 68
  loop : -0.78 (0.27), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 996 
 TYR   0.010   0.001   TYR C 456 
 PHE   0.011   0.001   PHE D 818 
 TRP   0.009   0.001   TRP B 515 
 HIS   0.005   0.001   HIS D 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (20404)
  covalent geometry    : angle       0.57695 (27472)
  hydrogen bonds       : bond        0.04829 ( 1164)
  hydrogen bonds       : angle       3.57486 ( 3456)

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

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

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 191
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
REVERT: A  544 LEU cc_start: 0.9204 (mt) cc_final: 0.8919 (mm)
REVERT: A  634 MET cc_start: 0.8914 (tpt) cc_final: 0.8703 (tpp)
REVERT: A  720 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.7911 (mpt)
REVERT: A  842 TYR cc_start: 0.9210 (OUTLIER) cc_final: 0.8893 (m-80)
REVERT: A  986 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8848 (tp)
REVERT: A 1059 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8087 (tm-30)
REVERT: B  483 MET cc_start: 0.8718 (mtp) cc_final: 0.8131 (mmt)
REVERT: B  681 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7676 (pp20)
REVERT: B  717 ARG cc_start: 0.8609 (ttt180) cc_final: 0.8371 (ttt90)
REVERT: B  822 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8255 (pt)
REVERT: B  852 ARG cc_start: 0.8620 (mpt-90) cc_final: 0.7905 (mtp180)
REVERT: B  877 PHE cc_start: 0.8543 (m-80) cc_final: 0.8308 (t80)
REVERT: D  488 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7998 (mm)
REVERT: D  720 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7387 (mpt)
REVERT: D  873 SER cc_start: 0.8412 (OUTLIER) cc_final: 0.8206 (p)
REVERT: D  941 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8644 (tp)
REVERT: D 1059 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8205 (tp30)
REVERT: C  733 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8259 (ttp)
REVERT: C  744 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7899 (mmm)
REVERT: C  785 TYR cc_start: 0.7835 (m-10) cc_final: 0.7629 (m-10)
REVERT: C  842 TYR cc_start: 0.9236 (OUTLIER) cc_final: 0.7465 (t80)
REVERT: C  873 SER cc_start: 0.8230 (t) cc_final: 0.7948 (p)
REVERT: C  941 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8634 (tp)
REVERT: C  981 GLU cc_start: 0.8509 (tp30) cc_final: 0.8185 (tp30)
REVERT: C 1059 GLU cc_start: 0.8795 (tp30) cc_final: 0.8355 (tp30)
  outliers start: 77
  outliers final: 29
  residues processed: 242
  average time/residue: 0.5354
  time to fit residues: 148.0947
Evaluate side-chains
  215 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 173
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  709 MET
Chi-restraints excluded: chain A residue  720 MET
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  842 TYR
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain B residue  466 LEU
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  510 SER
Chi-restraints excluded: chain B residue  681 GLU
Chi-restraints excluded: chain B residue  748 SER
Chi-restraints excluded: chain B residue  803 ILE
Chi-restraints excluded: chain B residue  819 VAL
Chi-restraints excluded: chain B residue  822 LEU
Chi-restraints excluded: chain B residue  844 MET
Chi-restraints excluded: chain B residue  995 LEU
Chi-restraints excluded: chain B residue  998 VAL
Chi-restraints excluded: chain D residue  484 THR
Chi-restraints excluded: chain D residue  488 LEU
Chi-restraints excluded: chain D residue  507 LEU
Chi-restraints excluded: chain D residue  709 MET
Chi-restraints excluded: chain D residue  720 MET
Chi-restraints excluded: chain D residue  748 SER
Chi-restraints excluded: chain D residue  779 LEU
Chi-restraints excluded: chain D residue  819 VAL
Chi-restraints excluded: chain D residue  852 ARG
Chi-restraints excluded: chain D residue  873 SER
Chi-restraints excluded: chain D residue  941 LEU
Chi-restraints excluded: chain D residue  998 VAL
Chi-restraints excluded: chain C residue  502 LEU
Chi-restraints excluded: chain C residue  510 SER
Chi-restraints excluded: chain C residue  627 ILE
Chi-restraints excluded: chain C residue  698 LEU
Chi-restraints excluded: chain C residue  719 HIS
Chi-restraints excluded: chain C residue  733 MET
Chi-restraints excluded: chain C residue  744 MET
Chi-restraints excluded: chain C residue  842 TYR
Chi-restraints excluded: chain C residue  941 LEU
Chi-restraints excluded: chain C residue 1047 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 63 optimal weight:    0.2980
   chunk 169 optimal weight:    0.6980
   chunk 133 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 60 optimal weight:   10.0000
   chunk 220 optimal weight:    0.9980
   chunk 192 optimal weight:    8.9990
   chunk 216 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 97 optimal weight:    3.9990
   chunk 211 optimal weight:    2.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 590 ASN
** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 590 ASN
** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.119680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.085495 restraints weight = 32195.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 2.49
r_work: 0.2940 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.3826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  20404  Z= 0.118
  Angle     :  0.545   8.756  27472  Z= 0.260
  Chirality :  0.040   0.199   3132
  Planarity :  0.004   0.056   3304
  Dihedral  : 20.411 166.906   3472
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 16.17 %
    Favored  : 80.41 %
  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:  1.62 (0.18), residues: 2376
  helix:  1.63 (0.12), residues: 1752
  sheet:  1.01 (0.77), residues: 68
  loop : -0.63 (0.28), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 872 
 TYR   0.010   0.001   TYR D 842 
 PHE   0.008   0.001   PHE B 583 
 TRP   0.010   0.001   TRP A 809 
 HIS   0.004   0.001   HIS B 481 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (20404)
  covalent geometry    : angle       0.54486 (27472)
  hydrogen bonds       : bond        0.04307 ( 1164)
  hydrogen bonds       : angle       3.47689 ( 3456)

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

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

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 196
  time to evaluate  : 0.800 
Fit side-chains
REVERT: A  483 MET cc_start: 0.8893 (mtm) cc_final: 0.8670 (mtp)
REVERT: A  544 LEU cc_start: 0.9194 (mt) cc_final: 0.8921 (mm)
REVERT: A  744 MET cc_start: 0.8033 (mmp) cc_final: 0.7589 (mtm)
REVERT: A  842 TYR cc_start: 0.9151 (OUTLIER) cc_final: 0.8926 (m-80)
REVERT: A  986 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8807 (tp)
REVERT: A 1059 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8079 (tm-30)
REVERT: B  464 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7900 (mtp180)
REVERT: B  483 MET cc_start: 0.8727 (mtp) cc_final: 0.8068 (mmt)
REVERT: B  681 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7565 (pp20)
REVERT: B  717 ARG cc_start: 0.8613 (ttt180) cc_final: 0.8351 (ttt90)
REVERT: B  720 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8345 (mmp)
REVERT: B  822 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8216 (pt)
REVERT: B  852 ARG cc_start: 0.8609 (mpt-90) cc_final: 0.7903 (mtp180)
REVERT: B  881 LEU cc_start: 0.8893 (tt) cc_final: 0.8448 (tp)
REVERT: D  530 MET cc_start: 0.8325 (mtp) cc_final: 0.8059 (mtt)
REVERT: D  720 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7898 (mmm)
REVERT: D  744 MET cc_start: 0.8058 (mmp) cc_final: 0.7783 (mmm)
REVERT: D  852 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7830 (mtp180)
REVERT: D  941 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8672 (tp)
REVERT: D  981 GLU cc_start: 0.8653 (tp30) cc_final: 0.8399 (tp30)
REVERT: D 1059 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8185 (tp30)
REVERT: C  475 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7949 (tp)
REVERT: C  733 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8336 (ttp)
REVERT: C  744 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7856 (mmm)
REVERT: C  842 TYR cc_start: 0.9138 (OUTLIER) cc_final: 0.7176 (t80)
REVERT: C  873 SER cc_start: 0.8175 (t) cc_final: 0.7882 (p)
REVERT: C  981 GLU cc_start: 0.8498 (tp30) cc_final: 0.8171 (tp30)
REVERT: C 1059 GLU cc_start: 0.8853 (tp30) cc_final: 0.8414 (tp30)
  outliers start: 69
  outliers final: 26
  residues processed: 242
  average time/residue: 0.5334
  time to fit residues: 148.1131
Evaluate side-chains
  222 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 183
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  709 MET
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain A residue  842 TYR
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain B residue  464 ARG
Chi-restraints excluded: chain B residue  466 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  510 SER
Chi-restraints excluded: chain B residue  681 GLU
Chi-restraints excluded: chain B residue  720 MET
Chi-restraints excluded: chain B residue  723 LEU
Chi-restraints excluded: chain B residue  748 SER
Chi-restraints excluded: chain B residue  819 VAL
Chi-restraints excluded: chain B residue  822 LEU
Chi-restraints excluded: chain B residue  995 LEU
Chi-restraints excluded: chain B residue  998 VAL
Chi-restraints excluded: chain D residue  484 THR
Chi-restraints excluded: chain D residue  507 LEU
Chi-restraints excluded: chain D residue  709 MET
Chi-restraints excluded: chain D residue  720 MET
Chi-restraints excluded: chain D residue  748 SER
Chi-restraints excluded: chain D residue  779 LEU
Chi-restraints excluded: chain D residue  819 VAL
Chi-restraints excluded: chain D residue  852 ARG
Chi-restraints excluded: chain D residue  941 LEU
Chi-restraints excluded: chain D residue  998 VAL
Chi-restraints excluded: chain C residue  475 LEU
Chi-restraints excluded: chain C residue  502 LEU
Chi-restraints excluded: chain C residue  504 LYS
Chi-restraints excluded: chain C residue  698 LEU
Chi-restraints excluded: chain C residue  719 HIS
Chi-restraints excluded: chain C residue  733 MET
Chi-restraints excluded: chain C residue  744 MET
Chi-restraints excluded: chain C residue  822 LEU
Chi-restraints excluded: chain C residue  842 TYR
Chi-restraints excluded: chain C residue 1047 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 197 optimal weight:    3.9990
   chunk 83 optimal weight:    0.8980
   chunk 139 optimal weight:    0.9980
   chunk 131 optimal weight:    0.0770
   chunk 170 optimal weight:    0.0270
   chunk 70 optimal weight:    1.9990
   chunk 113 optimal weight:    4.9990
   chunk 199 optimal weight:    0.9980
   chunk 189 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 619 ASN
B1047 GLN
** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 907 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.121140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.087445 restraints weight = 32161.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 2.47
r_work: 0.2982 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.3940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  20404  Z= 0.103
  Angle     :  0.536   9.146  27472  Z= 0.255
  Chirality :  0.039   0.167   3132
  Planarity :  0.004   0.053   3304
  Dihedral  : 19.959 169.117   3472
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.41 %
    Favored  : 79.86 %
  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:  1.82 (0.18), residues: 2376
  helix:  1.79 (0.13), residues: 1752
  sheet:  1.19 (0.78), residues: 68
  loop : -0.62 (0.28), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 996 
 TYR   0.017   0.001   TYR B 842 
 PHE   0.011   0.001   PHE B 877 
 TRP   0.009   0.001   TRP A 809 
 HIS   0.005   0.000   HIS B 487 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (20404)
  covalent geometry    : angle       0.53574 (27472)
  hydrogen bonds       : bond        0.03840 ( 1164)
  hydrogen bonds       : angle       3.38638 ( 3456)

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

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

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 200
  time to evaluate  : 0.654 
Fit side-chains
REVERT: A  483 MET cc_start: 0.8951 (mtm) cc_final: 0.8642 (mtp)
REVERT: A  544 LEU cc_start: 0.9194 (mt) cc_final: 0.8935 (mm)
REVERT: A  720 MET cc_start: 0.8450 (mmm) cc_final: 0.8134 (mmp)
REVERT: A  744 MET cc_start: 0.7995 (mmp) cc_final: 0.7606 (mtm)
REVERT: A  974 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7931 (tmtt)
REVERT: A  986 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8806 (tp)
REVERT: A 1059 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8019 (tm-30)
REVERT: B  464 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7930 (mtp180)
REVERT: B  483 MET cc_start: 0.8479 (mtp) cc_final: 0.7873 (mmt)
REVERT: B  681 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7545 (pp20)
REVERT: B  717 ARG cc_start: 0.8603 (ttt180) cc_final: 0.8355 (ttt90)
REVERT: B  720 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8361 (mmp)
REVERT: B  852 ARG cc_start: 0.8617 (mpt-90) cc_final: 0.7908 (mtp180)
REVERT: B  881 LEU cc_start: 0.8854 (tt) cc_final: 0.8415 (tp)
REVERT: B  987 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8635 (mt-10)
REVERT: D  530 MET cc_start: 0.8329 (mtp) cc_final: 0.8103 (mtt)
REVERT: D  720 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7892 (mmm)
REVERT: D  721 MET cc_start: 0.8197 (mmt) cc_final: 0.7947 (mtm)
REVERT: D  744 MET cc_start: 0.8041 (mmp) cc_final: 0.7784 (mmm)
REVERT: D  852 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7817 (mtp85)
REVERT: D  871 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8826 (mm)
REVERT: D  941 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8647 (tp)
REVERT: D  981 GLU cc_start: 0.8680 (tp30) cc_final: 0.8427 (tp30)
REVERT: D 1059 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8123 (tp30)
REVERT: C  475 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8008 (tp)
REVERT: C  483 MET cc_start: 0.8871 (mtm) cc_final: 0.8440 (mtp)
REVERT: C  720 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7953 (mmp)
REVERT: C  744 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7816 (mmm)
REVERT: C  873 SER cc_start: 0.8128 (t) cc_final: 0.7834 (p)
REVERT: C  981 GLU cc_start: 0.8487 (tp30) cc_final: 0.8157 (tp30)
REVERT: C 1047 GLN cc_start: 0.7064 (OUTLIER) cc_final: 0.6768 (mt0)
REVERT: C 1059 GLU cc_start: 0.8854 (tp30) cc_final: 0.8415 (tp30)
  outliers start: 55
  outliers final: 21
  residues processed: 233
  average time/residue: 0.5318
  time to fit residues: 141.8136
Evaluate side-chains
  218 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 183
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  709 MET
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  974 LYS
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue  998 VAL
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain B residue  464 ARG
Chi-restraints excluded: chain B residue  466 LEU
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  681 GLU
Chi-restraints excluded: chain B residue  720 MET
Chi-restraints excluded: chain B residue  819 VAL
Chi-restraints excluded: chain B residue  987 GLU
Chi-restraints excluded: chain B residue  998 VAL
Chi-restraints excluded: chain D residue  507 LEU
Chi-restraints excluded: chain D residue  709 MET
Chi-restraints excluded: chain D residue  720 MET
Chi-restraints excluded: chain D residue  779 LEU
Chi-restraints excluded: chain D residue  819 VAL
Chi-restraints excluded: chain D residue  852 ARG
Chi-restraints excluded: chain D residue  871 LEU
Chi-restraints excluded: chain D residue  941 LEU
Chi-restraints excluded: chain D residue  998 VAL
Chi-restraints excluded: chain C residue  475 LEU
Chi-restraints excluded: chain C residue  502 LEU
Chi-restraints excluded: chain C residue  504 LYS
Chi-restraints excluded: chain C residue  698 LEU
Chi-restraints excluded: chain C residue  719 HIS
Chi-restraints excluded: chain C residue  720 MET
Chi-restraints excluded: chain C residue  744 MET
Chi-restraints excluded: chain C residue  822 LEU
Chi-restraints excluded: chain C residue 1047 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 166 optimal weight:    2.9990
   chunk 123 optimal weight:    5.9990
   chunk 118 optimal weight:    4.9990
   chunk 153 optimal weight:    4.9990
   chunk 154 optimal weight:    0.9990
   chunk 149 optimal weight:    0.0010
   chunk 208 optimal weight:    0.6980
   chunk 91 optimal weight:    4.9990
   chunk 109 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.6588

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

Flipped N/Q/H residues before XYZ refinement:
** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 549 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.120858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.086225 restraints weight = 32271.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 2.54
r_work: 0.2968 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.4019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  20404  Z= 0.105
  Angle     :  0.545  10.341  27472  Z= 0.257
  Chirality :  0.039   0.218   3132
  Planarity :  0.004   0.053   3304
  Dihedral  : 19.633 171.410   3472
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 18.01 %
    Favored  : 79.56 %
  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:  1.94 (0.18), residues: 2376
  helix:  1.87 (0.13), residues: 1752
  sheet:  1.25 (0.79), residues: 68
  loop : -0.56 (0.28), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 996 
 TYR   0.015   0.001   TYR B 842 
 PHE   0.013   0.001   PHE B 877 
 TRP   0.021   0.001   TRP B 809 
 HIS   0.003   0.001   HIS B 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (20404)
  covalent geometry    : angle       0.54480 (27472)
  hydrogen bonds       : bond        0.03871 ( 1164)
  hydrogen bonds       : angle       3.36824 ( 3456)

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

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

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 188
  time to evaluate  : 0.756 
Fit side-chains
REVERT: A  483 MET cc_start: 0.8948 (mtm) cc_final: 0.8675 (mtp)
REVERT: A  544 LEU cc_start: 0.9190 (mt) cc_final: 0.8936 (mm)
REVERT: A  720 MET cc_start: 0.8507 (mmm) cc_final: 0.8180 (mmp)
REVERT: A  744 MET cc_start: 0.7936 (mmp) cc_final: 0.7603 (mtm)
REVERT: A  986 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8821 (tp)
REVERT: A 1059 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8031 (tm-30)
REVERT: B  464 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7902 (mtp180)
REVERT: B  483 MET cc_start: 0.8430 (mtp) cc_final: 0.7819 (mmt)
REVERT: B  681 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7543 (pp20)
REVERT: B  717 ARG cc_start: 0.8585 (ttt180) cc_final: 0.8328 (ttt90)
REVERT: B  720 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8380 (mmp)
REVERT: B  852 ARG cc_start: 0.8611 (mpt-90) cc_final: 0.7910 (mtp180)
REVERT: B  881 LEU cc_start: 0.8877 (tp) cc_final: 0.8441 (tp)
REVERT: B  987 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8639 (mt-10)
REVERT: D  530 MET cc_start: 0.8317 (mtp) cc_final: 0.8077 (mtt)
REVERT: D  720 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7745 (mmp)
REVERT: D  721 MET cc_start: 0.8185 (mmt) cc_final: 0.7939 (mtm)
REVERT: D  744 MET cc_start: 0.8021 (mmp) cc_final: 0.7759 (mmm)
REVERT: D  852 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7815 (mtp85)
REVERT: D  871 LEU cc_start: 0.9044 (tp) cc_final: 0.8744 (mt)
REVERT: D  941 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8635 (tp)
REVERT: D  981 GLU cc_start: 0.8685 (tp30) cc_final: 0.8435 (tp30)
REVERT: D 1059 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8158 (tp30)
REVERT: C  475 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8030 (tp)
REVERT: C  483 MET cc_start: 0.8894 (mtm) cc_final: 0.8531 (mtp)
REVERT: C  720 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7962 (mmp)
REVERT: C  744 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7753 (mmm)
REVERT: C  873 SER cc_start: 0.8177 (t) cc_final: 0.7877 (p)
REVERT: C  981 GLU cc_start: 0.8472 (tp30) cc_final: 0.8150 (tp30)
REVERT: C 1047 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6823 (mt0)
REVERT: C 1059 GLU cc_start: 0.8855 (tp30) cc_final: 0.8410 (tp30)
  outliers start: 49
  outliers final: 24
  residues processed: 217
  average time/residue: 0.5742
  time to fit residues: 142.2238
Evaluate side-chains
  215 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 179
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  709 MET
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain A residue  871 LEU
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue  998 VAL
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain B residue  464 ARG
Chi-restraints excluded: chain B residue  466 LEU
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  681 GLU
Chi-restraints excluded: chain B residue  720 MET
Chi-restraints excluded: chain B residue  748 SER
Chi-restraints excluded: chain B residue  819 VAL
Chi-restraints excluded: chain B residue  987 GLU
Chi-restraints excluded: chain B residue  998 VAL
Chi-restraints excluded: chain D residue  507 LEU
Chi-restraints excluded: chain D residue  709 MET
Chi-restraints excluded: chain D residue  720 MET
Chi-restraints excluded: chain D residue  748 SER
Chi-restraints excluded: chain D residue  779 LEU
Chi-restraints excluded: chain D residue  819 VAL
Chi-restraints excluded: chain D residue  852 ARG
Chi-restraints excluded: chain D residue  941 LEU
Chi-restraints excluded: chain D residue  998 VAL
Chi-restraints excluded: chain C residue  475 LEU
Chi-restraints excluded: chain C residue  502 LEU
Chi-restraints excluded: chain C residue  504 LYS
Chi-restraints excluded: chain C residue  698 LEU
Chi-restraints excluded: chain C residue  719 HIS
Chi-restraints excluded: chain C residue  720 MET
Chi-restraints excluded: chain C residue  744 MET
Chi-restraints excluded: chain C residue  822 LEU
Chi-restraints excluded: chain C residue 1047 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 96 optimal weight:    7.9990
   chunk 85 optimal weight:    2.9990
   chunk 209 optimal weight:    2.9990
   chunk 204 optimal weight:    0.0970
   chunk 78 optimal weight:    0.6980
   chunk 19 optimal weight:    5.9990
   chunk 205 optimal weight:    0.9990
   chunk 156 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 231 optimal weight:    6.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 619 ASN
** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.119968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.085185 restraints weight = 31963.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 2.52
r_work: 0.2955 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.4092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  20404  Z= 0.115
  Angle     :  0.553   9.240  27472  Z= 0.262
  Chirality :  0.040   0.204   3132
  Planarity :  0.004   0.053   3304
  Dihedral  : 19.355 175.935   3472
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 17.96 %
    Favored  : 79.61 %
  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:  1.98 (0.18), residues: 2376
  helix:  1.90 (0.13), residues: 1752
  sheet:  1.39 (0.79), residues: 68
  loop : -0.58 (0.28), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 996 
 TYR   0.015   0.001   TYR B 842 
 PHE   0.011   0.001   PHE B 877 
 TRP   0.009   0.001   TRP B 809 
 HIS   0.003   0.001   HIS D 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (20404)
  covalent geometry    : angle       0.55289 (27472)
  hydrogen bonds       : bond        0.04072 ( 1164)
  hydrogen bonds       : angle       3.38074 ( 3456)

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

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

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 183
  time to evaluate  : 0.705 
Fit side-chains
REVERT: A  483 MET cc_start: 0.8930 (mtm) cc_final: 0.8622 (mtp)
REVERT: A  544 LEU cc_start: 0.9198 (mt) cc_final: 0.8945 (mm)
REVERT: A  720 MET cc_start: 0.8556 (mmm) cc_final: 0.8234 (mmp)
REVERT: A  744 MET cc_start: 0.7936 (mmp) cc_final: 0.7612 (mtm)
REVERT: A  974 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.7977 (tmtt)
REVERT: A  986 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8823 (tp)
REVERT: A 1059 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8024 (tm-30)
REVERT: B  464 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7898 (mtp180)
REVERT: B  483 MET cc_start: 0.8423 (mtp) cc_final: 0.7768 (mmt)
REVERT: B  681 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7464 (pp20)
REVERT: B  717 ARG cc_start: 0.8605 (ttt180) cc_final: 0.8396 (ttm-80)
REVERT: B  720 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8406 (mmp)
REVERT: B  852 ARG cc_start: 0.8611 (mpt-90) cc_final: 0.7918 (mtp180)
REVERT: B  877 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.7930 (t80)
REVERT: B  881 LEU cc_start: 0.8858 (tp) cc_final: 0.8416 (tp)
REVERT: B  987 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8540 (mt-10)
REVERT: D  488 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7896 (mm)
REVERT: D  530 MET cc_start: 0.8329 (mtp) cc_final: 0.8101 (mtt)
REVERT: D  720 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7757 (mmp)
REVERT: D  721 MET cc_start: 0.8156 (mmt) cc_final: 0.7918 (mtm)
REVERT: D  744 MET cc_start: 0.7985 (mmp) cc_final: 0.7755 (mmm)
REVERT: D  852 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7834 (mtp85)
REVERT: D  871 LEU cc_start: 0.9047 (tp) cc_final: 0.8766 (mt)
REVERT: D  941 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8638 (tp)
REVERT: D  981 GLU cc_start: 0.8653 (tp30) cc_final: 0.8429 (tp30)
REVERT: D 1059 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8131 (tp30)
REVERT: C  483 MET cc_start: 0.8881 (mtm) cc_final: 0.8465 (mtp)
REVERT: C  720 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8013 (mmp)
REVERT: C  744 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7781 (mmm)
REVERT: C  785 TYR cc_start: 0.7604 (m-10) cc_final: 0.7393 (m-10)
REVERT: C  873 SER cc_start: 0.8227 (t) cc_final: 0.7943 (p)
REVERT: C  981 GLU cc_start: 0.8441 (tp30) cc_final: 0.8119 (tp30)
REVERT: C 1047 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6833 (mt0)
REVERT: C 1059 GLU cc_start: 0.8878 (tp30) cc_final: 0.8418 (tp30)
  outliers start: 49
  outliers final: 26
  residues processed: 213
  average time/residue: 0.5657
  time to fit residues: 137.6533
Evaluate side-chains
  218 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 178
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  709 MET
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain A residue  871 LEU
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  974 LYS
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue  998 VAL
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain B residue  464 ARG
Chi-restraints excluded: chain B residue  466 LEU
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  681 GLU
Chi-restraints excluded: chain B residue  720 MET
Chi-restraints excluded: chain B residue  748 SER
Chi-restraints excluded: chain B residue  803 ILE
Chi-restraints excluded: chain B residue  819 VAL
Chi-restraints excluded: chain B residue  877 PHE
Chi-restraints excluded: chain B residue  987 GLU
Chi-restraints excluded: chain B residue  998 VAL
Chi-restraints excluded: chain D residue  484 THR
Chi-restraints excluded: chain D residue  488 LEU
Chi-restraints excluded: chain D residue  507 LEU
Chi-restraints excluded: chain D residue  709 MET
Chi-restraints excluded: chain D residue  720 MET
Chi-restraints excluded: chain D residue  748 SER
Chi-restraints excluded: chain D residue  779 LEU
Chi-restraints excluded: chain D residue  819 VAL
Chi-restraints excluded: chain D residue  852 ARG
Chi-restraints excluded: chain D residue  941 LEU
Chi-restraints excluded: chain D residue  998 VAL
Chi-restraints excluded: chain C residue  502 LEU
Chi-restraints excluded: chain C residue  504 LYS
Chi-restraints excluded: chain C residue  698 LEU
Chi-restraints excluded: chain C residue  719 HIS
Chi-restraints excluded: chain C residue  720 MET
Chi-restraints excluded: chain C residue  744 MET
Chi-restraints excluded: chain C residue  822 LEU
Chi-restraints excluded: chain C residue 1047 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 72 optimal weight:    7.9990
   chunk 68 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 33 optimal weight:    5.9990
   chunk 154 optimal weight:    0.0870
   chunk 203 optimal weight:    3.9990
   chunk 218 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0870
   chunk 172 optimal weight:    3.9990
   chunk 217 optimal weight:    0.9980
   overall best weight:    0.5536

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

Flipped N/Q/H residues before XYZ refinement:
** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.121252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.086895 restraints weight = 32140.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 2.53
r_work: 0.2980 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.4158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  20404  Z= 0.103
  Angle     :  0.542  10.062  27472  Z= 0.258
  Chirality :  0.039   0.199   3132
  Planarity :  0.004   0.053   3304
  Dihedral  : 19.018 176.281   3472
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 18.40 %
    Favored  : 79.37 %
  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:  2.03 (0.18), residues: 2376
  helix:  1.94 (0.13), residues: 1752
  sheet:  1.39 (0.79), residues: 68
  loop : -0.56 (0.28), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 996 
 TYR   0.015   0.001   TYR B 842 
 PHE   0.010   0.001   PHE B 877 
 TRP   0.013   0.001   TRP B 809 
 HIS   0.003   0.000   HIS B 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (20404)
  covalent geometry    : angle       0.54157 (27472)
  hydrogen bonds       : bond        0.03755 ( 1164)
  hydrogen bonds       : angle       3.33710 ( 3456)

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

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

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4752 Ramachandran restraints generated.
    2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 188
  time to evaluate  : 0.798 
Fit side-chains
REVERT: A  483 MET cc_start: 0.8941 (mtm) cc_final: 0.8639 (mtp)
REVERT: A  544 LEU cc_start: 0.9173 (mt) cc_final: 0.8940 (mm)
REVERT: A  720 MET cc_start: 0.8549 (mmm) cc_final: 0.8230 (mmp)
REVERT: A  744 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7614 (mtm)
REVERT: A  974 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.7970 (tmtt)
REVERT: A  986 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8820 (tp)
REVERT: A 1059 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8026 (tm-30)
REVERT: B  464 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7876 (mtp180)
REVERT: B  483 MET cc_start: 0.8280 (mtp) cc_final: 0.7666 (mmt)
REVERT: B  681 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7460 (pp20)
REVERT: B  717 ARG cc_start: 0.8601 (ttt180) cc_final: 0.8391 (ttm-80)
REVERT: B  720 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8383 (mmp)
REVERT: B  852 ARG cc_start: 0.8618 (mpt-90) cc_final: 0.7943 (mtp180)
REVERT: B  877 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.7929 (t80)
REVERT: B  881 LEU cc_start: 0.8863 (tp) cc_final: 0.8437 (tp)
REVERT: B  987 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8584 (mt-10)
REVERT: D  488 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7906 (mm)
REVERT: D  530 MET cc_start: 0.8321 (mtp) cc_final: 0.8066 (mtt)
REVERT: D  720 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7736 (mmp)
REVERT: D  721 MET cc_start: 0.8216 (mmt) cc_final: 0.7956 (mtm)
REVERT: D  744 MET cc_start: 0.7905 (mmp) cc_final: 0.7701 (mmm)
REVERT: D  852 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7830 (mtp85)
REVERT: D  871 LEU cc_start: 0.9065 (tp) cc_final: 0.8783 (mt)
REVERT: D  941 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8626 (tp)
REVERT: D  981 GLU cc_start: 0.8643 (tp30) cc_final: 0.8429 (tp30)
REVERT: D 1059 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8135 (tp30)
REVERT: C  483 MET cc_start: 0.8892 (mtm) cc_final: 0.8530 (mtp)
REVERT: C  720 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7970 (mmp)
REVERT: C  744 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7814 (mmm)
REVERT: C  785 TYR cc_start: 0.7558 (m-10) cc_final: 0.7356 (m-10)
REVERT: C  873 SER cc_start: 0.8176 (t) cc_final: 0.7879 (p)
REVERT: C  881 LEU cc_start: 0.8540 (pp) cc_final: 0.8255 (mp)
REVERT: C  981 GLU cc_start: 0.8435 (tp30) cc_final: 0.8127 (tp30)
REVERT: C 1047 GLN cc_start: 0.7148 (OUTLIER) cc_final: 0.6846 (mt0)
REVERT: C 1059 GLU cc_start: 0.8876 (tp30) cc_final: 0.8412 (tp30)
  outliers start: 45
  outliers final: 24
  residues processed: 212
  average time/residue: 0.5963
  time to fit residues: 143.6411
Evaluate side-chains
  221 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 182
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  709 MET
Chi-restraints excluded: chain A residue  744 MET
Chi-restraints excluded: chain A residue  748 SER
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  974 LYS
Chi-restraints excluded: chain A residue  986 LEU
Chi-restraints excluded: chain A residue  998 VAL
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain B residue  464 ARG
Chi-restraints excluded: chain B residue  466 LEU
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  681 GLU
Chi-restraints excluded: chain B residue  720 MET
Chi-restraints excluded: chain B residue  748 SER
Chi-restraints excluded: chain B residue  803 ILE
Chi-restraints excluded: chain B residue  819 VAL
Chi-restraints excluded: chain B residue  877 PHE
Chi-restraints excluded: chain B residue  987 GLU
Chi-restraints excluded: chain B residue  998 VAL
Chi-restraints excluded: chain D residue  488 LEU
Chi-restraints excluded: chain D residue  507 LEU
Chi-restraints excluded: chain D residue  709 MET
Chi-restraints excluded: chain D residue  720 MET
Chi-restraints excluded: chain D residue  779 LEU
Chi-restraints excluded: chain D residue  819 VAL
Chi-restraints excluded: chain D residue  852 ARG
Chi-restraints excluded: chain D residue  941 LEU
Chi-restraints excluded: chain D residue  998 VAL
Chi-restraints excluded: chain C residue  502 LEU
Chi-restraints excluded: chain C residue  504 LYS
Chi-restraints excluded: chain C residue  698 LEU
Chi-restraints excluded: chain C residue  719 HIS
Chi-restraints excluded: chain C residue  720 MET
Chi-restraints excluded: chain C residue  744 MET
Chi-restraints excluded: chain C residue  822 LEU
Chi-restraints excluded: chain C residue  871 LEU
Chi-restraints excluded: chain C residue 1047 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 135 optimal weight:    0.7980
   chunk 157 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 173 optimal weight:    0.8980
   chunk 211 optimal weight:    0.8980
   chunk 92 optimal weight:    2.9990
   chunk 103 optimal weight:    0.4980
   chunk 223 optimal weight:    0.9990
   chunk 184 optimal weight:    2.9990
   chunk 162 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.120534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.086630 restraints weight = 32187.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 2.49
r_work: 0.2966 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.4217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  20404  Z= 0.111
  Angle     :  0.562   9.841  27472  Z= 0.266
  Chirality :  0.040   0.198   3132
  Planarity :  0.004   0.053   3304
  Dihedral  : 18.636 167.779   3472
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 18.40 %
    Favored  : 79.27 %
  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:  2.06 (0.18), residues: 2376
  helix:  1.96 (0.13), residues: 1752
  sheet:  1.53 (0.79), residues: 68
  loop : -0.54 (0.28), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 996 
 TYR   0.014   0.001   TYR B 842 
 PHE   0.011   0.001   PHE B 877 
 TRP   0.013   0.001   TRP D 515 
 HIS   0.003   0.001   HIS D 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (20404)
  covalent geometry    : angle       0.56199 (27472)
  hydrogen bonds       : bond        0.03936 ( 1164)
  hydrogen bonds       : angle       3.34722 ( 3456)

===============================================================================
Job complete
usr+sys time: 6190.09 seconds
wall clock time: 106 minutes 13.29 seconds (6373.29 seconds total)