Starting phenix.real_space_refine
on Fri Feb 14 08:18:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jxg_36700/02_2025/8jxg_36700.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jxg_36700/02_2025/8jxg_36700.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jxg_36700/02_2025/8jxg_36700.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jxg_36700/02_2025/8jxg_36700.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jxg_36700/02_2025/8jxg_36700.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jxg_36700/02_2025/8jxg_36700.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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
     Ca     21      9.91       5
     S     137      5.16       5
     C    5903      2.51       5
     N    1721      2.21       5
     O    2028      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9810
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "D"
      Number of atoms: 599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 599
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 1, 'TRANS': 70}
    Chain: "A"
      Number of atoms: 8739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1114, 8739
          Classifications: {'peptide': 1114}
          Link IDs: {'PTRANS': 55, 'TRANS': 1058}
          Chain breaks: 1
    Chain: "M"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 28
          Classifications: {'peptide': 5}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'TRANS': 4}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'UNK:plan-1': 4}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "F"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "G"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "H"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "I"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "A"
      Number of atoms: 105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 105
          Unusual residues: {' CA': 21, 'A2G': 4, 'NAG': 2}
          Classifications: {'undetermined': 27}
          Link IDs: {None: 26}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 6.25, per 1000 atoms: 0.64
  Number of scatterers: 9810
  At special positions: 0
  Unit cell: (95.948, 128.401, 145.333, 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)
     Ca     21     19.99
     S     137     16.00
     O    2028      8.00
     N    1721      7.00
     C    5903      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=61, symmetry=0
    Simple disulfide: pdb=" SG  CYS A1231 " - pdb=" SG  CYS A1244 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1238 " - pdb=" SG  CYS A1257 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1251 " - pdb=" SG  CYS A1267 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A2865 " - pdb=" SG  CYS A2878 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A2872 " - pdb=" SG  CYS A2891 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A2885 " - pdb=" SG  CYS A2901 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A2908 " - pdb=" SG  CYS A2920 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A2915 " - pdb=" SG  CYS A2933 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A2927 " - pdb=" SG  CYS A2945 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A2950 " - pdb=" SG  CYS A2967 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A2957 " - pdb=" SG  CYS A2980 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A2974 " - pdb=" SG  CYS A2990 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A2995 " - pdb=" SG  CYS A3007 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3002 " - pdb=" SG  CYS A3020 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3014 " - pdb=" SG  CYS A3029 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3034 " - pdb=" SG  CYS A3046 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3041 " - pdb=" SG  CYS A3059 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3053 " - pdb=" SG  CYS A3070 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3077 " - pdb=" SG  CYS A3089 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3084 " - pdb=" SG  CYS A3102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3096 " - pdb=" SG  CYS A3111 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A3116 " - pdb=" SG  CYS A3128 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3124 " - pdb=" SG  CYS A3137 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3139 " - pdb=" SG  CYS A3152 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3158 " - pdb=" SG  CYS A3169 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3165 " - pdb=" SG  CYS A3178 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3180 " - pdb=" SG  CYS A3193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3313 " - pdb=" SG  CYS A3321 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3471 " - pdb=" SG  CYS A3482 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3478 " - pdb=" SG  CYS A3493 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3495 " - pdb=" SG  CYS A3510 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3514 " - pdb=" SG  CYS A3527 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3521 " - pdb=" SG  CYS A3540 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3534 " - pdb=" SG  CYS A3550 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3555 " - pdb=" SG  CYS A3567 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3562 " - pdb=" SG  CYS A3580 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3574 " - pdb=" SG  CYS A3591 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3596 " - pdb=" SG  CYS A3608 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3603 " - pdb=" SG  CYS A3621 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3615 " - pdb=" SG  CYS A3632 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3637 " - pdb=" SG  CYS A3649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3644 " - pdb=" SG  CYS A3662 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3656 " - pdb=" SG  CYS A3673 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3680 " - pdb=" SG  CYS A3694 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3688 " - pdb=" SG  CYS A3707 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3701 " - pdb=" SG  CYS A3716 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3721 " - pdb=" SG  CYS A3734 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3729 " - pdb=" SG  CYS A3747 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3741 " - pdb=" SG  CYS A3756 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3761 " - pdb=" SG  CYS A3773 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3768 " - pdb=" SG  CYS A3786 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3780 " - pdb=" SG  CYS A3795 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3800 " - pdb=" SG  CYS A3812 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A3807 " - pdb=" SG  CYS A3825 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3819 " - pdb=" SG  CYS A3834 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3844 " - pdb=" SG  CYS A3856 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3851 " - pdb=" SG  CYS A3869 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3863 " - pdb=" SG  CYS A3880 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3885 " - pdb=" SG  CYS A3898 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3893 " - pdb=" SG  CYS A3911 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3905 " - pdb=" SG  CYS A3922 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=4, symmetry=0
  Links applied
    ALPHA1-3
      " BMA E   3 " - " MAN E   4 "
      " BMA H   3 " - " MAN H   4 "
      " BMA I   3 " - " MAN I   4 "
    ALPHA1-6
      " BMA E   3 " - " MAN E   5 "
      " BMA H   3 " - " MAN H   5 "
      " BMA I   3 " - " MAN I   5 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
      " NAG H   1 " - " NAG H   2 "
      " NAG H   2 " - " BMA H   3 "
      " NAG I   1 " - " NAG I   2 "
      " NAG I   2 " - " BMA I   3 "
    NAG-ASN
      " NAG A4701 " - " ASN A3448 "
      " NAG A4702 " - " ASN A3682 "
      " NAG B   1 " - " ASN A3127 "
      " NAG C   1 " - " ASN A3213 "
      " NAG E   1 " - " ASN A3259 "
      " NAG F   1 " - " ASN A3317 "
      " NAG G   1 " - " ASN A3357 "
      " NAG H   1 " - " ASN A3566 "
      " NAG I   1 " - " ASN A3840 "
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.16
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2224

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 28 sheets defined
      17.4% alpha, 16.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.37
  Creating SS restraints...
    Processing helix  chain 'D' and resid 59 through 72
    Processing helix  chain 'D' and resid 75 through 102
    Processing helix  chain 'D' and resid 108 through 125
      removed outlier: 4.419A  pdb=" N   ALA D 112 " --> pdb=" O   GLY D 108 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   LYS D 113 " --> pdb=" O   GLU D 109 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LEU D 114 " --> pdb=" O   LYS D 110 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ASN D 117 " --> pdb=" O   LYS D 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1248 through 1250
      No H-bonds generated for 'chain 'A' and resid 1248 through 1250'
    Processing helix  chain 'A' and resid 1260 through 1264
      removed outlier: 3.925A  pdb=" N   HIS A1264 " --> pdb=" O   SER A1261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2923 through 2927
    Processing helix  chain 'A' and resid 2936 through 2940
    Processing helix  chain 'A' and resid 2971 through 2973
      No H-bonds generated for 'chain 'A' and resid 2971 through 2973'
    Processing helix  chain 'A' and resid 3009 through 3013
    Processing helix  chain 'A' and resid 3050 through 3052
      No H-bonds generated for 'chain 'A' and resid 3050 through 3052'
    Processing helix  chain 'A' and resid 3091 through 3095
      removed outlier: 3.557A  pdb=" N   VAL A3095 " --> pdb=" O   MET A3092 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3156 through 3161
    Processing helix  chain 'A' and resid 3162 through 3165
      removed outlier: 3.523A  pdb=" N   CYS A3165 " --> pdb=" O   PRO A3162 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 3162 through 3165'
    Processing helix  chain 'A' and resid 3460 through 3464
    Processing helix  chain 'A' and resid 3474 through 3478
    Processing helix  chain 'A' and resid 3531 through 3533
      No H-bonds generated for 'chain 'A' and resid 3531 through 3533'
    Processing helix  chain 'A' and resid 3569 through 3573
    Processing helix  chain 'A' and resid 3583 through 3586
    Processing helix  chain 'A' and resid 3587 through 3592
    Processing helix  chain 'A' and resid 3630 through 3635
    Processing helix  chain 'A' and resid 3653 through 3655
      No H-bonds generated for 'chain 'A' and resid 3653 through 3655'
    Processing helix  chain 'A' and resid 3669 through 3674
    Processing helix  chain 'A' and resid 3675 through 3679
      removed outlier: 3.510A  pdb=" N   TYR A3678 " --> pdb=" O   THR A3675 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3698 through 3700
      No H-bonds generated for 'chain 'A' and resid 3698 through 3700'
    Processing helix  chain 'A' and resid 3710 through 3714
      removed outlier: 3.518A  pdb=" N   GLU A3713 " --> pdb=" O   ASN A3710 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3715 through 3719
    Processing helix  chain 'A' and resid 3738 through 3740
      No H-bonds generated for 'chain 'A' and resid 3738 through 3740'
    Processing helix  chain 'A' and resid 3777 through 3779
      No H-bonds generated for 'chain 'A' and resid 3777 through 3779'
    Processing helix  chain 'A' and resid 3789 through 3793
    Processing helix  chain 'A' and resid 3816 through 3818
      No H-bonds generated for 'chain 'A' and resid 3816 through 3818'
    Processing helix  chain 'A' and resid 3858 through 3862
    Processing helix  chain 'A' and resid 3872 through 3875
    Processing helix  chain 'A' and resid 3876 through 3882
      removed outlier: 4.094A  pdb=" N   ASN A3882 " --> pdb=" O   HIS A3878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3902 through 3904
      No H-bonds generated for 'chain 'A' and resid 3902 through 3904'
    Processing helix  chain 'A' and resid 3914 through 3922
      removed outlier: 6.658A  pdb=" N   GLU A3919 " --> pdb=" O   ASP A3916 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   GLU A3920 " --> pdb=" O   GLU A3917 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   HIS A3921 " --> pdb=" O   LYS A3918 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   CYS A3922 " --> pdb=" O   GLU A3919 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1235 through 1237
    Processing sheet with id=AA2, first strand: chain 'A' and resid 2869 through 2871
    Processing sheet with id=AA3, first strand: chain 'A' and resid 2913 through 2914
    Processing sheet with id=AA4, first strand: chain 'A' and resid 2954 through 2956
    Processing sheet with id=AA5, first strand: chain 'A' and resid 3000 through 3001
    Processing sheet with id=AA6, first strand: chain 'A' and resid 3038 through 3040
    Processing sheet with id=AA7, first strand: chain 'A' and resid 3127 through 3130
    Processing sheet with id=AA8, first strand: chain 'A' and resid 3143 through 3145
    Processing sheet with id=AA9, first strand: chain 'A' and resid 3168 through 3171
    Processing sheet with id=AB1, first strand: chain 'A' and resid 3184 through 3186
    Processing sheet with id=AB2, first strand: chain 'A' and resid 3221 through 3225
      removed outlier: 6.527A  pdb=" N   ILE A3211 " --> pdb=" O   ILE A3224 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   TYR A3202 " --> pdb=" O   TYR A3459 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   SER A3206 " --> pdb=" O   ASP A3455 " (cutoff:3.500A)
      removed outlier: 5.221A  pdb=" N   ASP A3455 " --> pdb=" O   SER A3206 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 3235 through 3237
      removed outlier: 6.748A  pdb=" N   ARG A3255 " --> pdb=" O   THR A3265 " (cutoff:3.500A)
      removed outlier: 5.255A  pdb=" N   THR A3265 " --> pdb=" O   ARG A3255 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 3274 through 3280
      removed outlier: 4.128A  pdb=" N   SER A3276 " --> pdb=" O   LEU A3289 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   TRP A3288 " --> pdb=" O   PHE A3297 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   LEU A3296 " --> pdb=" O   ILE A3309 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 3325 through 3331
      removed outlier: 4.285A  pdb=" N   ILE A3328 " --> pdb=" O   TYR A3338 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   TYR A3338 " --> pdb=" O   ILE A3328 " (cutoff:3.500A)
      removed outlier: 4.918A  pdb=" N   LEU A3330 " --> pdb=" O   HIS A3336 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   HIS A3336 " --> pdb=" O   LEU A3330 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   TRP A3339 " --> pdb=" O   GLY A3349 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   ILE A3348 " --> pdb=" O   ILE A3361 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 3371 through 3374
      removed outlier: 3.777A  pdb=" N   ALA A3371 " --> pdb=" O   ALA A3384 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   ILE A3391 " --> pdb=" O   VAL A3404 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 3412 through 3418
      removed outlier: 3.965A  pdb=" N   ALA A3414 " --> pdb=" O   THR A3425 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   VAL A3432 " --> pdb=" O   LEU A3446 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 3481 through 3484
    Processing sheet with id=AB9, first strand: chain 'A' and resid 3499 through 3503
    Processing sheet with id=AC1, first strand: chain 'A' and resid 3518 through 3520
    Processing sheet with id=AC2, first strand: chain 'A' and resid 3560 through 3561
    Processing sheet with id=AC3, first strand: chain 'A' and resid 3600 through 3602
    Processing sheet with id=AC4, first strand: chain 'A' and resid 3641 through 3643
    Processing sheet with id=AC5, first strand: chain 'A' and resid 3685 through 3687
    Processing sheet with id=AC6, first strand: chain 'A' and resid 3726 through 3728
    Processing sheet with id=AC7, first strand: chain 'A' and resid 3765 through 3767
    Processing sheet with id=AC8, first strand: chain 'A' and resid 3804 through 3806
    Processing sheet with id=AC9, first strand: chain 'A' and resid 3849 through 3850
    Processing sheet with id=AD1, first strand: chain 'A' and resid 3890 through 3893

    203 hydrogen bonds defined for protein.
    468 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: 3.90

  Time building geometry restraints manager: 3.62 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2833
        1.33 -     1.46: 2134
        1.46 -     1.58: 4890
        1.58 -     1.70: 1
        1.70 -     1.83: 151
  Bond restraints: 10009
  Sorted by residual:
  bond pdb=" N   MET A2936 "
       pdb=" CA  MET A2936 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 1.29e-02 6.01e+03 9.16e+00
  bond pdb=" N   THR A3799 "
       pdb=" CA  THR A3799 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.034 1.22e-02 6.72e+03 7.90e+00
  bond pdb=" N   THR A3836 "
       pdb=" CA  THR A3836 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.30e-02 5.92e+03 7.22e+00
  bond pdb=" N   CYS A3800 "
       pdb=" CA  CYS A3800 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.033 1.23e-02 6.61e+03 6.98e+00
  bond pdb=" N   MET A3848 "
       pdb=" CA  MET A3848 "
    ideal  model  delta    sigma   weight residual
    1.453  1.486 -0.033 1.31e-02 5.83e+03 6.42e+00
  ... (remaining 10004 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 12916
        1.75 -     3.50: 512
        3.50 -     5.25: 106
        5.25 -     7.00: 23
        7.00 -     8.76: 2
  Bond angle restraints: 13559
  Sorted by residual:
  angle pdb=" C   HIS A3312 "
        pdb=" CA  HIS A3312 "
        pdb=" CB  HIS A3312 "
      ideal   model   delta    sigma   weight residual
     117.23  110.60    6.63 1.36e+00 5.41e-01 2.37e+01
  angle pdb=" N   PRO A3845 "
        pdb=" CA  PRO A3845 "
        pdb=" C   PRO A3845 "
      ideal   model   delta    sigma   weight residual
     111.41  104.83    6.58 1.50e+00 4.44e-01 1.92e+01
  angle pdb=" CA  ASP A3379 "
        pdb=" CB  ASP A3379 "
        pdb=" CG  ASP A3379 "
      ideal   model   delta    sigma   weight residual
     112.60  116.46   -3.86 1.00e+00 1.00e+00 1.49e+01
  angle pdb=" C   GLY A3110 "
        pdb=" N   CYS A3111 "
        pdb=" CA  CYS A3111 "
      ideal   model   delta    sigma   weight residual
     121.54  127.90   -6.36 1.91e+00 2.74e-01 1.11e+01
  angle pdb=" CA  MET A3848 "
        pdb=" C   MET A3848 "
        pdb=" O   MET A3848 "
      ideal   model   delta    sigma   weight residual
     121.81  118.04    3.77 1.18e+00 7.18e-01 1.02e+01
  ... (remaining 13554 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.52: 5958
       22.52 -    45.04: 476
       45.04 -    67.57: 82
       67.57 -    90.09: 67
       90.09 -   112.61: 28
  Dihedral angle restraints: 6611
    sinusoidal: 3171
      harmonic: 3440
  Sorted by residual:
  dihedral pdb=" CB  CYS A3534 "
           pdb=" SG  CYS A3534 "
           pdb=" SG  CYS A3550 "
           pdb=" CB  CYS A3550 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  177.00  -84.00     1      1.00e+01 1.00e-02 8.60e+01
  dihedral pdb=" CB  CYS A2950 "
           pdb=" SG  CYS A2950 "
           pdb=" SG  CYS A2967 "
           pdb=" CB  CYS A2967 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  168.96  -75.96     1      1.00e+01 1.00e-02 7.27e+01
  dihedral pdb=" CB  CYS A1238 "
           pdb=" SG  CYS A1238 "
           pdb=" SG  CYS A1257 "
           pdb=" CB  CYS A1257 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.69  -73.69     1      1.00e+01 1.00e-02 6.90e+01
  ... (remaining 6608 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 1339
       0.084 -    0.168: 136
       0.168 -    0.252: 8
       0.252 -    0.336: 2
       0.336 -    0.420: 1
  Chirality restraints: 1486
  Sorted by residual:
  chirality pdb=" C1  NAG A4701 "
            pdb=" ND2 ASN A3448 "
            pdb=" C2  NAG A4701 "
            pdb=" O5  NAG A4701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.98   -0.42 2.00e-01 2.50e+01 4.40e+00
  chirality pdb=" C1  NAG H   1 "
            pdb=" ND2 ASN A3566 "
            pdb=" C2  NAG H   1 "
            pdb=" O5  NAG H   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.08   -0.32 2.00e-01 2.50e+01 2.50e+00
  chirality pdb=" C1  NAG A4702 "
            pdb=" ND2 ASN A3682 "
            pdb=" C2  NAG A4702 "
            pdb=" O5  NAG A4702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.10   -0.30 2.00e-01 2.50e+01 2.23e+00
  ... (remaining 1483 not shown)

  Planarity restraints: 1805
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A4701 "    0.323 2.00e-02 2.50e+03   2.74e-01 9.37e+02
        pdb=" C7  NAG A4701 "   -0.082 2.00e-02 2.50e+03
        pdb=" C8  NAG A4701 "    0.184 2.00e-02 2.50e+03
        pdb=" N2  NAG A4701 "   -0.477 2.00e-02 2.50e+03
        pdb=" O7  NAG A4701 "    0.052 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F   1 "    0.319 2.00e-02 2.50e+03   2.73e-01 9.33e+02
        pdb=" C7  NAG F   1 "   -0.078 2.00e-02 2.50e+03
        pdb=" C8  NAG F   1 "    0.172 2.00e-02 2.50e+03
        pdb=" N2  NAG F   1 "   -0.481 2.00e-02 2.50e+03
        pdb=" O7  NAG F   1 "    0.068 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG G   1 "    0.324 2.00e-02 2.50e+03   2.73e-01 9.32e+02
        pdb=" C7  NAG G   1 "   -0.083 2.00e-02 2.50e+03
        pdb=" C8  NAG G   1 "    0.193 2.00e-02 2.50e+03
        pdb=" N2  NAG G   1 "   -0.471 2.00e-02 2.50e+03
        pdb=" O7  NAG G   1 "    0.037 2.00e-02 2.50e+03
  ... (remaining 1802 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.74: 860
        2.74 -     3.28: 10370
        3.28 -     3.82: 16087
        3.82 -     4.36: 19577
        4.36 -     4.90: 32626
  Nonbonded interactions: 79520
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A3657 "
            pdb="CA    CA A4721 "
     model   vdw
     2.194 2.510
  nonbonded pdb=" N   ASP A2938 "
            pdb=" OD1 ASP A2938 "
     model   vdw
     2.200 3.120
  nonbonded pdb=" O   TRP A3778 "
            pdb="CA    CA A4724 "
     model   vdw
     2.203 2.510
  nonbonded pdb=" OD1 ASP A3820 "
            pdb="CA    CA A4725 "
     model   vdw
     2.203 2.510
  nonbonded pdb=" OD1 ASN A3575 "
            pdb="CA    CA A4719 "
     model   vdw
     2.210 2.510
  ... (remaining 79515 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
  selection = chain 'F'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'H'
  selection = chain 'I'
}

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:             1.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     26.980
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.094  10009  Z= 0.318
  Angle     :  0.825   8.755  13559  Z= 0.428
  Chirality :  0.052   0.420   1486
  Planarity :  0.015   0.274   1796
  Dihedral  : 19.602 112.608   4204
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  7.03 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.73 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.24), residues: 1180
  helix: -1.23 (0.53), residues: 88
  sheet: -0.79 (0.40), residues: 155
  loop : -0.42 (0.21), residues: 937

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP D  66 
 HIS   0.007   0.001   HIS A1254 
 PHE   0.023   0.001   PHE A2884 
 TYR   0.011   0.001   TYR A3459 
 ARG   0.005   0.000   ARG A3017 

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 68
  time to evaluate  : 1.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  114 LEU cc_start: 0.1135 (OUTLIER) cc_final: 0.0766 (pt)
  outliers start: 23
  outliers final: 21
  residues processed: 88
  average time/residue: 0.2170
  time to fit residues: 28.1003
Evaluate side-chains
  80 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 58
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  114 LEU
Chi-restraints excluded: chain A residue 1234 ASP
Chi-restraints excluded: chain A residue 1247 ASN
Chi-restraints excluded: chain A residue 2938 ASP
Chi-restraints excluded: chain A residue 2944 HIS
Chi-restraints excluded: chain A residue 3047 ILE
Chi-restraints excluded: chain A residue 3096 CYS
Chi-restraints excluded: chain A residue 3106 SER
Chi-restraints excluded: chain A residue 3220 SER
Chi-restraints excluded: chain A residue 3224 ILE
Chi-restraints excluded: chain A residue 3228 LEU
Chi-restraints excluded: chain A residue 3277 LEU
Chi-restraints excluded: chain A residue 3329 VAL
Chi-restraints excluded: chain A residue 3415 LEU
Chi-restraints excluded: chain A residue 3449 THR
Chi-restraints excluded: chain A residue 3450 THR
Chi-restraints excluded: chain A residue 3509 LEU
Chi-restraints excluded: chain A residue 3549 LEU
Chi-restraints excluded: chain A residue 3623 ASP
Chi-restraints excluded: chain A residue 3770 ASP
Chi-restraints excluded: chain A residue 3836 THR
Chi-restraints excluded: chain A residue 3874 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:    0.9980
   chunk 89 optimal weight:    0.5980
   chunk 49 optimal weight:    0.5980
   chunk 30 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   chunk 107 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A3066 GLN
A3262 ASN
A3523 ASN
A3878 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.153706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.108942 restraints weight = 16922.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 2.50
r_work: 0.3338 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.0878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10009  Z= 0.228
  Angle     :  0.688   9.283  13559  Z= 0.347
  Chirality :  0.049   0.355   1486
  Planarity :  0.004   0.042   1796
  Dihedral  : 14.410  92.323   1995
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 15.16 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.24), residues: 1180
  helix: -0.55 (0.53), residues: 88
  sheet: -0.89 (0.40), residues: 164
  loop : -0.42 (0.21), residues: 928

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D  66 
 HIS   0.009   0.001   HIS D 116 
 PHE   0.017   0.002   PHE A2884 
 TYR   0.012   0.002   TYR A3459 
 ARG   0.004   0.000   ARG D  78 

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 67
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   70 LYS cc_start: 0.5568 (mttt) cc_final: 0.5087 (mmtm)
REVERT: A 1230 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8367 (ttm)
REVERT: A 2919 ARG cc_start: 0.2630 (OUTLIER) cc_final: 0.1776 (mtp85)
REVERT: A 2961 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.6344 (mmt180)
REVERT: A 2992 MET cc_start: 0.4965 (mmm) cc_final: 0.4764 (mmm)
REVERT: A 3275 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7869 (mm-30)
REVERT: A 3680 CYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7656 (m)
REVERT: A 3807 CYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7437 (m)
  outliers start: 36
  outliers final: 22
  residues processed: 91
  average time/residue: 0.2271
  time to fit residues: 29.6863
Evaluate side-chains
  89 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 62
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   83 HIS
Chi-restraints excluded: chain D residue  114 LEU
Chi-restraints excluded: chain A residue 1230 MET
Chi-restraints excluded: chain A residue 2919 ARG
Chi-restraints excluded: chain A residue 2927 CYS
Chi-restraints excluded: chain A residue 2938 ASP
Chi-restraints excluded: chain A residue 2944 HIS
Chi-restraints excluded: chain A residue 2961 ARG
Chi-restraints excluded: chain A residue 2971 TYR
Chi-restraints excluded: chain A residue 3096 CYS
Chi-restraints excluded: chain A residue 3215 THR
Chi-restraints excluded: chain A residue 3228 LEU
Chi-restraints excluded: chain A residue 3277 LEU
Chi-restraints excluded: chain A residue 3329 VAL
Chi-restraints excluded: chain A residue 3353 MET
Chi-restraints excluded: chain A residue 3415 LEU
Chi-restraints excluded: chain A residue 3449 THR
Chi-restraints excluded: chain A residue 3450 THR
Chi-restraints excluded: chain A residue 3513 MET
Chi-restraints excluded: chain A residue 3549 LEU
Chi-restraints excluded: chain A residue 3680 CYS
Chi-restraints excluded: chain A residue 3695 ILE
Chi-restraints excluded: chain A residue 3757 VAL
Chi-restraints excluded: chain A residue 3797 MET
Chi-restraints excluded: chain A residue 3807 CYS
Chi-restraints excluded: chain A residue 3826 LEU
Chi-restraints excluded: chain A residue 3851 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 13 optimal weight:    8.9990
   chunk 14 optimal weight:    0.9990
   chunk 29 optimal weight:    0.2980
   chunk 36 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0980
   chunk 78 optimal weight:    0.2980
   overall best weight:    0.5384

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

Flipped N/Q/H residues before XYZ refinement:
** A1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1254 HIS
A3336 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.154263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.108518 restraints weight = 17179.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 2.19
r_work: 0.3363 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3259 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.1257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  10009  Z= 0.193
  Angle     :  0.625   7.059  13559  Z= 0.315
  Chirality :  0.049   0.306   1486
  Planarity :  0.004   0.038   1796
  Dihedral  : 11.695  78.987   1976
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 14.88 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.25), residues: 1180
  helix: -0.37 (0.53), residues: 95
  sheet: -0.94 (0.41), residues: 164
  loop : -0.38 (0.21), residues: 921

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  66 
 HIS   0.005   0.001   HIS D  73 
 PHE   0.017   0.002   PHE A3418 
 TYR   0.014   0.001   TYR D 125 
 ARG   0.003   0.000   ARG A3350 

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 69
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   70 LYS cc_start: 0.5733 (mttt) cc_final: 0.5391 (mmtm)
REVERT: A 2919 ARG cc_start: 0.2796 (OUTLIER) cc_final: 0.1973 (mtp85)
REVERT: A 2961 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6341 (mmt180)
REVERT: A 3146 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6573 (pmm)
REVERT: A 3150 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6776 (ttt-90)
REVERT: A 3275 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7824 (mm-30)
REVERT: A 3577 ARG cc_start: 0.8078 (mtt-85) cc_final: 0.7876 (mtm-85)
REVERT: A 3664 ASP cc_start: 0.8646 (t0) cc_final: 0.8410 (t0)
REVERT: A 3871 ASP cc_start: 0.7645 (t0) cc_final: 0.7439 (t0)
  outliers start: 39
  outliers final: 23
  residues processed: 97
  average time/residue: 0.2347
  time to fit residues: 32.1817
Evaluate side-chains
  92 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 65
  time to evaluate  : 1.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   83 HIS
Chi-restraints excluded: chain D residue  114 LEU
Chi-restraints excluded: chain A residue 1238 CYS
Chi-restraints excluded: chain A residue 2919 ARG
Chi-restraints excluded: chain A residue 2927 CYS
Chi-restraints excluded: chain A residue 2938 ASP
Chi-restraints excluded: chain A residue 2944 HIS
Chi-restraints excluded: chain A residue 2961 ARG
Chi-restraints excluded: chain A residue 2971 TYR
Chi-restraints excluded: chain A residue 2993 ARG
Chi-restraints excluded: chain A residue 3086 ASN
Chi-restraints excluded: chain A residue 3096 CYS
Chi-restraints excluded: chain A residue 3146 MET
Chi-restraints excluded: chain A residue 3150 ARG
Chi-restraints excluded: chain A residue 3215 THR
Chi-restraints excluded: chain A residue 3228 LEU
Chi-restraints excluded: chain A residue 3277 LEU
Chi-restraints excluded: chain A residue 3329 VAL
Chi-restraints excluded: chain A residue 3353 MET
Chi-restraints excluded: chain A residue 3415 LEU
Chi-restraints excluded: chain A residue 3450 THR
Chi-restraints excluded: chain A residue 3513 MET
Chi-restraints excluded: chain A residue 3757 VAL
Chi-restraints excluded: chain A residue 3770 ASP
Chi-restraints excluded: chain A residue 3797 MET
Chi-restraints excluded: chain A residue 3826 LEU
Chi-restraints excluded: chain A residue 3851 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 116 optimal weight:    4.9990
   chunk 90 optimal weight:    0.0050
   chunk 89 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 100 optimal weight:    4.9990
   overall best weight:    0.8796

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

Flipped N/Q/H residues before XYZ refinement:
** A1239 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 = 0.4081 r_free = 0.4081 target = 0.152751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.109469 restraints weight = 17080.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 2.70
r_work: 0.3311 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.1459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10009  Z= 0.247
  Angle     :  0.645   7.117  13559  Z= 0.325
  Chirality :  0.050   0.283   1486
  Planarity :  0.004   0.040   1796
  Dihedral  : 10.509  68.574   1973
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 15.35 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.25), residues: 1180
  helix: -0.14 (0.56), residues: 88
  sheet: -0.96 (0.41), residues: 164
  loop : -0.41 (0.21), residues: 928

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A3383 
 HIS   0.006   0.001   HIS D  73 
 PHE   0.018   0.002   PHE A3454 
 TYR   0.014   0.002   TYR A3459 
 ARG   0.003   0.000   ARG A3212 

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 62
  time to evaluate  : 1.399 
Fit side-chains
   revert: symmetry clash
REVERT: D   70 LYS cc_start: 0.5590 (mttt) cc_final: 0.5206 (mmtm)
REVERT: A 1230 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8335 (ttm)
REVERT: A 1245 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8243 (pp)
REVERT: A 2919 ARG cc_start: 0.2674 (OUTLIER) cc_final: 0.1707 (mmm-85)
REVERT: A 2961 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6341 (mmt180)
REVERT: A 3092 MET cc_start: 0.5964 (OUTLIER) cc_final: 0.5644 (pmt)
REVERT: A 3150 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6808 (ttt-90)
REVERT: A 3275 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7831 (mm-30)
REVERT: A 3577 ARG cc_start: 0.8094 (mtt-85) cc_final: 0.7869 (mtm-85)
REVERT: A 3622 LEU cc_start: 0.8169 (mm) cc_final: 0.7719 (mt)
REVERT: A 3664 ASP cc_start: 0.8630 (t0) cc_final: 0.8368 (t0)
  outliers start: 41
  outliers final: 21
  residues processed: 90
  average time/residue: 0.2627
  time to fit residues: 33.8594
Evaluate side-chains
  86 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 59
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   83 HIS
Chi-restraints excluded: chain D residue  114 LEU
Chi-restraints excluded: chain A residue 1230 MET
Chi-restraints excluded: chain A residue 1238 CYS
Chi-restraints excluded: chain A residue 1245 ILE
Chi-restraints excluded: chain A residue 2919 ARG
Chi-restraints excluded: chain A residue 2927 CYS
Chi-restraints excluded: chain A residue 2938 ASP
Chi-restraints excluded: chain A residue 2944 HIS
Chi-restraints excluded: chain A residue 2961 ARG
Chi-restraints excluded: chain A residue 2971 TYR
Chi-restraints excluded: chain A residue 3092 MET
Chi-restraints excluded: chain A residue 3150 ARG
Chi-restraints excluded: chain A residue 3215 THR
Chi-restraints excluded: chain A residue 3228 LEU
Chi-restraints excluded: chain A residue 3277 LEU
Chi-restraints excluded: chain A residue 3329 VAL
Chi-restraints excluded: chain A residue 3353 MET
Chi-restraints excluded: chain A residue 3415 LEU
Chi-restraints excluded: chain A residue 3450 THR
Chi-restraints excluded: chain A residue 3695 ILE
Chi-restraints excluded: chain A residue 3757 VAL
Chi-restraints excluded: chain A residue 3770 ASP
Chi-restraints excluded: chain A residue 3797 MET
Chi-restraints excluded: chain A residue 3826 LEU
Chi-restraints excluded: chain A residue 3851 CYS
Chi-restraints excluded: chain A residue 3859 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 16 optimal weight:    9.9990
   chunk 17 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 102 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 112 optimal weight:    0.0030
   chunk 46 optimal weight:    0.1980
   chunk 22 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   overall best weight:    0.4990

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

Flipped N/Q/H residues before XYZ refinement:
A1239 GLN
A3378 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.153999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.108338 restraints weight = 17138.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 2.21
r_work: 0.3354 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3248 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.1629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10009  Z= 0.177
  Angle     :  0.600   6.946  13559  Z= 0.303
  Chirality :  0.048   0.389   1486
  Planarity :  0.004   0.039   1796
  Dihedral  :  9.657  66.353   1972
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 15.25 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.25), residues: 1180
  helix: -0.08 (0.55), residues: 94
  sheet: -0.91 (0.42), residues: 164
  loop : -0.34 (0.22), residues: 922

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A3383 
 HIS   0.005   0.001   HIS D  73 
 PHE   0.016   0.002   PHE A2884 
 TYR   0.009   0.001   TYR A3459 
 ARG   0.005   0.000   ARG A2993 

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 66
  time to evaluate  : 1.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   70 LYS cc_start: 0.5808 (mttt) cc_final: 0.5453 (mmtm)
REVERT: A 1230 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8195 (ttm)
REVERT: A 1245 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8217 (pp)
REVERT: A 2919 ARG cc_start: 0.2674 (OUTLIER) cc_final: 0.1697 (mmm-85)
REVERT: A 3092 MET cc_start: 0.5970 (OUTLIER) cc_final: 0.5664 (pmt)
REVERT: A 3150 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6855 (ttt-90)
REVERT: A 3577 ARG cc_start: 0.8034 (mtt-85) cc_final: 0.7822 (mtm-85)
REVERT: A 3609 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8993 (pp)
REVERT: A 3622 LEU cc_start: 0.8091 (mm) cc_final: 0.7643 (mt)
REVERT: A 3664 ASP cc_start: 0.8665 (t0) cc_final: 0.8424 (t0)
  outliers start: 45
  outliers final: 28
  residues processed: 100
  average time/residue: 0.2182
  time to fit residues: 31.9483
Evaluate side-chains
  98 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 64
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   83 HIS
Chi-restraints excluded: chain A residue 1230 MET
Chi-restraints excluded: chain A residue 1238 CYS
Chi-restraints excluded: chain A residue 1239 GLN
Chi-restraints excluded: chain A residue 1245 ILE
Chi-restraints excluded: chain A residue 2919 ARG
Chi-restraints excluded: chain A residue 2927 CYS
Chi-restraints excluded: chain A residue 2938 ASP
Chi-restraints excluded: chain A residue 2944 HIS
Chi-restraints excluded: chain A residue 2971 TYR
Chi-restraints excluded: chain A residue 3020 CYS
Chi-restraints excluded: chain A residue 3086 ASN
Chi-restraints excluded: chain A residue 3092 MET
Chi-restraints excluded: chain A residue 3096 CYS
Chi-restraints excluded: chain A residue 3145 LEU
Chi-restraints excluded: chain A residue 3150 ARG
Chi-restraints excluded: chain A residue 3215 THR
Chi-restraints excluded: chain A residue 3228 LEU
Chi-restraints excluded: chain A residue 3277 LEU
Chi-restraints excluded: chain A residue 3295 CYS
Chi-restraints excluded: chain A residue 3329 VAL
Chi-restraints excluded: chain A residue 3353 MET
Chi-restraints excluded: chain A residue 3406 ASP
Chi-restraints excluded: chain A residue 3415 LEU
Chi-restraints excluded: chain A residue 3450 THR
Chi-restraints excluded: chain A residue 3513 MET
Chi-restraints excluded: chain A residue 3609 ILE
Chi-restraints excluded: chain A residue 3695 ILE
Chi-restraints excluded: chain A residue 3757 VAL
Chi-restraints excluded: chain A residue 3770 ASP
Chi-restraints excluded: chain A residue 3797 MET
Chi-restraints excluded: chain A residue 3826 LEU
Chi-restraints excluded: chain A residue 3851 CYS
Chi-restraints excluded: chain A residue 3859 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 53 optimal weight:    0.5980
   chunk 80 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 91 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 16 optimal weight:    7.9990
   chunk 104 optimal weight:    0.0870
   overall best weight:    0.6158

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.153613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.107942 restraints weight = 17259.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.22
r_work: 0.3347 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10009  Z= 0.196
  Angle     :  0.605   9.918  13559  Z= 0.304
  Chirality :  0.048   0.358   1486
  Planarity :  0.004   0.040   1796
  Dihedral  :  9.148  64.443   1970
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 15.07 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.25), residues: 1180
  helix: -0.04 (0.55), residues: 94
  sheet: -0.90 (0.42), residues: 164
  loop : -0.33 (0.22), residues: 922

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A3383 
 HIS   0.005   0.001   HIS D  73 
 PHE   0.016   0.002   PHE A2884 
 TYR   0.011   0.001   TYR A3459 
 ARG   0.003   0.000   ARG A3017 

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 62
  time to evaluate  : 1.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   70 LYS cc_start: 0.5817 (mttt) cc_final: 0.5436 (mmtm)
REVERT: A 1230 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8255 (ttm)
REVERT: A 1245 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8141 (pp)
REVERT: A 2919 ARG cc_start: 0.2699 (OUTLIER) cc_final: 0.1732 (mmm-85)
REVERT: A 3092 MET cc_start: 0.5964 (OUTLIER) cc_final: 0.5701 (pmt)
REVERT: A 3150 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6740 (ttt-90)
REVERT: A 3557 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8238 (mm)
REVERT: A 3577 ARG cc_start: 0.8034 (mtt-85) cc_final: 0.7823 (mtm-85)
REVERT: A 3609 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8990 (pp)
REVERT: A 3664 ASP cc_start: 0.8659 (t0) cc_final: 0.8421 (t0)
  outliers start: 46
  outliers final: 28
  residues processed: 96
  average time/residue: 0.2233
  time to fit residues: 31.3171
Evaluate side-chains
  96 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 61
  time to evaluate  : 1.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   83 HIS
Chi-restraints excluded: chain A residue 1230 MET
Chi-restraints excluded: chain A residue 1238 CYS
Chi-restraints excluded: chain A residue 1245 ILE
Chi-restraints excluded: chain A residue 2919 ARG
Chi-restraints excluded: chain A residue 2920 CYS
Chi-restraints excluded: chain A residue 2927 CYS
Chi-restraints excluded: chain A residue 2938 ASP
Chi-restraints excluded: chain A residue 2944 HIS
Chi-restraints excluded: chain A residue 2971 TYR
Chi-restraints excluded: chain A residue 3020 CYS
Chi-restraints excluded: chain A residue 3086 ASN
Chi-restraints excluded: chain A residue 3092 MET
Chi-restraints excluded: chain A residue 3145 LEU
Chi-restraints excluded: chain A residue 3150 ARG
Chi-restraints excluded: chain A residue 3215 THR
Chi-restraints excluded: chain A residue 3220 SER
Chi-restraints excluded: chain A residue 3228 LEU
Chi-restraints excluded: chain A residue 3277 LEU
Chi-restraints excluded: chain A residue 3295 CYS
Chi-restraints excluded: chain A residue 3329 VAL
Chi-restraints excluded: chain A residue 3353 MET
Chi-restraints excluded: chain A residue 3406 ASP
Chi-restraints excluded: chain A residue 3415 LEU
Chi-restraints excluded: chain A residue 3450 THR
Chi-restraints excluded: chain A residue 3513 MET
Chi-restraints excluded: chain A residue 3557 LEU
Chi-restraints excluded: chain A residue 3609 ILE
Chi-restraints excluded: chain A residue 3636 THR
Chi-restraints excluded: chain A residue 3695 ILE
Chi-restraints excluded: chain A residue 3757 VAL
Chi-restraints excluded: chain A residue 3797 MET
Chi-restraints excluded: chain A residue 3826 LEU
Chi-restraints excluded: chain A residue 3851 CYS
Chi-restraints excluded: chain A residue 3859 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 100 optimal weight:    0.0870
   chunk 108 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0030
   chunk 97 optimal weight:    5.9990
   chunk 10 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0770
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.2926

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.154490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.110622 restraints weight = 17148.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.16
r_work: 0.3372 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3269 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049  10009  Z= 0.155
  Angle     :  0.585   9.088  13559  Z= 0.295
  Chirality :  0.047   0.329   1486
  Planarity :  0.004   0.039   1796
  Dihedral  :  8.532  62.363   1970
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 15.16 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.25), residues: 1180
  helix: -0.01 (0.55), residues: 94
  sheet: -0.83 (0.42), residues: 164
  loop : -0.28 (0.22), residues: 922

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A3383 
 HIS   0.005   0.001   HIS D  73 
 PHE   0.015   0.001   PHE A2884 
 TYR   0.008   0.001   TYR A3459 
 ARG   0.002   0.000   ARG A3017 

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 69
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
REVERT: D   70 LYS cc_start: 0.5790 (mttt) cc_final: 0.5443 (mmtm)
REVERT: A 1230 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8254 (ttm)
REVERT: A 1245 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8152 (pp)
REVERT: A 2919 ARG cc_start: 0.2848 (OUTLIER) cc_final: 0.1943 (mmm-85)
REVERT: A 3092 MET cc_start: 0.5997 (OUTLIER) cc_final: 0.5732 (pmt)
REVERT: A 3146 MET cc_start: 0.7729 (mmt) cc_final: 0.7352 (ptp)
REVERT: A 3150 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6774 (ttt-90)
REVERT: A 3261 THR cc_start: 0.8944 (t) cc_final: 0.8734 (p)
REVERT: A 3379 ASP cc_start: 0.8512 (p0) cc_final: 0.8306 (m-30)
REVERT: A 3557 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8186 (mm)
REVERT: A 3577 ARG cc_start: 0.8117 (mtt-85) cc_final: 0.7846 (mtm-85)
REVERT: A 3609 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8887 (pp)
REVERT: A 3622 LEU cc_start: 0.8074 (mm) cc_final: 0.7681 (mt)
REVERT: A 3664 ASP cc_start: 0.8586 (t0) cc_final: 0.8382 (t0)
  outliers start: 43
  outliers final: 25
  residues processed: 102
  average time/residue: 0.2170
  time to fit residues: 32.2207
Evaluate side-chains
  97 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 65
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   83 HIS
Chi-restraints excluded: chain A residue 1230 MET
Chi-restraints excluded: chain A residue 1238 CYS
Chi-restraints excluded: chain A residue 1245 ILE
Chi-restraints excluded: chain A residue 2919 ARG
Chi-restraints excluded: chain A residue 2920 CYS
Chi-restraints excluded: chain A residue 2927 CYS
Chi-restraints excluded: chain A residue 2938 ASP
Chi-restraints excluded: chain A residue 2944 HIS
Chi-restraints excluded: chain A residue 2971 TYR
Chi-restraints excluded: chain A residue 3020 CYS
Chi-restraints excluded: chain A residue 3086 ASN
Chi-restraints excluded: chain A residue 3092 MET
Chi-restraints excluded: chain A residue 3132 ILE
Chi-restraints excluded: chain A residue 3145 LEU
Chi-restraints excluded: chain A residue 3150 ARG
Chi-restraints excluded: chain A residue 3215 THR
Chi-restraints excluded: chain A residue 3220 SER
Chi-restraints excluded: chain A residue 3228 LEU
Chi-restraints excluded: chain A residue 3277 LEU
Chi-restraints excluded: chain A residue 3295 CYS
Chi-restraints excluded: chain A residue 3329 VAL
Chi-restraints excluded: chain A residue 3415 LEU
Chi-restraints excluded: chain A residue 3450 THR
Chi-restraints excluded: chain A residue 3557 LEU
Chi-restraints excluded: chain A residue 3609 ILE
Chi-restraints excluded: chain A residue 3695 ILE
Chi-restraints excluded: chain A residue 3757 VAL
Chi-restraints excluded: chain A residue 3797 MET
Chi-restraints excluded: chain A residue 3826 LEU
Chi-restraints excluded: chain A residue 3851 CYS
Chi-restraints excluded: chain A residue 3859 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 96 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 117 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 5 optimal weight:    7.9990
   chunk 40 optimal weight:    0.6980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** D 116 HIS ** 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 = 0.4074 r_free = 0.4074 target = 0.152157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.109675 restraints weight = 17291.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.65
r_work: 0.3312 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  10009  Z= 0.277
  Angle     :  0.646   9.234  13559  Z= 0.325
  Chirality :  0.049   0.324   1486
  Planarity :  0.004   0.044   1796
  Dihedral  :  8.719  59.767   1970
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 15.63 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.25), residues: 1180
  helix:  0.42 (0.57), residues: 88
  sheet: -0.88 (0.42), residues: 166
  loop : -0.36 (0.22), residues: 926

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A3288 
 HIS   0.004   0.001   HIS D  73 
 PHE   0.020   0.002   PHE A3454 
 TYR   0.016   0.002   TYR A3459 
 ARG   0.004   0.000   ARG A3463 

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 60
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
REVERT: D   70 LYS cc_start: 0.5834 (mttt) cc_final: 0.5411 (mmtm)
REVERT: A 1230 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8265 (ttm)
REVERT: A 1245 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8196 (pp)
REVERT: A 2919 ARG cc_start: 0.2730 (OUTLIER) cc_final: 0.1750 (mmm-85)
REVERT: A 2992 MET cc_start: 0.5215 (mmm) cc_final: 0.4964 (mmm)
REVERT: A 3092 MET cc_start: 0.5967 (OUTLIER) cc_final: 0.5695 (pmt)
REVERT: A 3135 PHE cc_start: 0.6815 (p90) cc_final: 0.6524 (p90)
REVERT: A 3146 MET cc_start: 0.7844 (mmt) cc_final: 0.7414 (ptp)
REVERT: A 3150 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6871 (ttt-90)
REVERT: A 3261 THR cc_start: 0.9070 (t) cc_final: 0.8816 (p)
REVERT: A 3392 GLU cc_start: 0.8325 (tt0) cc_final: 0.7982 (mt-10)
REVERT: A 3557 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8279 (mm)
REVERT: A 3577 ARG cc_start: 0.8154 (mtt-85) cc_final: 0.7930 (mtm-85)
REVERT: A 3609 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8996 (pp)
REVERT: A 3664 ASP cc_start: 0.8646 (t0) cc_final: 0.8421 (t0)
  outliers start: 40
  outliers final: 27
  residues processed: 92
  average time/residue: 0.2307
  time to fit residues: 30.3299
Evaluate side-chains
  93 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 59
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   83 HIS
Chi-restraints excluded: chain A residue 1230 MET
Chi-restraints excluded: chain A residue 1238 CYS
Chi-restraints excluded: chain A residue 1245 ILE
Chi-restraints excluded: chain A residue 2919 ARG
Chi-restraints excluded: chain A residue 2920 CYS
Chi-restraints excluded: chain A residue 2927 CYS
Chi-restraints excluded: chain A residue 2938 ASP
Chi-restraints excluded: chain A residue 2944 HIS
Chi-restraints excluded: chain A residue 2971 TYR
Chi-restraints excluded: chain A residue 3020 CYS
Chi-restraints excluded: chain A residue 3086 ASN
Chi-restraints excluded: chain A residue 3092 MET
Chi-restraints excluded: chain A residue 3132 ILE
Chi-restraints excluded: chain A residue 3145 LEU
Chi-restraints excluded: chain A residue 3150 ARG
Chi-restraints excluded: chain A residue 3215 THR
Chi-restraints excluded: chain A residue 3220 SER
Chi-restraints excluded: chain A residue 3228 LEU
Chi-restraints excluded: chain A residue 3277 LEU
Chi-restraints excluded: chain A residue 3295 CYS
Chi-restraints excluded: chain A residue 3329 VAL
Chi-restraints excluded: chain A residue 3406 ASP
Chi-restraints excluded: chain A residue 3415 LEU
Chi-restraints excluded: chain A residue 3450 THR
Chi-restraints excluded: chain A residue 3509 LEU
Chi-restraints excluded: chain A residue 3557 LEU
Chi-restraints excluded: chain A residue 3609 ILE
Chi-restraints excluded: chain A residue 3695 ILE
Chi-restraints excluded: chain A residue 3757 VAL
Chi-restraints excluded: chain A residue 3797 MET
Chi-restraints excluded: chain A residue 3826 LEU
Chi-restraints excluded: chain A residue 3851 CYS
Chi-restraints excluded: chain A residue 3859 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 103 optimal weight:    0.3980
   chunk 37 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 115 optimal weight:    4.9990
   chunk 77 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0050
   chunk 55 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    0.7996

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

Flipped N/Q/H residues before XYZ refinement:
** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2988 GLN
A3801 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.152565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.108548 restraints weight = 17296.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 2.18
r_work: 0.3345 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  10009  Z= 0.231
  Angle     :  0.624   9.189  13559  Z= 0.313
  Chirality :  0.048   0.323   1486
  Planarity :  0.004   0.045   1796
  Dihedral  :  8.544  58.086   1970
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 16.38 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.25), residues: 1180
  helix:  0.40 (0.57), residues: 88
  sheet: -0.93 (0.42), residues: 164
  loop : -0.35 (0.22), residues: 928

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  66 
 HIS   0.004   0.001   HIS D  73 
 PHE   0.016   0.002   PHE A2884 
 TYR   0.012   0.002   TYR A3459 
 ARG   0.003   0.000   ARG A2993 

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 62
  time to evaluate  : 1.125 
Fit side-chains
   revert: symmetry clash
REVERT: D   70 LYS cc_start: 0.5830 (mttt) cc_final: 0.5408 (mmtm)
REVERT: A 1230 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8213 (ttm)
REVERT: A 1245 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8162 (pp)
REVERT: A 2919 ARG cc_start: 0.2707 (OUTLIER) cc_final: 0.1720 (mmm-85)
REVERT: A 3092 MET cc_start: 0.6003 (OUTLIER) cc_final: 0.5745 (pmt)
REVERT: A 3135 PHE cc_start: 0.6797 (p90) cc_final: 0.6483 (p90)
REVERT: A 3150 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6847 (ttt-90)
REVERT: A 3261 THR cc_start: 0.9012 (t) cc_final: 0.8795 (p)
REVERT: A 3392 GLU cc_start: 0.8252 (tt0) cc_final: 0.7895 (mt-10)
REVERT: A 3557 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8215 (mm)
REVERT: A 3577 ARG cc_start: 0.8093 (mtt-85) cc_final: 0.7881 (mtm-85)
REVERT: A 3609 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8991 (pp)
REVERT: A 3664 ASP cc_start: 0.8575 (t0) cc_final: 0.8365 (t0)
  outliers start: 34
  outliers final: 24
  residues processed: 89
  average time/residue: 0.2434
  time to fit residues: 31.7955
Evaluate side-chains
  92 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 61
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   83 HIS
Chi-restraints excluded: chain A residue 1230 MET
Chi-restraints excluded: chain A residue 1238 CYS
Chi-restraints excluded: chain A residue 1245 ILE
Chi-restraints excluded: chain A residue 2919 ARG
Chi-restraints excluded: chain A residue 2920 CYS
Chi-restraints excluded: chain A residue 2927 CYS
Chi-restraints excluded: chain A residue 2938 ASP
Chi-restraints excluded: chain A residue 2944 HIS
Chi-restraints excluded: chain A residue 2971 TYR
Chi-restraints excluded: chain A residue 3020 CYS
Chi-restraints excluded: chain A residue 3086 ASN
Chi-restraints excluded: chain A residue 3092 MET
Chi-restraints excluded: chain A residue 3132 ILE
Chi-restraints excluded: chain A residue 3150 ARG
Chi-restraints excluded: chain A residue 3215 THR
Chi-restraints excluded: chain A residue 3220 SER
Chi-restraints excluded: chain A residue 3228 LEU
Chi-restraints excluded: chain A residue 3277 LEU
Chi-restraints excluded: chain A residue 3295 CYS
Chi-restraints excluded: chain A residue 3329 VAL
Chi-restraints excluded: chain A residue 3406 ASP
Chi-restraints excluded: chain A residue 3450 THR
Chi-restraints excluded: chain A residue 3557 LEU
Chi-restraints excluded: chain A residue 3609 ILE
Chi-restraints excluded: chain A residue 3695 ILE
Chi-restraints excluded: chain A residue 3757 VAL
Chi-restraints excluded: chain A residue 3797 MET
Chi-restraints excluded: chain A residue 3826 LEU
Chi-restraints excluded: chain A residue 3851 CYS
Chi-restraints excluded: chain A residue 3859 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 55 optimal weight:    0.5980
   chunk 67 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 20 optimal weight:    8.9990
   chunk 98 optimal weight:    0.8980
   chunk 50 optimal weight:    0.2980
   chunk 88 optimal weight:    0.6980
   chunk 96 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A2988 GLN
A3801 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.152913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.108979 restraints weight = 17143.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 2.58
r_work: 0.3335 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  10009  Z= 0.206
  Angle     :  0.621   9.121  13559  Z= 0.311
  Chirality :  0.047   0.314   1486
  Planarity :  0.004   0.043   1796
  Dihedral  :  8.313  58.906   1968
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 16.67 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.25), residues: 1180
  helix:  0.43 (0.58), residues: 88
  sheet: -0.90 (0.42), residues: 164
  loop : -0.34 (0.22), residues: 928

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A3383 
 HIS   0.004   0.001   HIS D  73 
 PHE   0.016   0.002   PHE A2884 
 TYR   0.012   0.001   TYR A3244 
 ARG   0.002   0.000   ARG A3017 

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

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

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2360 Ramachandran restraints generated.
    1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 60
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
REVERT: D   70 LYS cc_start: 0.5710 (mttt) cc_final: 0.5357 (mmtm)
REVERT: A 1230 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8285 (ttm)
REVERT: A 1245 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8187 (pp)
REVERT: A 2919 ARG cc_start: 0.2728 (OUTLIER) cc_final: 0.1754 (mmm-85)
REVERT: A 2927 CYS cc_start: 0.4055 (OUTLIER) cc_final: 0.3640 (p)
REVERT: A 3017 ARG cc_start: 0.6910 (mpp-170) cc_final: 0.6705 (mpp-170)
REVERT: A 3092 MET cc_start: 0.5937 (OUTLIER) cc_final: 0.5687 (pmt)
REVERT: A 3135 PHE cc_start: 0.6786 (p90) cc_final: 0.6509 (p90)
REVERT: A 3150 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6824 (ttt-90)
REVERT: A 3261 THR cc_start: 0.9038 (t) cc_final: 0.8792 (p)
REVERT: A 3557 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8195 (mm)
REVERT: A 3577 ARG cc_start: 0.8126 (mtt-85) cc_final: 0.7908 (mtm-85)
REVERT: A 3609 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8904 (pp)
REVERT: A 3664 ASP cc_start: 0.8691 (t0) cc_final: 0.8454 (t0)
  outliers start: 33
  outliers final: 24
  residues processed: 86
  average time/residue: 0.2324
  time to fit residues: 28.6940
Evaluate side-chains
  90 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 58
  time to evaluate  : 1.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   83 HIS
Chi-restraints excluded: chain A residue 1230 MET
Chi-restraints excluded: chain A residue 1238 CYS
Chi-restraints excluded: chain A residue 1245 ILE
Chi-restraints excluded: chain A residue 2919 ARG
Chi-restraints excluded: chain A residue 2920 CYS
Chi-restraints excluded: chain A residue 2927 CYS
Chi-restraints excluded: chain A residue 2938 ASP
Chi-restraints excluded: chain A residue 2944 HIS
Chi-restraints excluded: chain A residue 2971 TYR
Chi-restraints excluded: chain A residue 3020 CYS
Chi-restraints excluded: chain A residue 3086 ASN
Chi-restraints excluded: chain A residue 3092 MET
Chi-restraints excluded: chain A residue 3132 ILE
Chi-restraints excluded: chain A residue 3150 ARG
Chi-restraints excluded: chain A residue 3215 THR
Chi-restraints excluded: chain A residue 3220 SER
Chi-restraints excluded: chain A residue 3228 LEU
Chi-restraints excluded: chain A residue 3277 LEU
Chi-restraints excluded: chain A residue 3295 CYS
Chi-restraints excluded: chain A residue 3329 VAL
Chi-restraints excluded: chain A residue 3406 ASP
Chi-restraints excluded: chain A residue 3450 THR
Chi-restraints excluded: chain A residue 3509 LEU
Chi-restraints excluded: chain A residue 3557 LEU
Chi-restraints excluded: chain A residue 3609 ILE
Chi-restraints excluded: chain A residue 3695 ILE
Chi-restraints excluded: chain A residue 3757 VAL
Chi-restraints excluded: chain A residue 3797 MET
Chi-restraints excluded: chain A residue 3826 LEU
Chi-restraints excluded: chain A residue 3851 CYS
Chi-restraints excluded: chain A residue 3859 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 111 optimal weight:    0.0980
   chunk 80 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 87 optimal weight:    0.6980
   chunk 68 optimal weight:    0.8980
   chunk 90 optimal weight:    0.6980
   chunk 40 optimal weight:    0.3980
   chunk 63 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A3801 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.153620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.109690 restraints weight = 17134.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.59
r_work: 0.3349 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.2224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10009  Z= 0.182
  Angle     :  0.605   9.114  13559  Z= 0.303
  Chirality :  0.047   0.305   1486
  Planarity :  0.004   0.042   1796
  Dihedral  :  7.946  58.810   1968
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 16.48 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.25), residues: 1180
  helix:  0.45 (0.57), residues: 88
  sheet: -0.79 (0.43), residues: 154
  loop : -0.33 (0.22), residues: 938

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A3383 
 HIS   0.004   0.001   HIS D  73 
 PHE   0.016   0.001   PHE A2884 
 TYR   0.013   0.001   TYR A3244 
 ARG   0.003   0.000   ARG A2961 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6808.64 seconds
wall clock time: 120 minutes 49.04 seconds (7249.04 seconds total)