Starting phenix.real_space_refine
on Thu May 22 22:52:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bm1_44684/05_2025/9bm1_44684.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bm1_44684/05_2025/9bm1_44684.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bm1_44684/05_2025/9bm1_44684.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bm1_44684/05_2025/9bm1_44684.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bm1_44684/05_2025/9bm1_44684.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bm1_44684/05_2025/9bm1_44684.cif"
  }
  resolution = 3.02
  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=   0.030
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: 6
    Type Number    sf(0)   Gaussians
     P       9      5.49       5
     Mg      2      5.21       5
     S     113      5.16       5
     C   14644      2.51       5
     N    3981      2.21       5
     O    4302      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.07s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 23051
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 22937
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 2859, 22925
          Classifications: {'peptide': 2859}
          Link IDs: {'PTRANS': 130, 'TRANS': 2728}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 2859, 22925
          Classifications: {'peptide': 2859}
          Link IDs: {'PTRANS': 130, 'TRANS': 2728}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 23395
    Chain: "A"
      Number of atoms: 114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 114
          Unusual residues: {' MG': 2, 'ADP': 3, 'ATP': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR A2022 " occ=0.52
      ... (22 atoms not shown)
      pdb=" OH BTYR A2022 " occ=0.48
  Time building chain proxies: 23.19, per 1000 atoms: 1.01
  Number of scatterers: 23051
  At special positions: 0
  Unit cell: (116.48, 188.864, 164.736, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S     113     16.00
     P       9     15.00
     Mg      2     11.99
     O    4302      8.00
     N    3981      7.00
     C   14644      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 5.94
  Conformation dependent library (CDL) restraints added in 5.6 seconds
  

  5708 Ramachandran restraints generated.
    2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5436

  Finding SS restraints...
    Secondary structure from input PDB file:
      133 helices and 19 sheets defined
      64.1% alpha, 9.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 4.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1535 through 1554
      removed outlier: 4.195A  pdb=" N   ASP A1539 " --> pdb=" O   ASP A1535 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   TYR A1546 " --> pdb=" O   ARG A1542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1556 through 1561
    Processing helix  chain 'A' and resid 1561 through 1585
      removed outlier: 3.559A  pdb=" N   THR A1565 " --> pdb=" O   LEU A1561 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   SER A1585 " --> pdb=" O   LYS A1581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1587 through 1593
    Processing helix  chain 'A' and resid 1596 through 1614
    Processing helix  chain 'A' and resid 1615 through 1626
      removed outlier: 3.527A  pdb=" N   PHE A1626 " --> pdb=" O   GLU A1622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1627 through 1632
    Processing helix  chain 'A' and resid 1633 through 1643
    Processing helix  chain 'A' and resid 1646 through 1651
      removed outlier: 3.676A  pdb=" N   LYS A1649 " --> pdb=" O   ASN A1646 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLN A1651 " --> pdb=" O   ALA A1648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1653 through 1658
      removed outlier: 3.913A  pdb=" N   MET A1657 " --> pdb=" O   HIS A1653 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1697 through 1728
      removed outlier: 3.658A  pdb=" N   ILE A1726 " --> pdb=" O   THR A1722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1734 through 1745
    Processing helix  chain 'A' and resid 1746 through 1769
      removed outlier: 3.765A  pdb=" N   VAL A1751 " --> pdb=" O   ALA A1747 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LEU A1752 " --> pdb=" O   GLN A1748 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1770 through 1772
      No H-bonds generated for 'chain 'A' and resid 1770 through 1772'
    Processing helix  chain 'A' and resid 1777 through 1798
      removed outlier: 3.713A  pdb=" N   MET A1798 " --> pdb=" O   ASP A1794 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1801 through 1828
      removed outlier: 3.536A  pdb=" N   HIS A1817 " --> pdb=" O   THR A1813 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1835 through 1840
    Processing helix  chain 'A' and resid 1852 through 1855
    Processing helix  chain 'A' and resid 1882 through 1898
    Processing helix  chain 'A' and resid 1911 through 1923
    Processing helix  chain 'A' and resid 1937 through 1952
    Processing helix  chain 'A' and resid 1960 through 1963
      removed outlier: 3.755A  pdb=" N   LEU A1963 " --> pdb=" O   PHE A1960 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1960 through 1963'
    Processing helix  chain 'A' and resid 1964 through 1987
      removed outlier: 3.729A  pdb=" N   GLN A1973 " --> pdb=" O   SER A1969 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   GLN A1974 " --> pdb=" O   ALA A1970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2029 through 2034
    Processing helix  chain 'A' and resid 2045 through 2057
    Processing helix  chain 'A' and resid 2061 through 2080
      Proline residue:  A2071  - end of helix
      removed outlier: 3.654A  pdb=" N   LEU A2080 " --> pdb=" O   CYS A2076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2089 through 2118
    Processing helix  chain 'A' and resid 2123 through 2130
    Processing helix  chain 'A' and resid 2132 through 2145
    Processing helix  chain 'A' and resid 2146 through 2149
    Processing helix  chain 'A' and resid 2153 through 2165
    Processing helix  chain 'A' and resid 2175 through 2189
      removed outlier: 3.728A  pdb=" N   GLU A2181 " --> pdb=" O   ALA A2177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2200 through 2217
    Processing helix  chain 'A' and resid 2229 through 2246
    Processing helix  chain 'A' and resid 2255 through 2259
      removed outlier: 3.933A  pdb=" N   ILE A2259 " --> pdb=" O   PRO A2256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2260 through 2265
    Processing helix  chain 'A' and resid 2278 through 2290
    Processing helix  chain 'A' and resid 2293 through 2297
    Processing helix  chain 'A' and resid 2311 through 2314
      removed outlier: 3.529A  pdb=" N   ASN A2314 " --> pdb=" O   TRP A2311 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2311 through 2314'
    Processing helix  chain 'A' and resid 2315 through 2320
    Processing helix  chain 'A' and resid 2352 through 2357
    Processing helix  chain 'A' and resid 2370 through 2385
    Processing helix  chain 'A' and resid 2411 through 2424
    Processing helix  chain 'A' and resid 2425 through 2428
      removed outlier: 4.034A  pdb=" N   THR A2428 " --> pdb=" O   PRO A2425 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2425 through 2428'
    Processing helix  chain 'A' and resid 2431 through 2441
    Processing helix  chain 'A' and resid 2450 through 2476
      removed outlier: 3.554A  pdb=" N   CYS A2454 " --> pdb=" O   THR A2450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2482 through 2503
    Processing helix  chain 'A' and resid 2507 through 2522
    Processing helix  chain 'A' and resid 2533 through 2535
      No H-bonds generated for 'chain 'A' and resid 2533 through 2535'
    Processing helix  chain 'A' and resid 2549 through 2552
    Processing helix  chain 'A' and resid 2558 through 2562
    Processing helix  chain 'A' and resid 2571 through 2587
      removed outlier: 4.019A  pdb=" N   GLU A2587 " --> pdb=" O   THR A2583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2600 through 2611
      removed outlier: 3.870A  pdb=" N   ALA A2611 " --> pdb=" O   SER A2607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2627 through 2638
      removed outlier: 4.228A  pdb=" N   LEU A2631 " --> pdb=" O   THR A2627 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2677 through 2689
    Processing helix  chain 'A' and resid 2724 through 2729
    Processing helix  chain 'A' and resid 2740 through 2757
    Processing helix  chain 'A' and resid 2758 through 2764
      removed outlier: 6.605A  pdb=" N   SER A2761 " --> pdb=" O   LEU A2758 " (cutoff:3.500A)
      removed outlier: 4.767A  pdb=" N   THR A2764 " --> pdb=" O   SER A2761 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2765 through 2784
    Processing helix  chain 'A' and resid 2795 through 2811
      removed outlier: 3.818A  pdb=" N   MET A2799 " --> pdb=" O   SER A2795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2817 through 2834
    Processing helix  chain 'A' and resid 2839 through 2858
    Processing helix  chain 'A' and resid 2862 through 2868
      removed outlier: 4.178A  pdb=" N   ALA A2866 " --> pdb=" O   ASP A2862 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2885 through 2904
    Processing helix  chain 'A' and resid 2912 through 2927
    Processing helix  chain 'A' and resid 2942 through 2954
    Processing helix  chain 'A' and resid 2968 through 2985
    Processing helix  chain 'A' and resid 2997 through 2999
      No H-bonds generated for 'chain 'A' and resid 2997 through 2999'
    Processing helix  chain 'A' and resid 3001 through 3015
      removed outlier: 3.712A  pdb=" N   LEU A3005 " --> pdb=" O   ASP A3001 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3023 through 3041
    Processing helix  chain 'A' and resid 3046 through 3061
    Processing helix  chain 'A' and resid 3071 through 3082
      removed outlier: 3.571A  pdb=" N   LYS A3076 " --> pdb=" O   SER A3072 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ALA A3080 " --> pdb=" O   LYS A3076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3083 through 3088
    Processing helix  chain 'A' and resid 3098 through 3110
    Processing helix  chain 'A' and resid 3138 through 3165
      removed outlier: 3.617A  pdb=" N   LEU A3154 " --> pdb=" O   VAL A3150 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   HIS A3155 " --> pdb=" O   HIS A3151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3172 through 3241
      removed outlier: 3.690A  pdb=" N   TYR A3176 " --> pdb=" O   THR A3172 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLU A3217 " --> pdb=" O   ASP A3213 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LYS A3241 " --> pdb=" O   ASN A3237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3450 through 3495
      removed outlier: 4.827A  pdb=" N   ALA A3484 " --> pdb=" O   LYS A3480 " (cutoff:3.500A)
      removed outlier: 4.954A  pdb=" N   GLU A3485 " --> pdb=" O   SER A3481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3495 through 3517
      removed outlier: 5.032A  pdb=" N   ALA A3504 " --> pdb=" O   MET A3500 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   GLY A3505 " --> pdb=" O   SER A3501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3521 through 3539
    Processing helix  chain 'A' and resid 3548 through 3554
    Processing helix  chain 'A' and resid 3555 through 3565
    Processing helix  chain 'A' and resid 3570 through 3582
    Processing helix  chain 'A' and resid 3594 through 3604
    Processing helix  chain 'A' and resid 3618 through 3630
    Processing helix  chain 'A' and resid 3637 through 3641
      removed outlier: 3.717A  pdb=" N   SER A3640 " --> pdb=" O   ASP A3637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3642 through 3644
      No H-bonds generated for 'chain 'A' and resid 3642 through 3644'
    Processing helix  chain 'A' and resid 3645 through 3650
    Processing helix  chain 'A' and resid 3689 through 3696
      removed outlier: 3.635A  pdb=" N   ARG A3695 " --> pdb=" O   ASP A3691 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL A3696 " --> pdb=" O   LEU A3692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3704 through 3721
    Processing helix  chain 'A' and resid 3721 through 3756
    Processing helix  chain 'A' and resid 3763 through 3817
      removed outlier: 3.525A  pdb=" N   VAL A3797 " --> pdb=" O   GLU A3793 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   GLN A3800 " --> pdb=" O   THR A3796 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   TYR A3801 " --> pdb=" O   VAL A3797 " (cutoff:3.500A)
      Proline residue:  A3803  - end of helix
    Processing helix  chain 'A' and resid 3818 through 3821
    Processing helix  chain 'A' and resid 3828 through 3841
      removed outlier: 3.619A  pdb=" N   PHE A3832 " --> pdb=" O   SER A3828 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3843 through 3847
    Processing helix  chain 'A' and resid 3851 through 3874
      removed outlier: 3.523A  pdb=" N   PHE A3864 " --> pdb=" O   THR A3860 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   GLY A3874 " --> pdb=" O   ARG A3870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3876 through 3894
      removed outlier: 4.489A  pdb=" N   ILE A3881 " --> pdb=" O   HIS A3877 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   THR A3882 " --> pdb=" O   GLN A3878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3901 through 3910
    Processing helix  chain 'A' and resid 3911 through 3914
    Processing helix  chain 'A' and resid 3917 through 3921
      removed outlier: 3.559A  pdb=" N   THR A3921 " --> pdb=" O   ALA A3918 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3928 through 3939
    Processing helix  chain 'A' and resid 3940 through 3945
      removed outlier: 6.162A  pdb=" N   ALA A3943 " --> pdb=" O   CYS A3940 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LYS A3945 " --> pdb=" O   PRO A3942 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3946 through 3954
      removed outlier: 3.541A  pdb=" N   LYS A3950 " --> pdb=" O   ASP A3946 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3956 through 3962
    Processing helix  chain 'A' and resid 3981 through 3997
    Processing helix  chain 'A' and resid 4000 through 4014
    Processing helix  chain 'A' and resid 4026 through 4033
      removed outlier: 3.653A  pdb=" N   ILE A4030 " --> pdb=" O   ASP A4026 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4051 through 4063
    Processing helix  chain 'A' and resid 4073 through 4091
      removed outlier: 3.926A  pdb=" N   LYS A4089 " --> pdb=" O   ASN A4085 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4098 through 4101
    Processing helix  chain 'A' and resid 4102 through 4115
      removed outlier: 3.703A  pdb=" N   MET A4107 " --> pdb=" O   PRO A4103 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   GLN A4108 " --> pdb=" O   GLY A4104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4135 through 4142
    Processing helix  chain 'A' and resid 4152 through 4164
    Processing helix  chain 'A' and resid 4165 through 4170
      removed outlier: 3.562A  pdb=" N   ILE A4169 " --> pdb=" O   PRO A4165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4174 through 4193
      removed outlier: 4.431A  pdb=" N   ARG A4178 " --> pdb=" O   ASN A4174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4196 through 4201
    Processing helix  chain 'A' and resid 4208 through 4227
    Processing helix  chain 'A' and resid 4234 through 4238
    Processing helix  chain 'A' and resid 4239 through 4250
    Processing helix  chain 'A' and resid 4258 through 4273
    Processing helix  chain 'A' and resid 4274 through 4279
    Processing helix  chain 'A' and resid 4301 through 4311
    Processing helix  chain 'A' and resid 4317 through 4322
    Processing helix  chain 'A' and resid 4324 through 4327
    Processing helix  chain 'A' and resid 4328 through 4346
    Processing helix  chain 'A' and resid 4375 through 4391
    Processing helix  chain 'A' and resid 4401 through 4406
      removed outlier: 4.468A  pdb=" N   LYS A4406 " --> pdb=" O   VAL A4402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4407 through 4439
    Processing helix  chain 'A' and resid 4445 through 4458
    Processing helix  chain 'A' and resid 4474 through 4499
    Processing helix  chain 'A' and resid 4500 through 4506
      removed outlier: 3.781A  pdb=" N   LYS A4505 " --> pdb=" O   ALA A4501 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   ASN A4506 " --> pdb=" O   LYS A4502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4516 through 4533
    Processing helix  chain 'A' and resid 4535 through 4537
      No H-bonds generated for 'chain 'A' and resid 4535 through 4537'
    Processing helix  chain 'A' and resid 4631 through 4638
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1663 through 1666
      removed outlier: 7.735A  pdb=" N   GLY A1675 " --> pdb=" O   THR A1688 " (cutoff:3.500A)
      removed outlier: 10.689A  pdb=" N   THR A1688 " --> pdb=" O   GLY A1675 " (cutoff:3.500A)
      removed outlier: 11.571A  pdb=" N   SER A1677 " --> pdb=" O   PHE A1686 " (cutoff:3.500A)
      removed outlier: 11.318A  pdb=" N   PHE A1686 " --> pdb=" O   SER A1677 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1842 through 1846
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1901 through 1905
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1927 through 1931
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1998 through 2001
    Processing sheet with id=AA6, first strand: chain 'A' and resid 2249 through 2254
      removed outlier: 6.883A  pdb=" N   GLY A2219 " --> pdb=" O   GLY A2360 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   VAL A2362 " --> pdb=" O   GLY A2219 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   MET A2221 " --> pdb=" O   VAL A2362 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 2266 through 2268
    Processing sheet with id=AA8, first strand: chain 'A' and resid 2324 through 2326
    Processing sheet with id=AA9, first strand: chain 'A' and resid 2537 through 2539
    Processing sheet with id=AB1, first strand: chain 'A' and resid 2615 through 2620
      removed outlier: 6.197A  pdb=" N   LEU A2659 " --> pdb=" O   GLN A2707 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   VAL A2709 " --> pdb=" O   LEU A2659 " (cutoff:3.500A)
      removed outlier: 5.864A  pdb=" N   LEU A2661 " --> pdb=" O   VAL A2709 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   ALA A2711 " --> pdb=" O   LEU A2661 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   CYS A2663 " --> pdb=" O   ALA A2711 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 2639 through 2644
      removed outlier: 4.204A  pdb=" N   VAL A2648 " --> pdb=" O   TRP A2700 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 2873 through 2874
      removed outlier: 3.829A  pdb=" N   ILE A2882 " --> pdb=" O   SER A2874 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 2957 through 2959
      removed outlier: 6.236A  pdb=" N   SER A2957 " --> pdb=" O   ALA A2991 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   ILE A2993 " --> pdb=" O   SER A2957 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   TYR A2959 " --> pdb=" O   ILE A2993 " (cutoff:3.500A)
      removed outlier: 7.966A  pdb=" N   ASP A2995 " --> pdb=" O   TYR A2959 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 3610 through 3612
      removed outlier: 6.307A  pdb=" N   LEU A3588 " --> pdb=" O   VAL A3699 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 3654 through 3656
    Processing sheet with id=AB7, first strand: chain 'A' and resid 4066 through 4070
      removed outlier: 6.100A  pdb=" N   THR A4067 " --> pdb=" O   MET A4095 " (cutoff:3.500A)
      removed outlier: 7.425A  pdb=" N   LYS A4097 " --> pdb=" O   THR A4067 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   ILE A4069 " --> pdb=" O   LYS A4097 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   VAL A4094 " --> pdb=" O   PHE A4125 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   THR A4127 " --> pdb=" O   VAL A4094 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   LEU A4096 " --> pdb=" O   THR A4127 " (cutoff:3.500A)
      removed outlier: 8.568A  pdb=" N   GLU A4129 " --> pdb=" O   LEU A4096 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   MET A4128 " --> pdb=" O   MET A4043 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 4283 through 4289
      removed outlier: 5.627A  pdb=" N   CYS A4286 " --> pdb=" O   ILE A4294 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   ILE A4294 " --> pdb=" O   CYS A4286 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   LYS A4292 " --> pdb=" O   VAL A4288 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 4509 through 4510
    Processing sheet with id=AC1, first strand: chain 'A' and resid 4564 through 4571
      removed outlier: 7.436A  pdb=" N   ILE A4581 " --> pdb=" O   GLY A4567 " (cutoff:3.500A)
      removed outlier: 9.556A  pdb=" N   THR A4569 " --> pdb=" O   ASN A4579 " (cutoff:3.500A)
      removed outlier: 9.643A  pdb=" N   ASN A4579 " --> pdb=" O   THR A4569 " (cutoff:3.500A)
      removed outlier: 10.058A  pdb=" N   ASN A4571 " --> pdb=" O   LEU A4577 " (cutoff:3.500A)
      removed outlier: 10.144A  pdb=" N   LEU A4577 " --> pdb=" O   ASN A4571 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   PHE A4620 " --> pdb=" O   VAL A4609 " (cutoff:3.500A)
      removed outlier: 8.380A  pdb=" N   VAL A4642 " --> pdb=" O   THR A4606 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ALA A4641 " --> pdb=" O   GLN A4566 " (cutoff:3.500A)

    1393 hydrogen bonds defined for protein.
    4047 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: 14.17

  Time building geometry restraints manager: 6.89 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 7605
        1.34 -     1.46: 4909
        1.46 -     1.58: 10826
        1.58 -     1.70: 14
        1.70 -     1.81: 189
  Bond restraints: 23543
  Sorted by residual:
  bond pdb=" C4  ADP A4703 "
       pdb=" C5  ADP A4703 "
    ideal  model  delta    sigma   weight residual
    1.490  1.380  0.110 2.00e-02 2.50e+03 3.01e+01
  bond pdb=" C4  ADP A4701 "
       pdb=" C5  ADP A4701 "
    ideal  model  delta    sigma   weight residual
    1.490  1.381  0.109 2.00e-02 2.50e+03 2.97e+01
  bond pdb=" C4  ADP A4704 "
       pdb=" C5  ADP A4704 "
    ideal  model  delta    sigma   weight residual
    1.490  1.381  0.109 2.00e-02 2.50e+03 2.95e+01
  bond pdb=" C5  ADP A4703 "
       pdb=" C6  ADP A4703 "
    ideal  model  delta    sigma   weight residual
    1.490  1.407  0.083 2.00e-02 2.50e+03 1.71e+01
  bond pdb=" C5  ADP A4704 "
       pdb=" C6  ADP A4704 "
    ideal  model  delta    sigma   weight residual
    1.490  1.408  0.082 2.00e-02 2.50e+03 1.69e+01
  ... (remaining 23538 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.57: 31617
        2.57 -     5.15: 279
        5.15 -     7.72: 25
        7.72 -    10.30: 9
       10.30 -    12.87: 6
  Bond angle restraints: 31936
  Sorted by residual:
  angle pdb=" PB  ATP A4702 "
        pdb=" O3B ATP A4702 "
        pdb=" PG  ATP A4702 "
      ideal   model   delta    sigma   weight residual
     139.87  132.79    7.08 1.00e+00 1.00e+00 5.02e+01
  angle pdb=" PA  ATP A4702 "
        pdb=" O3A ATP A4702 "
        pdb=" PB  ATP A4702 "
      ideal   model   delta    sigma   weight residual
     136.83  130.39    6.44 1.00e+00 1.00e+00 4.14e+01
  angle pdb=" PA  ADP A4704 "
        pdb=" O3A ADP A4704 "
        pdb=" PB  ADP A4704 "
      ideal   model   delta    sigma   weight residual
     120.50  133.37  -12.87 3.00e+00 1.11e-01 1.84e+01
  angle pdb=" PA  ADP A4703 "
        pdb=" O3A ADP A4703 "
        pdb=" PB  ADP A4703 "
      ideal   model   delta    sigma   weight residual
     120.50  132.26  -11.76 3.00e+00 1.11e-01 1.54e+01
  angle pdb=" PA  ADP A4701 "
        pdb=" O3A ADP A4701 "
        pdb=" PB  ADP A4701 "
      ideal   model   delta    sigma   weight residual
     120.50  131.80  -11.30 3.00e+00 1.11e-01 1.42e+01
  ... (remaining 31931 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.81: 13490
       25.81 -    51.62: 670
       51.62 -    77.43: 111
       77.43 -   103.24: 15
      103.24 -   129.05: 3
  Dihedral angle restraints: 14289
    sinusoidal: 5917
      harmonic: 8372
  Sorted by residual:
  dihedral pdb=" C5' ADP A4703 "
           pdb=" O5' ADP A4703 "
           pdb=" PA  ADP A4703 "
           pdb=" O2A ADP A4703 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  170.95  129.05     1      2.00e+01 2.50e-03 3.91e+01
  dihedral pdb=" O1B ADP A4701 "
           pdb=" O3A ADP A4701 "
           pdb=" PB  ADP A4701 "
           pdb=" PA  ADP A4701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -172.32  112.32     1      2.00e+01 2.50e-03 3.31e+01
  dihedral pdb=" C5' ADP A4701 "
           pdb=" O5' ADP A4701 "
           pdb=" PA  ADP A4701 "
           pdb=" O2A ADP A4701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   46.51 -106.51     1      2.00e+01 2.50e-03 3.08e+01
  ... (remaining 14286 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 2729
       0.041 -    0.082: 611
       0.082 -    0.123: 233
       0.123 -    0.164: 13
       0.164 -    0.205: 10
  Chirality restraints: 3596
  Sorted by residual:
  chirality pdb=" CA  ILE A2049 "
            pdb=" N   ILE A2049 "
            pdb=" C   ILE A2049 "
            pdb=" CB  ILE A2049 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  VAL A1880 "
            pdb=" N   VAL A1880 "
            pdb=" C   VAL A1880 "
            pdb=" CB  VAL A1880 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.60e-01
  chirality pdb=" CA  VAL A2568 "
            pdb=" N   VAL A2568 "
            pdb=" C   VAL A2568 "
            pdb=" CB  VAL A2568 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.63e-01
  ... (remaining 3593 not shown)

  Planarity restraints: 4093
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA BTYR A2022 "    0.028 2.00e-02 2.50e+03   5.78e-02 3.34e+01
        pdb=" C  BTYR A2022 "   -0.100 2.00e-02 2.50e+03
        pdb=" O  BTYR A2022 "    0.037 2.00e-02 2.50e+03
        pdb=" N   ALA A2023 "    0.035 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA ATYR A2022 "    0.027 2.00e-02 2.50e+03   5.44e-02 2.96e+01
        pdb=" C  ATYR A2022 "   -0.094 2.00e-02 2.50e+03
        pdb=" O  ATYR A2022 "    0.035 2.00e-02 2.50e+03
        pdb=" N   ALA A2023 "    0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A2021 "    0.026 2.00e-02 2.50e+03   5.33e-02 2.84e+01
        pdb=" C   GLY A2021 "   -0.092 2.00e-02 2.50e+03
        pdb=" O   GLY A2021 "    0.034 2.00e-02 2.50e+03
        pdb=" N  ATYR A2022 "    0.032 2.00e-02 2.50e+03
  ... (remaining 4090 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.34: 22
        2.34 -     2.98: 11062
        2.98 -     3.62: 35242
        3.62 -     4.26: 54891
        4.26 -     4.90: 93375
  Nonbonded interactions: 194592
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A2344 "
            pdb="MG    MG A4706 "
     model   vdw
     1.694 2.170
  nonbonded pdb=" O   LEU A1561 "
            pdb=" OG1 THR A1565 "
     model   vdw
     2.166 3.040
  nonbonded pdb=" O   THR A3110 "
            pdb=" NH1 ARG A3140 "
     model   vdw
     2.200 3.120
  nonbonded pdb=" OH  TYR A3825 "
            pdb=" OD2 ASP A3879 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OE1 GLN A3499 "
            pdb=" NH2 ARG A3544 "
     model   vdw
     2.224 3.120
  ... (remaining 194587 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.00 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:             4.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.880
  Check model and map are aligned:         0.150
  Set scattering table:                    0.200
  Process input model:                     72.830
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.150
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   81.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
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      :  0.004   0.110  23543  Z= 0.219
  Angle     :  0.607  12.875  31936  Z= 0.337
  Chirality :  0.040   0.205   3596
  Planarity :  0.005   0.170   4093
  Dihedral  : 15.284 129.048   8853
  Min Nonbonded Distance : 1.694

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  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:  2.10 (0.16), residues: 2854
  helix:  2.23 (0.13), residues: 1630
  sheet: -0.51 (0.35), residues: 220
  loop :  0.57 (0.20), residues: 1004

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A2234 
 HIS   0.002   0.000   HIS A3837 
 PHE   0.014   0.001   PHE A3109 
 TYR   0.015   0.001   TYR A2496 
 ARG   0.008   0.000   ARG A2060 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13946 ( 1393)
  hydrogen bonds       : angle       5.45225 ( 4047)
  covalent geometry    : bond        0.00364 (23543)
  covalent geometry    : angle       0.60688 (31936)

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

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

  5708 Ramachandran restraints generated.
    2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5708 Ramachandran restraints generated.
    2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  423 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 423
  time to evaluate  : 2.481 
Fit side-chains
   revert: symmetry clash
REVERT: A 1814 GLU cc_start: 0.7586 (tp30) cc_final: 0.7197 (tp30)
REVERT: A 2124 GLU cc_start: 0.7479 (mp0) cc_final: 0.7121 (pm20)
REVERT: A 3132 LYS cc_start: 0.8445 (mmmt) cc_final: 0.7945 (mttp)
REVERT: A 3199 MET cc_start: 0.8584 (tmm) cc_final: 0.8342 (ppp)
REVERT: A 3201 LEU cc_start: 0.8635 (mt) cc_final: 0.8382 (mp)
REVERT: A 3610 THR cc_start: 0.8395 (t) cc_final: 0.7886 (m)
REVERT: A 3895 THR cc_start: 0.7409 (m) cc_final: 0.7020 (p)
REVERT: A 4287 LYS cc_start: 0.7861 (mtmm) cc_final: 0.7622 (mttm)
REVERT: A 4457 LYS cc_start: 0.7787 (ttpp) cc_final: 0.7505 (ttmm)
REVERT: A 4502 LYS cc_start: 0.7526 (pttp) cc_final: 0.7257 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 423
  average time/residue: 0.4008
  time to fit residues: 252.0128
Evaluate side-chains
  256 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 256
  time to evaluate  : 2.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 285
   random chunks:
   chunk 240 optimal weight:    2.9990
   chunk 216 optimal weight:    0.6980
   chunk 119 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 145 optimal weight:    3.9990
   chunk 115 optimal weight:    1.9990
   chunk 223 optimal weight:    3.9990
   chunk 86 optimal weight:    0.5980
   chunk 135 optimal weight:    1.9990
   chunk 166 optimal weight:    5.9990
   chunk 258 optimal weight:    1.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
** A1643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1867 ASN
A1894 GLN
A1922 GLN
A2471 GLN
A2476 HIS
A2752 ASN
A2827 HIS
A3200 HIS
A3538 GLN
A3751 GLN
A3772 ASN
A4012 ASN
A4029 HIS
A4098 ASN
A4397 HIS
A4589 GLN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.138993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.105745 restraints weight = 47068.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 2.64
r_work: 0.3229 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3289
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3289
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.1524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  23543  Z= 0.153
  Angle     :  0.549   8.636  31936  Z= 0.278
  Chirality :  0.042   0.283   3596
  Planarity :  0.004   0.046   4093
  Dihedral  :  6.472 128.428   3178
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  5.88 %
    Favored  : 93.45 %
  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:  2.12 (0.16), residues: 2854
  helix:  2.16 (0.13), residues: 1667
  sheet: -0.60 (0.35), residues: 209
  loop :  0.69 (0.21), residues: 978

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A2234 
 HIS   0.008   0.001   HIS A4029 
 PHE   0.013   0.001   PHE A4260 
 TYR   0.014   0.001   TYR A2496 
 ARG   0.006   0.001   ARG A2801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04276 ( 1393)
  hydrogen bonds       : angle       4.35408 ( 4047)
  covalent geometry    : bond        0.00353 (23543)
  covalent geometry    : angle       0.54944 (31936)

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

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

  5708 Ramachandran restraints generated.
    2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5708 Ramachandran restraints generated.
    2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 272
  time to evaluate  : 2.495 
Fit side-chains
REVERT: A 1769 MET cc_start: 0.7898 (mtp) cc_final: 0.7641 (mtp)
REVERT: A 1814 GLU cc_start: 0.7605 (tp30) cc_final: 0.6993 (tp30)
REVERT: A 2074 LYS cc_start: 0.8207 (tttm) cc_final: 0.7760 (ttmt)
REVERT: A 2124 GLU cc_start: 0.7641 (mp0) cc_final: 0.7138 (pm20)
REVERT: A 2573 ASP cc_start: 0.8744 (m-30) cc_final: 0.8518 (m-30)
REVERT: A 3132 LYS cc_start: 0.8396 (mmmt) cc_final: 0.7689 (mttt)
REVERT: A 3734 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8060 (tp)
REVERT: A 4281 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7765 (tm-30)
REVERT: A 4287 LYS cc_start: 0.8007 (mtmm) cc_final: 0.7558 (mttm)
  outliers start: 17
  outliers final: 10
  residues processed: 285
  average time/residue: 0.4089
  time to fit residues: 175.6355
Evaluate side-chains
  240 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 229
  time to evaluate  : 2.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1666 LEU
Chi-restraints excluded: chain A residue 2276 THR
Chi-restraints excluded: chain A residue 2429 SER
Chi-restraints excluded: chain A residue 2557 VAL
Chi-restraints excluded: chain A residue 2655 LEU
Chi-restraints excluded: chain A residue 2822 ILE
Chi-restraints excluded: chain A residue 3697 THR
Chi-restraints excluded: chain A residue 3734 LEU
Chi-restraints excluded: chain A residue 3749 LEU
Chi-restraints excluded: chain A residue 4061 GLU
Chi-restraints excluded: chain A residue 4065 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 285
   random chunks:
   chunk 272 optimal weight:    0.7980
   chunk 173 optimal weight:    2.9990
   chunk 220 optimal weight:    0.0870
   chunk 209 optimal weight:    2.9990
   chunk 174 optimal weight:    0.7980
   chunk 249 optimal weight:    0.3980
   chunk 283 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   overall best weight:    0.8160

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

Flipped N/Q/H residues before XYZ refinement:
** A1989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2827 HIS
A3751 GLN
A4532 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.139324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.106959 restraints weight = 43390.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.70
r_work: 0.3262 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3123
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3123
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  23543  Z= 0.124
  Angle     :  0.503   8.024  31936  Z= 0.255
  Chirality :  0.040   0.258   3596
  Planarity :  0.004   0.045   4093
  Dihedral  :  6.271 121.879   3178
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  6.55 %
    Favored  : 92.62 %
  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:  2.15 (0.16), residues: 2854
  helix:  2.23 (0.13), residues: 1669
  sheet: -0.63 (0.33), residues: 227
  loop :  0.65 (0.21), residues: 958

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A2234 
 HIS   0.005   0.001   HIS A1695 
 PHE   0.019   0.001   PHE A2949 
 TYR   0.016   0.001   TYR A2496 
 ARG   0.008   0.001   ARG A3164 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03912 ( 1393)
  hydrogen bonds       : angle       4.15801 ( 4047)
  covalent geometry    : bond        0.00272 (23543)
  covalent geometry    : angle       0.50335 (31936)

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

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

  5708 Ramachandran restraints generated.
    2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5708 Ramachandran restraints generated.
    2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 249
  time to evaluate  : 2.590 
Fit side-chains
REVERT: A 1769 MET cc_start: 0.7811 (mtp) cc_final: 0.7599 (mtp)
REVERT: A 2124 GLU cc_start: 0.7740 (mp0) cc_final: 0.7190 (pm20)
REVERT: A 2573 ASP cc_start: 0.8908 (m-30) cc_final: 0.8633 (m-30)
REVERT: A 3006 GLU cc_start: 0.7855 (tp30) cc_final: 0.7638 (tp30)
REVERT: A 3132 LYS cc_start: 0.8452 (mmmt) cc_final: 0.7718 (mttt)
REVERT: A 3734 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8112 (tp)
REVERT: A 4056 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8458 (mt-10)
REVERT: A 4287 LYS cc_start: 0.8056 (mtmm) cc_final: 0.7596 (mttm)
REVERT: A 4457 LYS cc_start: 0.7855 (ttpp) cc_final: 0.7404 (ttmm)
REVERT: A 4502 LYS cc_start: 0.7663 (pttp) cc_final: 0.7198 (mttp)
  outliers start: 21
  outliers final: 13
  residues processed: 263
  average time/residue: 0.3786
  time to fit residues: 153.9205
Evaluate side-chains
  235 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 221
  time to evaluate  : 2.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1666 LEU
Chi-restraints excluded: chain A residue 1797 LEU
Chi-restraints excluded: chain A residue 2135 GLU
Chi-restraints excluded: chain A residue 2157 LEU
Chi-restraints excluded: chain A residue 2655 LEU
Chi-restraints excluded: chain A residue 2822 ILE
Chi-restraints excluded: chain A residue 3478 LEU
Chi-restraints excluded: chain A residue 3610 THR
Chi-restraints excluded: chain A residue 3697 THR
Chi-restraints excluded: chain A residue 3734 LEU
Chi-restraints excluded: chain A residue 3796 THR
Chi-restraints excluded: chain A residue 4061 GLU
Chi-restraints excluded: chain A residue 4065 GLN
Chi-restraints excluded: chain A residue 4390 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 285
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 187 optimal weight:    0.4980
   chunk 36 optimal weight:    4.9990
   chunk 270 optimal weight:    6.9990
   chunk 163 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 199 optimal weight:    8.9990
   chunk 229 optimal weight:    0.1980
   chunk 42 optimal weight:    0.6980
   chunk 58 optimal weight:    0.3980
   chunk 80 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A3751 GLN
A4532 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.142202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.109841 restraints weight = 37481.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 2.36
r_work: 0.3274 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3198
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3198 r_free = 0.3198    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3198 r_free = 0.3198    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3198
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  23543  Z= 0.106
  Angle     :  0.491   9.573  31936  Z= 0.247
  Chirality :  0.039   0.278   3596
  Planarity :  0.004   0.045   4093
  Dihedral  :  5.997 114.415   3178
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  7.70 %
    Favored  : 91.59 %
  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:  2.25 (0.16), residues: 2854
  helix:  2.32 (0.13), residues: 1666
  sheet: -0.69 (0.33), residues: 232
  loop :  0.73 (0.21), residues: 956

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A2234 
 HIS   0.004   0.000   HIS A1695 
 PHE   0.023   0.001   PHE A2949 
 TYR   0.016   0.001   TYR A2496 
 ARG   0.007   0.000   ARG A2801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03585 ( 1393)
  hydrogen bonds       : angle       4.02341 ( 4047)
  covalent geometry    : bond        0.00229 (23543)
  covalent geometry    : angle       0.49138 (31936)

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

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

  5708 Ramachandran restraints generated.
    2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5708 Ramachandran restraints generated.
    2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 241
  time to evaluate  : 2.572 
Fit side-chains
REVERT: A 1726 ILE cc_start: 0.8328 (mt) cc_final: 0.8066 (tt)
REVERT: A 1769 MET cc_start: 0.7703 (mtp) cc_final: 0.7496 (mtp)
REVERT: A 1814 GLU cc_start: 0.7862 (tp30) cc_final: 0.7224 (tp30)
REVERT: A 2006 VAL cc_start: 0.8919 (t) cc_final: 0.8683 (p)
REVERT: A 2124 GLU cc_start: 0.7675 (mp0) cc_final: 0.7234 (pm20)
REVERT: A 2476 HIS cc_start: 0.7210 (m-70) cc_final: 0.6997 (m170)
REVERT: A 2573 ASP cc_start: 0.8881 (m-30) cc_final: 0.8602 (m-30)
REVERT: A 3132 LYS cc_start: 0.8425 (mmmt) cc_final: 0.7685 (mtmt)
REVERT: A 3497 LYS cc_start: 0.8420 (pptt) cc_final: 0.7873 (tttm)
REVERT: A 3734 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8105 (tp)
REVERT: A 4056 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8444 (mt-10)
REVERT: A 4281 GLU cc_start: 0.8274 (tm-30) cc_final: 0.8034 (tm-30)
REVERT: A 4287 LYS cc_start: 0.8036 (mtmm) cc_final: 0.7567 (mttm)
REVERT: A 4502 LYS cc_start: 0.7681 (pttp) cc_final: 0.7211 (mttp)
  outliers start: 18
  outliers final: 13
  residues processed: 257
  average time/residue: 0.3826
  time to fit residues: 151.1368
Evaluate side-chains
  239 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 225
  time to evaluate  : 2.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1666 LEU
Chi-restraints excluded: chain A residue 2135 GLU
Chi-restraints excluded: chain A residue 2157 LEU
Chi-restraints excluded: chain A residue 2276 THR
Chi-restraints excluded: chain A residue 2478 ASP
Chi-restraints excluded: chain A residue 2557 VAL
Chi-restraints excluded: chain A residue 2822 ILE
Chi-restraints excluded: chain A residue 3478 LEU
Chi-restraints excluded: chain A residue 3560 LEU
Chi-restraints excluded: chain A residue 3610 THR
Chi-restraints excluded: chain A residue 3697 THR
Chi-restraints excluded: chain A residue 3734 LEU
Chi-restraints excluded: chain A residue 4065 GLN
Chi-restraints excluded: chain A residue 4588 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 285
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 1 optimal weight:    5.9990
   chunk 166 optimal weight:    2.9990
   chunk 154 optimal weight:    3.9990
   chunk 156 optimal weight:    3.9990
   chunk 214 optimal weight:    3.9990
   chunk 158 optimal weight:    0.0970
   chunk 280 optimal weight:    1.9990
   chunk 113 optimal weight:    0.8980
   chunk 119 optimal weight:    0.8980
   chunk 195 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A3751 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.141366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.109786 restraints weight = 46516.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.57
r_work: 0.3266 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3172
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3172
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  23543  Z= 0.116
  Angle     :  0.489   8.200  31936  Z= 0.245
  Chirality :  0.040   0.273   3596
  Planarity :  0.004   0.048   4093
  Dihedral  :  5.891 106.667   3178
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  8.09 %
    Favored  : 91.00 %
  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:  2.27 (0.16), residues: 2854
  helix:  2.32 (0.13), residues: 1670
  sheet: -0.74 (0.33), residues: 232
  loop :  0.75 (0.21), residues: 952

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A2234 
 HIS   0.003   0.001   HIS A2588 
 PHE   0.013   0.001   PHE A2912 
 TYR   0.017   0.001   TYR A2748 
 ARG   0.008   0.000   ARG A3164 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03573 ( 1393)
  hydrogen bonds       : angle       3.96292 ( 4047)
  covalent geometry    : bond        0.00263 (23543)
  covalent geometry    : angle       0.48928 (31936)

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

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

  5708 Ramachandran restraints generated.
    2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5708 Ramachandran restraints generated.
    2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 243
  time to evaluate  : 2.640 
Fit side-chains
REVERT: A 1694 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7737 (mp0)
REVERT: A 1726 ILE cc_start: 0.8343 (mt) cc_final: 0.8095 (tt)
REVERT: A 1769 MET cc_start: 0.7796 (mtp) cc_final: 0.7573 (mtp)
REVERT: A 2124 GLU cc_start: 0.7669 (mp0) cc_final: 0.7267 (pm20)
REVERT: A 2573 ASP cc_start: 0.8885 (m-30) cc_final: 0.8613 (m-30)
REVERT: A 3049 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8130 (mt-10)
REVERT: A 3132 LYS cc_start: 0.8469 (mmmt) cc_final: 0.7739 (mtmt)
REVERT: A 3497 LYS cc_start: 0.8419 (pptt) cc_final: 0.7944 (tttm)
REVERT: A 3734 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8172 (tp)
REVERT: A 4056 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8463 (mt-10)
REVERT: A 4281 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7971 (tm-30)
REVERT: A 4287 LYS cc_start: 0.8109 (mtmm) cc_final: 0.7650 (mttm)
REVERT: A 4502 LYS cc_start: 0.7730 (pttp) cc_final: 0.7214 (mttp)
  outliers start: 23
  outliers final: 15
  residues processed: 263
  average time/residue: 0.3849
  time to fit residues: 155.4508
Evaluate side-chains
  241 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 224
  time to evaluate  : 2.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1666 LEU
Chi-restraints excluded: chain A residue 1694 GLU
Chi-restraints excluded: chain A residue 1705 VAL
Chi-restraints excluded: chain A residue 2135 GLU
Chi-restraints excluded: chain A residue 2157 LEU
Chi-restraints excluded: chain A residue 2276 THR
Chi-restraints excluded: chain A residue 2429 SER
Chi-restraints excluded: chain A residue 2478 ASP
Chi-restraints excluded: chain A residue 2557 VAL
Chi-restraints excluded: chain A residue 2822 ILE
Chi-restraints excluded: chain A residue 3610 THR
Chi-restraints excluded: chain A residue 3697 THR
Chi-restraints excluded: chain A residue 3734 LEU
Chi-restraints excluded: chain A residue 4061 GLU
Chi-restraints excluded: chain A residue 4065 GLN
Chi-restraints excluded: chain A residue 4390 LEU
Chi-restraints excluded: chain A residue 4516 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 285
   random chunks:
   chunk 158 optimal weight:    6.9990
   chunk 176 optimal weight:    1.9990
   chunk 228 optimal weight:    2.9990
   chunk 128 optimal weight:    5.9990
   chunk 174 optimal weight:    0.8980
   chunk 140 optimal weight:    4.9990
   chunk 94 optimal weight:    0.5980
   chunk 215 optimal weight:   10.0000
   chunk 188 optimal weight:    0.8980
   chunk 217 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0970
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A2476 HIS
A3751 GLN
A4589 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.138758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.106018 restraints weight = 45150.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 2.57
r_work: 0.3241 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3121
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3121 r_free = 0.3121    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3121 r_free = 0.3121    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3121
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8656
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  23543  Z= 0.121
  Angle     :  0.490   9.168  31936  Z= 0.246
  Chirality :  0.040   0.270   3596
  Planarity :  0.004   0.048   4093
  Dihedral  :  5.773 103.092   3178
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  8.57 %
    Favored  : 90.60 %
  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:  2.27 (0.16), residues: 2854
  helix:  2.33 (0.13), residues: 1671
  sheet: -0.81 (0.32), residues: 238
  loop :  0.76 (0.21), residues: 945

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A2234 
 HIS   0.002   0.001   HIS A1810 
 PHE   0.013   0.001   PHE A2912 
 TYR   0.016   0.001   TYR A1546 
 ARG   0.006   0.000   ARG A2801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03560 ( 1393)
  hydrogen bonds       : angle       3.94738 ( 4047)
  covalent geometry    : bond        0.00276 (23543)
  covalent geometry    : angle       0.48962 (31936)

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

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

  5708 Ramachandran restraints generated.
    2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5708 Ramachandran restraints generated.
    2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 240
  time to evaluate  : 2.683 
Fit side-chains
REVERT: A 1707 LYS cc_start: 0.8112 (tttm) cc_final: 0.7653 (ttmt)
REVERT: A 1726 ILE cc_start: 0.8392 (mt) cc_final: 0.8141 (tt)
REVERT: A 2124 GLU cc_start: 0.7709 (mp0) cc_final: 0.7285 (pm20)
REVERT: A 2573 ASP cc_start: 0.8892 (m-30) cc_final: 0.8593 (m-30)
REVERT: A 2614 ASP cc_start: 0.8704 (m-30) cc_final: 0.7735 (t0)
REVERT: A 3049 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8105 (mt-10)
REVERT: A 3132 LYS cc_start: 0.8470 (mmmt) cc_final: 0.7693 (mttt)
REVERT: A 3497 LYS cc_start: 0.8427 (pptt) cc_final: 0.7911 (tttm)
REVERT: A 3734 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8128 (tp)
REVERT: A 4056 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8402 (mt-10)
REVERT: A 4281 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7953 (tm-30)
REVERT: A 4287 LYS cc_start: 0.8139 (mtmm) cc_final: 0.7661 (mttm)
REVERT: A 4502 LYS cc_start: 0.7731 (pttp) cc_final: 0.7059 (mttp)
  outliers start: 21
  outliers final: 17
  residues processed: 259
  average time/residue: 0.3906
  time to fit residues: 155.9257
Evaluate side-chains
  248 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 230
  time to evaluate  : 2.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1666 LEU
Chi-restraints excluded: chain A residue 1705 VAL
Chi-restraints excluded: chain A residue 1797 LEU
Chi-restraints excluded: chain A residue 1830 ILE
Chi-restraints excluded: chain A residue 2135 GLU
Chi-restraints excluded: chain A residue 2157 LEU
Chi-restraints excluded: chain A residue 2276 THR
Chi-restraints excluded: chain A residue 2372 ASP
Chi-restraints excluded: chain A residue 2429 SER
Chi-restraints excluded: chain A residue 2478 ASP
Chi-restraints excluded: chain A residue 2557 VAL
Chi-restraints excluded: chain A residue 2822 ILE
Chi-restraints excluded: chain A residue 3560 LEU
Chi-restraints excluded: chain A residue 3610 THR
Chi-restraints excluded: chain A residue 3697 THR
Chi-restraints excluded: chain A residue 3734 LEU
Chi-restraints excluded: chain A residue 4065 GLN
Chi-restraints excluded: chain A residue 4516 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 285
   random chunks:
   chunk 160 optimal weight:    4.9990
   chunk 220 optimal weight:    0.0000
   chunk 91 optimal weight:    4.9990
   chunk 254 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0770
   chunk 277 optimal weight:    4.9990
   chunk 284 optimal weight:    2.9990
   chunk 236 optimal weight:    4.9990
   chunk 215 optimal weight:   10.0000
   chunk 87 optimal weight:    0.9990
   chunk 272 optimal weight:    0.9990
   overall best weight:    1.0148

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

Flipped N/Q/H residues before XYZ refinement:
A3751 GLN
A4589 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.141219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.107289 restraints weight = 53121.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 2.82
r_work: 0.3234 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3282
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3282
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.2196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  23543  Z= 0.128
  Angle     :  0.494   8.063  31936  Z= 0.248
  Chirality :  0.040   0.265   3596
  Planarity :  0.004   0.048   4093
  Dihedral  :  5.669 100.354   3178
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  8.88 %
    Favored  : 90.21 %
  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:  2.23 (0.16), residues: 2854
  helix:  2.30 (0.13), residues: 1673
  sheet: -0.88 (0.32), residues: 240
  loop :  0.77 (0.21), residues: 941

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A2234 
 HIS   0.003   0.001   HIS A2588 
 PHE   0.020   0.001   PHE A2949 
 TYR   0.018   0.001   TYR A2748 
 ARG   0.005   0.000   ARG A2801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03624 ( 1393)
  hydrogen bonds       : angle       3.92475 ( 4047)
  covalent geometry    : bond        0.00296 (23543)
  covalent geometry    : angle       0.49395 (31936)

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

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

  5708 Ramachandran restraints generated.
    2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5708 Ramachandran restraints generated.
    2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 235
  time to evaluate  : 2.473 
Fit side-chains
REVERT: A 1694 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7649 (mp0)
REVERT: A 1707 LYS cc_start: 0.8010 (tttm) cc_final: 0.7540 (ttmt)
REVERT: A 1726 ILE cc_start: 0.8404 (mt) cc_final: 0.8164 (tt)
REVERT: A 1814 GLU cc_start: 0.7570 (tp30) cc_final: 0.6968 (tp30)
REVERT: A 2124 GLU cc_start: 0.7564 (mp0) cc_final: 0.7278 (pm20)
REVERT: A 2573 ASP cc_start: 0.8682 (m-30) cc_final: 0.8406 (m-30)
REVERT: A 2614 ASP cc_start: 0.8506 (m-30) cc_final: 0.7716 (t0)
REVERT: A 3049 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8049 (mt-10)
REVERT: A 3132 LYS cc_start: 0.8449 (mmmt) cc_final: 0.7733 (mttt)
REVERT: A 3497 LYS cc_start: 0.8405 (pptt) cc_final: 0.7926 (tttm)
REVERT: A 3551 GLU cc_start: 0.7719 (mp0) cc_final: 0.7431 (mp0)
REVERT: A 3734 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8151 (tp)
REVERT: A 3770 LEU cc_start: 0.8589 (mp) cc_final: 0.8285 (tt)
REVERT: A 3847 LYS cc_start: 0.7964 (ttmm) cc_final: 0.7633 (mtmt)
REVERT: A 4056 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8292 (mt-10)
REVERT: A 4281 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7920 (tm-30)
REVERT: A 4287 LYS cc_start: 0.8067 (mtmm) cc_final: 0.7622 (mttm)
REVERT: A 4457 LYS cc_start: 0.7815 (ttpp) cc_final: 0.7456 (ttmm)
REVERT: A 4502 LYS cc_start: 0.7712 (pttp) cc_final: 0.7065 (mttp)
  outliers start: 23
  outliers final: 17
  residues processed: 256
  average time/residue: 0.3804
  time to fit residues: 149.8935
Evaluate side-chains
  246 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 227
  time to evaluate  : 2.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1666 LEU
Chi-restraints excluded: chain A residue 1694 GLU
Chi-restraints excluded: chain A residue 1705 VAL
Chi-restraints excluded: chain A residue 1797 LEU
Chi-restraints excluded: chain A residue 2135 GLU
Chi-restraints excluded: chain A residue 2157 LEU
Chi-restraints excluded: chain A residue 2276 THR
Chi-restraints excluded: chain A residue 2372 ASP
Chi-restraints excluded: chain A residue 2429 SER
Chi-restraints excluded: chain A residue 2478 ASP
Chi-restraints excluded: chain A residue 2557 VAL
Chi-restraints excluded: chain A residue 3478 LEU
Chi-restraints excluded: chain A residue 3560 LEU
Chi-restraints excluded: chain A residue 3610 THR
Chi-restraints excluded: chain A residue 3687 GLU
Chi-restraints excluded: chain A residue 3697 THR
Chi-restraints excluded: chain A residue 3734 LEU
Chi-restraints excluded: chain A residue 4065 GLN
Chi-restraints excluded: chain A residue 4516 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 285
   random chunks:
   chunk 175 optimal weight:    2.9990
   chunk 260 optimal weight:    0.7980
   chunk 193 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9980
   chunk 150 optimal weight:    0.9980
   chunk 92 optimal weight:    0.0870
   chunk 53 optimal weight:    2.9990
   chunk 15 optimal weight:    0.1980
   chunk 184 optimal weight:    0.9990
   chunk 116 optimal weight:    0.0980
   chunk 250 optimal weight:    0.9990
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
A3751 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.142970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.110189 restraints weight = 47835.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.82
r_work: 0.3267 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3304
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3304 r_free = 0.3304    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3304 r_free = 0.3304    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3304
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  23543  Z= 0.099
  Angle     :  0.479   9.865  31936  Z= 0.239
  Chirality :  0.039   0.270   3596
  Planarity :  0.003   0.047   4093
  Dihedral  :  5.490  95.149   3178
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  9.32 %
    Favored  : 89.97 %
  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:  2.33 (0.16), residues: 2854
  helix:  2.39 (0.13), residues: 1668
  sheet: -0.84 (0.32), residues: 238
  loop :  0.79 (0.21), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A2234 
 HIS   0.002   0.000   HIS A2445 
 PHE   0.012   0.001   PHE A2912 
 TYR   0.016   0.001   TYR A2748 
 ARG   0.007   0.000   ARG A3164 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03374 ( 1393)
  hydrogen bonds       : angle       3.84136 ( 4047)
  covalent geometry    : bond        0.00212 (23543)
  covalent geometry    : angle       0.47851 (31936)

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

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

  5708 Ramachandran restraints generated.
    2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5708 Ramachandran restraints generated.
    2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 250
  time to evaluate  : 2.711 
Fit side-chains
REVERT: A 1707 LYS cc_start: 0.7976 (tttm) cc_final: 0.7509 (ttmt)
REVERT: A 1726 ILE cc_start: 0.8322 (mt) cc_final: 0.8105 (tt)
REVERT: A 1814 GLU cc_start: 0.7570 (tp30) cc_final: 0.6966 (tp30)
REVERT: A 2113 ARG cc_start: 0.7888 (mmp80) cc_final: 0.7674 (mmp80)
REVERT: A 2124 GLU cc_start: 0.7537 (mp0) cc_final: 0.7300 (pm20)
REVERT: A 2320 ASP cc_start: 0.8161 (m-30) cc_final: 0.7923 (m-30)
REVERT: A 2481 MET cc_start: 0.8478 (tpp) cc_final: 0.8112 (ttt)
REVERT: A 2573 ASP cc_start: 0.8654 (m-30) cc_final: 0.8374 (m-30)
REVERT: A 2614 ASP cc_start: 0.8500 (m-30) cc_final: 0.7762 (t0)
REVERT: A 3049 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8044 (mt-10)
REVERT: A 3132 LYS cc_start: 0.8447 (mmmt) cc_final: 0.7700 (mtmt)
REVERT: A 3497 LYS cc_start: 0.8374 (pptt) cc_final: 0.7906 (tttm)
REVERT: A 3734 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8076 (tp)
REVERT: A 3847 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7624 (mtmt)
REVERT: A 4056 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8228 (mt-10)
REVERT: A 4281 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7863 (tm-30)
REVERT: A 4287 LYS cc_start: 0.8053 (mtmm) cc_final: 0.7612 (mttm)
REVERT: A 4502 LYS cc_start: 0.7724 (pttp) cc_final: 0.7066 (mttp)
  outliers start: 18
  outliers final: 13
  residues processed: 266
  average time/residue: 0.3878
  time to fit residues: 160.4048
Evaluate side-chains
  247 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 233
  time to evaluate  : 2.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1666 LEU
Chi-restraints excluded: chain A residue 1705 VAL
Chi-restraints excluded: chain A residue 1797 LEU
Chi-restraints excluded: chain A residue 2135 GLU
Chi-restraints excluded: chain A residue 2157 LEU
Chi-restraints excluded: chain A residue 2276 THR
Chi-restraints excluded: chain A residue 2372 ASP
Chi-restraints excluded: chain A residue 2557 VAL
Chi-restraints excluded: chain A residue 3478 LEU
Chi-restraints excluded: chain A residue 3560 LEU
Chi-restraints excluded: chain A residue 3610 THR
Chi-restraints excluded: chain A residue 3697 THR
Chi-restraints excluded: chain A residue 3734 LEU
Chi-restraints excluded: chain A residue 4516 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 285
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 254 optimal weight:    0.5980
   chunk 73 optimal weight:    0.2980
   chunk 27 optimal weight:    0.8980
   chunk 176 optimal weight:    4.9990
   chunk 184 optimal weight:    2.9990
   chunk 188 optimal weight:    9.9990
   chunk 24 optimal weight:    0.0870
   chunk 243 optimal weight:    3.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A3751 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.142837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.110473 restraints weight = 46707.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 2.72
r_work: 0.3280 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3320
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3320 r_free = 0.3320    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3320 r_free = 0.3320    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3320
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  23543  Z= 0.104
  Angle     :  0.486   9.204  31936  Z= 0.243
  Chirality :  0.039   0.285   3596
  Planarity :  0.004   0.049   4093
  Dihedral  :  5.395  90.645   3178
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  9.75 %
    Favored  : 89.58 %
  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:  2.35 (0.16), residues: 2854
  helix:  2.42 (0.13), residues: 1670
  sheet: -0.81 (0.31), residues: 245
  loop :  0.79 (0.21), residues: 939

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A2234 
 HIS   0.003   0.000   HIS A2588 
 PHE   0.013   0.001   PHE A2912 
 TYR   0.016   0.001   TYR A1546 
 ARG   0.007   0.000   ARG A3164 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03379 ( 1393)
  hydrogen bonds       : angle       3.82262 ( 4047)
  covalent geometry    : bond        0.00230 (23543)
  covalent geometry    : angle       0.48595 (31936)

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

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

  5708 Ramachandran restraints generated.
    2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5708 Ramachandran restraints generated.
    2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 247
  time to evaluate  : 2.534 
Fit side-chains
REVERT: A 1707 LYS cc_start: 0.7960 (tttm) cc_final: 0.7524 (ttmt)
REVERT: A 1726 ILE cc_start: 0.8374 (mt) cc_final: 0.8167 (tt)
REVERT: A 1814 GLU cc_start: 0.7499 (tp30) cc_final: 0.6900 (tp30)
REVERT: A 2320 ASP cc_start: 0.8189 (m-30) cc_final: 0.7942 (m-30)
REVERT: A 2481 MET cc_start: 0.8462 (tpp) cc_final: 0.8106 (ttt)
REVERT: A 2573 ASP cc_start: 0.8600 (m-30) cc_final: 0.8321 (m-30)
REVERT: A 2614 ASP cc_start: 0.8421 (m-30) cc_final: 0.7778 (t0)
REVERT: A 2953 MET cc_start: 0.8335 (mmm) cc_final: 0.7982 (mmt)
REVERT: A 3132 LYS cc_start: 0.8423 (mmmt) cc_final: 0.7727 (mtmt)
REVERT: A 3497 LYS cc_start: 0.8398 (pptt) cc_final: 0.7973 (tttm)
REVERT: A 3551 GLU cc_start: 0.7679 (mp0) cc_final: 0.7414 (mp0)
REVERT: A 3734 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8150 (tp)
REVERT: A 3847 LYS cc_start: 0.7914 (ttmm) cc_final: 0.7604 (mtmt)
REVERT: A 4247 MET cc_start: 0.8825 (mmm) cc_final: 0.8575 (mtp)
REVERT: A 4281 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7861 (tm-30)
REVERT: A 4287 LYS cc_start: 0.8021 (mtmm) cc_final: 0.7599 (mttm)
REVERT: A 4502 LYS cc_start: 0.7786 (pttp) cc_final: 0.7131 (mttp)
  outliers start: 17
  outliers final: 14
  residues processed: 261
  average time/residue: 0.3856
  time to fit residues: 155.1298
Evaluate side-chains
  247 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 232
  time to evaluate  : 2.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1666 LEU
Chi-restraints excluded: chain A residue 1705 VAL
Chi-restraints excluded: chain A residue 1797 LEU
Chi-restraints excluded: chain A residue 2135 GLU
Chi-restraints excluded: chain A residue 2157 LEU
Chi-restraints excluded: chain A residue 2276 THR
Chi-restraints excluded: chain A residue 2372 ASP
Chi-restraints excluded: chain A residue 2557 VAL
Chi-restraints excluded: chain A residue 3478 LEU
Chi-restraints excluded: chain A residue 3560 LEU
Chi-restraints excluded: chain A residue 3610 THR
Chi-restraints excluded: chain A residue 3687 GLU
Chi-restraints excluded: chain A residue 3697 THR
Chi-restraints excluded: chain A residue 3734 LEU
Chi-restraints excluded: chain A residue 4516 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 285
   random chunks:
   chunk 255 optimal weight:    0.9980
   chunk 62 optimal weight:    0.0980
   chunk 88 optimal weight:    1.9990
   chunk 180 optimal weight:    0.0170
   chunk 125 optimal weight:    0.9990
   chunk 280 optimal weight:    0.9980
   chunk 213 optimal weight:    0.6980
   chunk 253 optimal weight:    0.9980
   chunk 258 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 191 optimal weight:    0.1980
   overall best weight:    0.4018

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

Flipped N/Q/H residues before XYZ refinement:
A1855 GLN
A1867 ASN
A3751 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.140583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.108252 restraints weight = 45167.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 2.57
r_work: 0.3289 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3197
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3197
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  23543  Z= 0.098
  Angle     :  0.484   9.261  31936  Z= 0.242
  Chirality :  0.039   0.276   3596
  Planarity :  0.004   0.048   4093
  Dihedral  :  5.291  86.602   3178
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  9.87 %
    Favored  : 89.58 %
  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:  2.38 (0.16), residues: 2854
  helix:  2.44 (0.13), residues: 1670
  sheet: -0.84 (0.32), residues: 242
  loop :  0.81 (0.21), residues: 942

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A2234 
 HIS   0.004   0.000   HIS A2588 
 PHE   0.011   0.001   PHE A2912 
 TYR   0.016   0.001   TYR A2748 
 ARG   0.007   0.000   ARG A4230 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03280 ( 1393)
  hydrogen bonds       : angle       3.77816 ( 4047)
  covalent geometry    : bond        0.00210 (23543)
  covalent geometry    : angle       0.48439 (31936)

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

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

  5708 Ramachandran restraints generated.
    2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5708 Ramachandran restraints generated.
    2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 249
  time to evaluate  : 2.539 
Fit side-chains
REVERT: A 1707 LYS cc_start: 0.8114 (tttm) cc_final: 0.7659 (ttmt)
REVERT: A 1726 ILE cc_start: 0.8384 (mt) cc_final: 0.8169 (tt)
REVERT: A 1814 GLU cc_start: 0.7749 (tp30) cc_final: 0.7230 (tp30)
REVERT: A 1867 ASN cc_start: 0.8473 (m-40) cc_final: 0.8057 (p0)
REVERT: A 2481 MET cc_start: 0.8467 (tpp) cc_final: 0.8177 (ttt)
REVERT: A 2573 ASP cc_start: 0.8812 (m-30) cc_final: 0.8518 (m-30)
REVERT: A 2614 ASP cc_start: 0.8640 (m-30) cc_final: 0.8000 (t0)
REVERT: A 3132 LYS cc_start: 0.8458 (mmmt) cc_final: 0.7691 (mtmt)
REVERT: A 3497 LYS cc_start: 0.8367 (pptt) cc_final: 0.7939 (tttm)
REVERT: A 3551 GLU cc_start: 0.7872 (mp0) cc_final: 0.7610 (mp0)
REVERT: A 3732 LEU cc_start: 0.9201 (mp) cc_final: 0.8998 (mt)
REVERT: A 3734 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8158 (tp)
REVERT: A 3770 LEU cc_start: 0.8556 (mp) cc_final: 0.8241 (tt)
REVERT: A 3847 LYS cc_start: 0.8058 (ttmm) cc_final: 0.7669 (mtmt)
REVERT: A 4281 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7882 (tm-30)
REVERT: A 4287 LYS cc_start: 0.8090 (mtmm) cc_final: 0.7638 (mttm)
REVERT: A 4502 LYS cc_start: 0.7815 (pttp) cc_final: 0.7125 (mttp)
  outliers start: 14
  outliers final: 13
  residues processed: 261
  average time/residue: 0.3877
  time to fit residues: 156.9045
Evaluate side-chains
  251 residues out of total 2531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 237
  time to evaluate  : 3.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1666 LEU
Chi-restraints excluded: chain A residue 1705 VAL
Chi-restraints excluded: chain A residue 1797 LEU
Chi-restraints excluded: chain A residue 2135 GLU
Chi-restraints excluded: chain A residue 2157 LEU
Chi-restraints excluded: chain A residue 2276 THR
Chi-restraints excluded: chain A residue 2372 ASP
Chi-restraints excluded: chain A residue 2557 VAL
Chi-restraints excluded: chain A residue 3478 LEU
Chi-restraints excluded: chain A residue 3560 LEU
Chi-restraints excluded: chain A residue 3610 THR
Chi-restraints excluded: chain A residue 3697 THR
Chi-restraints excluded: chain A residue 3734 LEU
Chi-restraints excluded: chain A residue 4516 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 285
   random chunks:
   chunk 123 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 133 optimal weight:    0.0980
   chunk 90 optimal weight:    2.9990
   chunk 157 optimal weight:    0.0980
   chunk 25 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0570
   chunk 212 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9990
   chunk 250 optimal weight:    0.9990
   chunk 80 optimal weight:    0.6980
   overall best weight:    0.3900

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

Flipped N/Q/H residues before XYZ refinement:
A3527 ASN
A3751 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.142868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.109084 restraints weight = 59027.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 3.02
r_work: 0.3251 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3304
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3304 r_free = 0.3304    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3304 r_free = 0.3304    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3304
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.2472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  23543  Z= 0.097
  Angle     :  0.483   9.097  31936  Z= 0.241
  Chirality :  0.039   0.274   3596
  Planarity :  0.004   0.049   4093
  Dihedral  :  5.215  84.217   3178
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  9.99 %
    Favored  : 89.38 %
  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:  2.40 (0.16), residues: 2854
  helix:  2.45 (0.13), residues: 1670
  sheet: -0.81 (0.32), residues: 244
  loop :  0.82 (0.21), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A2234 
 HIS   0.003   0.000   HIS A2588 
 PHE   0.014   0.001   PHE A2165 
 TYR   0.016   0.001   TYR A1546 
 ARG   0.007   0.000   ARG A3164 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03250 ( 1393)
  hydrogen bonds       : angle       3.76287 ( 4047)
  covalent geometry    : bond        0.00208 (23543)
  covalent geometry    : angle       0.48310 (31936)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 14602.00 seconds
wall clock time: 252 minutes 37.67 seconds (15157.67 seconds total)