Starting phenix.real_space_refine
on Fri Sep 19 10:08:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dha_46861/09_2025/9dha_46861.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dha_46861/09_2025/9dha_46861.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dha_46861/09_2025/9dha_46861.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dha_46861/09_2025/9dha_46861.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dha_46861/09_2025/9dha_46861.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dha_46861/09_2025/9dha_46861.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.028
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      10      5.49       5
     Mg      1      5.21       5
     S     122      5.16       5
     C   15626      2.51       5
     N    4246      2.21       5
     O    4583      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 24588
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 24471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3038, 24471
          Classifications: {'peptide': 3038}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 130, 'TRANS': 2904}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 117
          Unusual residues: {' MG': 1, 'ADP': 2, 'ANP': 1, 'ATP': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 5.61, per 1000 atoms: 0.23
  Number of scatterers: 24588
  At special positions: 0
  Unit cell: (119.202, 170.123, 172.438, 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     122     16.00
     P      10     15.00
     Mg      1     11.99
     O    4583      8.00
     N    4246      7.00
     C   15626      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: 2.34
  Conformation dependent library (CDL) restraints added in 878.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  6056 Ramachandran restraints generated.
    3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5780

  Finding SS restraints...
    Secondary structure from input PDB file:
      138 helices and 20 sheets defined
      63.9% alpha, 8.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1327 through 1349
      removed outlier: 3.730A  pdb=" N   GLN A1349 " --> pdb=" O   GLN A1345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1355 through 1372
    Processing helix  chain 'A' and resid 1375 through 1379
      removed outlier: 3.552A  pdb=" N   GLN A1379 " --> pdb=" O   ARG A1376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1380 through 1404
      removed outlier: 4.360A  pdb=" N   MET A1398 " --> pdb=" O   MET A1394 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   LEU A1399 " --> pdb=" O   LYS A1395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1410 through 1421
    Processing helix  chain 'A' and resid 1430 through 1437
      removed outlier: 3.621A  pdb=" N   ILE A1434 " --> pdb=" O   THR A1430 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL A1437 " --> pdb=" O   GLN A1433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1442 through 1473
      removed outlier: 3.519A  pdb=" N   VAL A1446 " --> pdb=" O   ASN A1442 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   THR A1472 " --> pdb=" O   GLU A1468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1489 through 1508
      removed outlier: 3.507A  pdb=" N   LEU A1493 " --> pdb=" O   GLY A1489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1516 through 1552
      removed outlier: 3.682A  pdb=" N   ASP A1539 " --> pdb=" O   ASP A1535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1555 through 1561
    Processing helix  chain 'A' and resid 1561 through 1585
      removed outlier: 3.572A  pdb=" N   SER A1585 " --> pdb=" O   LYS A1581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1587 through 1594
    Processing helix  chain 'A' and resid 1596 through 1626
    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: 3.638A  pdb=" N   LYS A1649 " --> pdb=" O   ASN A1646 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLN A1651 " --> pdb=" O   ALA A1648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1653 through 1657
    Processing helix  chain 'A' and resid 1697 through 1729
      removed outlier: 4.075A  pdb=" N   ILE A1726 " --> pdb=" O   THR A1722 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   PHE A1727 " --> pdb=" O   GLU A1723 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1734 through 1745
      removed outlier: 3.648A  pdb=" N   TYR A1745 " --> pdb=" O   TRP A1741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1746 through 1773
      removed outlier: 4.136A  pdb=" N   GLY A1771 " --> pdb=" O   SER A1767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1775 through 1798
      removed outlier: 3.556A  pdb=" N   MET A1798 " --> pdb=" O   ASP A1794 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1801 through 1829
      removed outlier: 3.686A  pdb=" N   HIS A1817 " --> pdb=" O   THR A1813 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LYS A1829 " --> pdb=" O   LEU A1825 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1835 through 1841
    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 1939 through 1952
      removed outlier: 4.592A  pdb=" N   ARG A1943 " --> pdb=" O   GLN A1939 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1959 through 1963
    Processing helix  chain 'A' and resid 1964 through 1985
      removed outlier: 3.566A  pdb=" N   HIS A1985 " --> pdb=" O   ALA A1981 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2029 through 2034
      removed outlier: 4.618A  pdb=" N   LYS A2034 " --> pdb=" O   ASP A2030 " (cutoff:3.500A)
    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: 3.940A  pdb=" N   GLU A2078 " --> pdb=" O   LYS A2074 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2089 through 2118
    Processing helix  chain 'A' and resid 2123 through 2130
      removed outlier: 3.852A  pdb=" N   ASN A2130 " --> pdb=" O   GLU A2126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2132 through 2146
      removed outlier: 3.632A  pdb=" N   ILE A2136 " --> pdb=" O   PRO A2132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2147 through 2149
      No H-bonds generated for 'chain 'A' and resid 2147 through 2149'
    Processing helix  chain 'A' and resid 2153 through 2165
    Processing helix  chain 'A' and resid 2175 through 2189
    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: 3.507A  pdb=" N   ILE A2259 " --> pdb=" O   PRO A2256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2260 through 2266
      removed outlier: 3.647A  pdb=" N   TYR A2265 " --> pdb=" O   LYS A2261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2278 through 2290
    Processing helix  chain 'A' and resid 2315 through 2320
    Processing helix  chain 'A' and resid 2352 through 2359
    Processing helix  chain 'A' and resid 2365 through 2369
    Processing helix  chain 'A' and resid 2370 through 2385
    Processing helix  chain 'A' and resid 2395 through 2400
    Processing helix  chain 'A' and resid 2410 through 2424
    Processing helix  chain 'A' and resid 2425 through 2428
      removed outlier: 3.722A  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 2443
      removed outlier: 3.950A  pdb=" N   GLN A2442 " --> pdb=" O   GLU A2438 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU A2443 " --> pdb=" O   HIS A2439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2450 through 2476
      removed outlier: 3.578A  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 2571 through 2587
      removed outlier: 4.026A  pdb=" N   GLU A2587 " --> pdb=" O   THR A2583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2600 through 2612
      removed outlier: 3.797A  pdb=" N   LEU A2612 " --> pdb=" O   ALA A2608 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2627 through 2638
      removed outlier: 4.221A  pdb=" N   LEU A2631 " --> pdb=" O   THR A2627 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2677 through 2690
      removed outlier: 3.505A  pdb=" N   HIS A2689 " --> pdb=" O   GLN A2685 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2724 through 2729
    Processing helix  chain 'A' and resid 2740 through 2757
    Processing helix  chain 'A' and resid 2762 through 2764
      No H-bonds generated for 'chain 'A' and resid 2762 through 2764'
    Processing helix  chain 'A' and resid 2765 through 2784
      removed outlier: 3.545A  pdb=" N   THR A2770 " --> pdb=" O   ALA A2766 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ALA A2771 " --> pdb=" O   GLU A2767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2795 through 2811
      removed outlier: 3.932A  pdb=" N   MET A2799 " --> pdb=" O   SER A2795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2817 through 2834
      removed outlier: 3.535A  pdb=" N   LEU A2821 " --> pdb=" O   PRO A2817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2839 through 2858
    Processing helix  chain 'A' and resid 2885 through 2903
      removed outlier: 3.813A  pdb=" N   GLU A2902 " --> pdb=" O   LYS A2898 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   GLU A2903 " --> pdb=" O   VAL A2899 " (cutoff:3.500A)
    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 3001 through 3015
      removed outlier: 3.793A  pdb=" N   LEU A3005 " --> pdb=" O   ASP A3001 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   THR A3010 " --> pdb=" O   GLU A3006 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   LEU A3011 " --> pdb=" O   ARG A3007 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3022 through 3041
    Processing helix  chain 'A' and resid 3046 through 3062
    Processing helix  chain 'A' and resid 3082 through 3089
      removed outlier: 3.608A  pdb=" N   PHE A3086 " --> pdb=" O   SER A3082 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   CYS A3089 " --> pdb=" O   LEU A3085 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3098 through 3110
    Processing helix  chain 'A' and resid 3138 through 3164
    Processing helix  chain 'A' and resid 3172 through 3221
      removed outlier: 3.577A  pdb=" N   TYR A3176 " --> pdb=" O   THR A3172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3471 through 3516
      removed outlier: 4.774A  pdb=" N   ALA A3504 " --> pdb=" O   MET A3500 " (cutoff:3.500A)
      removed outlier: 5.166A  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 3553
    Processing helix  chain 'A' and resid 3555 through 3565
      removed outlier: 3.547A  pdb=" N   ARG A3559 " --> pdb=" O   ASN A3555 " (cutoff:3.500A)
    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 3642 through 3644
      No H-bonds generated for 'chain 'A' and resid 3642 through 3644'
    Processing helix  chain 'A' and resid 3645 through 3651
    Processing helix  chain 'A' and resid 3689 through 3696
    Processing helix  chain 'A' and resid 3704 through 3721
    Processing helix  chain 'A' and resid 3721 through 3734
    Processing helix  chain 'A' and resid 3736 through 3755
      removed outlier: 3.672A  pdb=" N   GLU A3755 " --> pdb=" O   GLN A3751 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3766 through 3786
      removed outlier: 3.721A  pdb=" N   LEU A3770 " --> pdb=" O   ILE A3766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3786 through 3818
      Proline residue:  A3803  - end of helix
    Processing helix  chain 'A' and resid 3819 through 3821
      No H-bonds generated for 'chain 'A' and resid 3819 through 3821'
    Processing helix  chain 'A' and resid 3828 through 3841
    Processing helix  chain 'A' and resid 3843 through 3847
    Processing helix  chain 'A' and resid 3851 through 3874
      removed outlier: 3.633A  pdb=" N   PHE A3864 " --> pdb=" O   THR A3860 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   GLY A3874 " --> pdb=" O   ARG A3870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3875 through 3878
      removed outlier: 6.066A  pdb=" N   GLN A3878 " --> pdb=" O   MET A3875 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 3875 through 3878'
    Processing helix  chain 'A' and resid 3879 through 3895
    Processing helix  chain 'A' and resid 3901 through 3911
    Processing helix  chain 'A' and resid 3912 through 3914
      No H-bonds generated for 'chain 'A' and resid 3912 through 3914'
    Processing helix  chain 'A' and resid 3928 through 3939
    Processing helix  chain 'A' and resid 3940 through 3945
      removed outlier: 6.845A  pdb=" N   ALA A3943 " --> pdb=" O   CYS A3940 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   LYS A3945 " --> pdb=" O   PRO A3942 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3946 through 3954
    Processing helix  chain 'A' and resid 3956 through 3962
    Processing helix  chain 'A' and resid 3965 through 3969
    Processing helix  chain 'A' and resid 3981 through 3997
    Processing helix  chain 'A' and resid 4000 through 4014
    Processing helix  chain 'A' and resid 4017 through 4023
      removed outlier: 4.232A  pdb=" N   ILE A4020 " --> pdb=" O   PHE A4017 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4026 through 4034
      removed outlier: 3.804A  pdb=" N   ILE A4030 " --> pdb=" O   ASP A4026 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4051 through 4063
      removed outlier: 3.806A  pdb=" N   VAL A4055 " --> pdb=" O   ALA A4051 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4073 through 4089
      removed outlier: 3.662A  pdb=" N   LYS A4089 " --> pdb=" O   ASN A4085 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4099 through 4101
      No H-bonds generated for 'chain 'A' and resid 4099 through 4101'
    Processing helix  chain 'A' and resid 4102 through 4116
      removed outlier: 3.920A  pdb=" N   SER A4115 " --> pdb=" O   LYS A4111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4135 through 4141
      removed outlier: 3.676A  pdb=" N   LEU A4139 " --> pdb=" O   PRO A4135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4152 through 4164
    Processing helix  chain 'A' and resid 4165 through 4170
      removed outlier: 3.580A  pdb=" N   ILE A4169 " --> pdb=" O   PRO A4165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4174 through 4192
      removed outlier: 4.121A  pdb=" N   ARG A4178 " --> pdb=" O   ASN A4174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4193 through 4197
    Processing helix  chain 'A' and resid 4208 through 4228
      removed outlier: 3.752A  pdb=" N   LEU A4212 " --> pdb=" O   GLY A4208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4234 through 4238
    Processing helix  chain 'A' and resid 4239 through 4250
    Processing helix  chain 'A' and resid 4252 through 4256
      removed outlier: 3.616A  pdb=" N   ARG A4255 " --> pdb=" O   TYR A4252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4258 through 4273
    Processing helix  chain 'A' and resid 4274 through 4279
    Processing helix  chain 'A' and resid 4287 through 4291
    Processing helix  chain 'A' and resid 4301 through 4311
    Processing helix  chain 'A' and resid 4317 through 4322
    Processing helix  chain 'A' and resid 4326 through 4346
    Processing helix  chain 'A' and resid 4376 through 4391
    Processing helix  chain 'A' and resid 4401 through 4406
      removed outlier: 3.831A  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 4506
      removed outlier: 7.718A  pdb=" N   ALA A4501 " --> pdb=" O   ALA A4497 " (cutoff:3.500A)
      removed outlier: 8.282A  pdb=" N   LYS A4502 " --> pdb=" O   SER A4498 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLU A4503 " --> pdb=" O   GLY A4499 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   LEU A4504 " --> pdb=" O   GLY A4500 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ASN A4506 " --> pdb=" O   LYS A4502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4512 through 4514
      No H-bonds generated for 'chain 'A' and resid 4512 through 4514'
    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 1477 through 1480
      removed outlier: 3.753A  pdb=" N   CYS A1484 " --> pdb=" O   TYR A1480 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1663 through 1666
      removed outlier: 10.511A  pdb=" N   VAL A1672 " --> pdb=" O   THR A1688 " (cutoff:3.500A)
      removed outlier: 10.976A  pdb=" N   THR A1688 " --> pdb=" O   VAL A1672 " (cutoff:3.500A)
      removed outlier: 7.518A  pdb=" N   LEU A1674 " --> pdb=" O   PHE A1686 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1843 through 1846
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1901 through 1905
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1930
      removed outlier: 6.291A  pdb=" N   GLY A1955 " --> pdb=" O   PHE A2015 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1998 through 2001
    Processing sheet with id=AA7, first strand: chain 'A' and resid 2249 through 2254
      removed outlier: 6.405A  pdb=" N   VAL A2250 " --> pdb=" O   TRP A2300 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   VAL A2302 " --> pdb=" O   VAL A2250 " (cutoff:3.500A)
      removed outlier: 5.975A  pdb=" N   HIS A2252 " --> pdb=" O   VAL A2302 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   GLN A2299 " --> pdb=" O   ARG A2340 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   MET A2342 " --> pdb=" O   GLN A2299 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   ILE A2301 " --> pdb=" O   MET A2342 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   GLU A2344 " --> pdb=" O   ILE A2301 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   PHE A2303 " --> pdb=" O   GLU A2344 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 2267 through 2268
    Processing sheet with id=AA9, first strand: chain 'A' and resid 2324 through 2326
    Processing sheet with id=AB1, first strand: chain 'A' and resid 2537 through 2539
    Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2620
      removed outlier: 6.228A  pdb=" N   LEU A2659 " --> pdb=" O   GLN A2707 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   VAL A2709 " --> pdb=" O   LEU A2659 " (cutoff:3.500A)
      removed outlier: 5.992A  pdb=" N   LEU A2661 " --> pdb=" O   VAL A2709 " (cutoff:3.500A)
      removed outlier: 7.770A  pdb=" N   ALA A2711 " --> pdb=" O   LEU A2661 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   CYS A2663 " --> pdb=" O   ALA A2711 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   LEU A2591 " --> pdb=" O   PHE A2708 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   VAL A2592 " --> pdb=" O   VAL A2734 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2644
      removed outlier: 6.705A  pdb=" N   VAL A2648 " --> pdb=" O   LYS A2702 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 2873 through 2874
    Processing sheet with id=AB5, first strand: chain 'A' and resid 2957 through 2960
      removed outlier: 6.189A  pdb=" N   ILE A2990 " --> pdb=" O   HIS A3063 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   VAL A3065 " --> pdb=" O   ILE A2990 " (cutoff:3.500A)
      removed outlier: 5.959A  pdb=" N   PHE A2992 " --> pdb=" O   VAL A3065 " (cutoff:3.500A)
      removed outlier: 7.474A  pdb=" N   THR A3067 " --> pdb=" O   PHE A2992 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   MET A2994 " --> pdb=" O   THR A3067 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   HIS A2932 " --> pdb=" O   VAL A3090 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   ASN A3092 " --> pdb=" O   HIS A2932 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   LEU A2934 " --> pdb=" O   ASN A3092 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   PHE A3094 " --> pdb=" O   LEU A2934 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   ILE A2936 " --> pdb=" O   PHE A3094 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 3610 through 3613
      removed outlier: 6.095A  pdb=" N   THR A3610 " --> pdb=" O   LEU A3634 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   GLN A3636 " --> pdb=" O   THR A3610 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   THR A3612 " --> pdb=" O   GLN A3636 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 3654 through 3656
    Processing sheet with id=AB8, first strand: chain 'A' and resid 4066 through 4070
      removed outlier: 6.022A  pdb=" N   THR A4067 " --> pdb=" O   MET A4095 " (cutoff:3.500A)
      removed outlier: 7.339A  pdb=" N   LYS A4097 " --> pdb=" O   THR A4067 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   ILE A4069 " --> pdb=" O   LYS A4097 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   VAL A4094 " --> pdb=" O   PHE A4125 " (cutoff:3.500A)
      removed outlier: 7.880A  pdb=" N   THR A4127 " --> pdb=" O   VAL A4094 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   LEU A4096 " --> pdb=" O   THR A4127 " (cutoff:3.500A)
      removed outlier: 9.017A  pdb=" N   GLU A4129 " --> pdb=" O   LEU A4096 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 4283 through 4285
      removed outlier: 3.894A  pdb=" N   ALA A4285 " --> pdb=" O   ILE A4294 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 4509 through 4510
      removed outlier: 6.229A  pdb=" N   VAL A4509 " --> pdb=" O   THR A4561 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 4563 through 4571
      removed outlier: 4.501A  pdb=" N   LEU A4563 " --> pdb=" O   LEU A4585 " (cutoff:3.500A)
      removed outlier: 7.497A  pdb=" N   ILE A4581 " --> pdb=" O   GLY A4567 " (cutoff:3.500A)
      removed outlier: 9.599A  pdb=" N   THR A4569 " --> pdb=" O   ASN A4579 " (cutoff:3.500A)
      removed outlier: 9.800A  pdb=" N   ASN A4579 " --> pdb=" O   THR A4569 " (cutoff:3.500A)
      removed outlier: 9.950A  pdb=" N   ASN A4571 " --> pdb=" O   LEU A4577 " (cutoff:3.500A)
      removed outlier: 10.162A  pdb=" N   LEU A4577 " --> pdb=" O   ASN A4571 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   PHE A4620 " --> pdb=" O   VAL A4609 " (cutoff:3.500A)
      removed outlier: 8.632A  pdb=" N   VAL A4642 " --> pdb=" O   THR A4606 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ALA A4641 " --> pdb=" O   GLN A4566 " (cutoff:3.500A)

    1456 hydrogen bonds defined for protein.
    4224 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: 7.59

  Time building geometry restraints manager: 2.94 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 7000
        1.33 -     1.45: 4042
        1.45 -     1.57: 13848
        1.57 -     1.69: 17
        1.69 -     1.81: 206
  Bond restraints: 25113
  Sorted by residual:
  bond pdb=" O3A ANP A4703 "
       pdb=" PB  ANP A4703 "
    ideal  model  delta    sigma   weight residual
    1.700  1.557  0.143 2.00e-02 2.50e+03 5.08e+01
  bond pdb=" N3B ANP A4703 "
       pdb=" PG  ANP A4703 "
    ideal  model  delta    sigma   weight residual
    1.795  1.692  0.103 2.00e-02 2.50e+03 2.64e+01
  bond pdb=" O5' ANP A4703 "
       pdb=" PA  ANP A4703 "
    ideal  model  delta    sigma   weight residual
    1.655  1.584  0.071 2.00e-02 2.50e+03 1.26e+01
  bond pdb=" O3G ANP A4703 "
       pdb=" PG  ANP A4703 "
    ideal  model  delta    sigma   weight residual
    1.528  1.580 -0.052 2.00e-02 2.50e+03 6.65e+00
  bond pdb=" O2B ANP A4703 "
       pdb=" PB  ANP A4703 "
    ideal  model  delta    sigma   weight residual
    1.508  1.556 -0.048 2.00e-02 2.50e+03 5.73e+00
  ... (remaining 25108 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.55: 33914
        3.55 -     7.11: 123
        7.11 -    10.66: 13
       10.66 -    14.22: 1
       14.22 -    17.77: 1
  Bond angle restraints: 34052
  Sorted by residual:
  angle pdb=" PB  ANP A4703 "
        pdb=" N3B ANP A4703 "
        pdb=" PG  ANP A4703 "
      ideal   model   delta    sigma   weight residual
     126.95  109.18   17.77 3.00e+00 1.11e-01 3.51e+01
  angle pdb=" CB  ARG A3206 "
        pdb=" CG  ARG A3206 "
        pdb=" CD  ARG A3206 "
      ideal   model   delta    sigma   weight residual
     111.30  120.53   -9.23 2.30e+00 1.89e-01 1.61e+01
  angle pdb=" O1B ANP A4703 "
        pdb=" PB  ANP A4703 "
        pdb=" O2B ANP A4703 "
      ideal   model   delta    sigma   weight residual
     120.08  109.39   10.69 3.00e+00 1.11e-01 1.27e+01
  angle pdb=" CA  ARG A1388 "
        pdb=" CB  ARG A1388 "
        pdb=" CG  ARG A1388 "
      ideal   model   delta    sigma   weight residual
     114.10  120.78   -6.68 2.00e+00 2.50e-01 1.11e+01
  angle pdb=" N   GLN A3792 "
        pdb=" CA  GLN A3792 "
        pdb=" CB  GLN A3792 "
      ideal   model   delta    sigma   weight residual
     110.28  115.45   -5.17 1.55e+00 4.16e-01 1.11e+01
  ... (remaining 34047 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 13728
       17.98 -    35.95: 1227
       35.95 -    53.93: 190
       53.93 -    71.90: 65
       71.90 -    89.88: 47
  Dihedral angle restraints: 15257
    sinusoidal: 6361
      harmonic: 8896
  Sorted by residual:
  dihedral pdb=" CA  LYS A2349 "
           pdb=" C   LYS A2349 "
           pdb=" N   TYR A2350 "
           pdb=" CA  TYR A2350 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.50   27.50     0      5.00e+00 4.00e-02 3.03e+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 -149.33   89.33     1      2.00e+01 2.50e-03 2.37e+01
  dihedral pdb=" CA  THR A4628 "
           pdb=" C   THR A4628 "
           pdb=" N   LYS A4629 "
           pdb=" CA  LYS A4629 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.15  -23.85     0      5.00e+00 4.00e-02 2.28e+01
  ... (remaining 15254 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 3206
       0.055 -    0.109: 561
       0.109 -    0.164: 47
       0.164 -    0.219: 1
       0.219 -    0.273: 1
  Chirality restraints: 3816
  Sorted by residual:
  chirality pdb=" C3' ANP A4703 "
            pdb=" C2' ANP A4703 "
            pdb=" C4' ANP A4703 "
            pdb=" O3' ANP A4703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.63    0.27 2.00e-01 2.50e+01 1.87e+00
  chirality pdb=" CG  LEU A3753 "
            pdb=" CB  LEU A3753 "
            pdb=" CD1 LEU A3753 "
            pdb=" CD2 LEU A3753 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 7.75e-01
  chirality pdb=" CB  THR A3685 "
            pdb=" CA  THR A3685 "
            pdb=" OG1 THR A3685 "
            pdb=" CG2 THR A3685 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.60e-01
  ... (remaining 3813 not shown)

  Planarity restraints: 4362
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1388 "    0.172 9.50e-02 1.11e+02   7.76e-02 4.63e+00
        pdb=" NE  ARG A1388 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1388 "    0.015 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1388 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1388 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A2524 "    0.033 5.00e-02 4.00e+02   4.99e-02 3.98e+00
        pdb=" N   PRO A2525 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A2525 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A2525 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A2731 "    0.029 5.00e-02 4.00e+02   4.36e-02 3.04e+00
        pdb=" N   PRO A2732 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A2732 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A2732 "    0.024 5.00e-02 4.00e+02
  ... (remaining 4359 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 256
        2.57 -     3.15: 20918
        3.15 -     3.73: 40959
        3.73 -     4.32: 53455
        4.32 -     4.90: 88391
  Nonbonded interactions: 203979
  Sorted by model distance:
  nonbonded pdb=" O1B ATP A4702 "
            pdb="MG    MG A4705 "
     model   vdw
     1.985 2.170
  nonbonded pdb=" O2G ATP A4702 "
            pdb="MG    MG A4705 "
     model   vdw
     2.113 2.170
  nonbonded pdb=" O   PRO A1511 "
            pdb=" NZ  LYS A1514 "
     model   vdw
     2.114 3.120
  nonbonded pdb=" OH  TYR A2265 "
            pdb=" O   TRP A2311 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" NH1 ARG A3167 "
            pdb=" O   THR A3168 "
     model   vdw
     2.196 3.120
  ... (remaining 203974 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.940
  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:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     26.010
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.050
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
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      :  0.003   0.143  25113  Z= 0.144
  Angle     :  0.624  17.771  34052  Z= 0.319
  Chirality :  0.040   0.273   3816
  Planarity :  0.004   0.078   4362
  Dihedral  : 14.917  89.877   9477
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.16), residues: 3028
  helix:  1.59 (0.13), residues: 1730
  sheet: -0.50 (0.33), residues: 239
  loop : -0.18 (0.20), residues: 1059

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A1388 
 TYR   0.017   0.001   TYR A1393 
 PHE   0.028   0.001   PHE A2682 
 TRP   0.021   0.001   TRP A3489 
 HIS   0.007   0.001   HIS A2730 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (25113)
  covalent geometry    : angle       0.62383 (34052)
  hydrogen bonds       : bond        0.12980 ( 1456)
  hydrogen bonds       : angle       5.79652 ( 4224)

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

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

  6056 Ramachandran restraints generated.
    3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6056 Ramachandran restraints generated.
    3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 232
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1457 MET cc_start: 0.8976 (ttt) cc_final: 0.8557 (mtp)
REVERT: A 1531 MET cc_start: 0.8765 (tpt) cc_final: 0.8534 (tpt)
REVERT: A 2953 MET cc_start: 0.7708 (ttm) cc_final: 0.7392 (mtp)
REVERT: A 3205 LEU cc_start: 0.9076 (mt) cc_final: 0.8150 (mt)
REVERT: A 3776 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8413 (tm-30)
REVERT: A 4063 ASN cc_start: 0.8850 (m-40) cc_final: 0.8641 (m-40)
REVERT: A 4190 ILE cc_start: 0.9065 (pt) cc_final: 0.8790 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 232
  average time/residue: 0.1592
  time to fit residues: 59.3627
Evaluate side-chains
  171 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 303
   random chunks:
   chunk 197 optimal weight:    0.7980
   chunk 215 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 132 optimal weight:    9.9990
   chunk 261 optimal weight:    6.9990
   chunk 248 optimal weight:    0.8980
   chunk 207 optimal weight:    0.9990
   chunk 155 optimal weight:    8.9990
   chunk 244 optimal weight:    0.0770
   chunk 183 optimal weight:    1.9990
   chunk 298 optimal weight:    0.0270
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
** A1397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1495 ASN
A1500 HIS
** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A4012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A4137 ASN
** A4347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A4549 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.075430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.060228 restraints weight = 88643.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.061962 restraints weight = 42501.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.063076 restraints weight = 26787.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 70)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.063821 restraints weight = 20044.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.064265 restraints weight = 16618.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.0917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  25113  Z= 0.117
  Angle     :  0.547   8.903  34052  Z= 0.277
  Chirality :  0.039   0.179   3816
  Planarity :  0.004   0.050   4362
  Dihedral  :  6.553  97.619   3391
  Min Nonbonded Distance : 1.875

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  5.77 %
    Favored  : 93.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.38 (0.16), residues: 3028
  helix:  1.77 (0.12), residues: 1770
  sheet: -0.56 (0.32), residues: 252
  loop : -0.13 (0.21), residues: 1006

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A3167 
 TYR   0.020   0.001   TYR A3812 
 PHE   0.037   0.001   PHE A3698 
 TRP   0.014   0.001   TRP A2234 
 HIS   0.009   0.001   HIS A4389 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (25113)
  covalent geometry    : angle       0.54729 (34052)
  hydrogen bonds       : bond        0.04042 ( 1456)
  hydrogen bonds       : angle       4.48638 ( 4224)

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

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

  6056 Ramachandran restraints generated.
    3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6056 Ramachandran restraints generated.
    3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 218
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1531 MET cc_start: 0.8789 (tpt) cc_final: 0.8566 (tpt)
REVERT: A 1814 GLU cc_start: 0.8369 (tp30) cc_final: 0.8140 (tp30)
REVERT: A 3169 MET cc_start: 0.7179 (mtp) cc_final: 0.6920 (mtp)
REVERT: A 3776 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8098 (tm-30)
REVERT: A 3788 ASP cc_start: 0.7859 (t0) cc_final: 0.7581 (t0)
REVERT: A 4063 ASN cc_start: 0.8863 (m-40) cc_final: 0.8627 (m-40)
REVERT: A 4192 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7816 (mm-30)
REVERT: A 4344 LEU cc_start: 0.9153 (tp) cc_final: 0.8880 (tp)
  outliers start: 13
  outliers final: 6
  residues processed: 230
  average time/residue: 0.1560
  time to fit residues: 58.5388
Evaluate side-chains
  175 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 169
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1344 ASP
Chi-restraints excluded: chain A residue 1533 LEU
Chi-restraints excluded: chain A residue 2976 LEU
Chi-restraints excluded: chain A residue 3044 LEU
Chi-restraints excluded: chain A residue 3154 LEU
Chi-restraints excluded: chain A residue 4597 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 303
   random chunks:
   chunk 276 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 151 optimal weight:    0.9990
   chunk 268 optimal weight:    4.9990
   chunk 18 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 51 optimal weight:    1.9990
   chunk 213 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 109 optimal weight:    1.9990
   chunk 264 optimal weight:    0.1980
   overall best weight:    1.2388

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

Flipped N/Q/H residues before XYZ refinement:
A1495 ASN
** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A4012 ASN
A4291 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.074600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.059610 restraints weight = 88708.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.061281 restraints weight = 43525.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.062375 restraints weight = 27765.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.063074 restraints weight = 20852.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.063512 restraints weight = 17451.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.1217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  25113  Z= 0.133
  Angle     :  0.530  11.487  34052  Z= 0.266
  Chirality :  0.039   0.140   3816
  Planarity :  0.004   0.053   4362
  Dihedral  :  6.429  99.278   3391
  Min Nonbonded Distance : 1.852

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  8.51 %
    Favored  : 90.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.16), residues: 3028
  helix:  1.90 (0.12), residues: 1772
  sheet: -0.54 (0.32), residues: 252
  loop : -0.12 (0.21), residues: 1004

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2726 
 TYR   0.017   0.001   TYR A3812 
 PHE   0.023   0.001   PHE A3698 
 TRP   0.015   0.001   TRP A2234 
 HIS   0.004   0.001   HIS A2918 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (25113)
  covalent geometry    : angle       0.52951 (34052)
  hydrogen bonds       : bond        0.03879 ( 1456)
  hydrogen bonds       : angle       4.34200 ( 4224)

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

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

  6056 Ramachandran restraints generated.
    3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6056 Ramachandran restraints generated.
    3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 178
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2863 ARG cc_start: 0.8473 (ptp90) cc_final: 0.7481 (tmm160)
REVERT: A 4063 ASN cc_start: 0.8852 (m-40) cc_final: 0.8623 (m-40)
REVERT: A 4192 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7796 (mm-30)
REVERT: A 4344 LEU cc_start: 0.9153 (tp) cc_final: 0.8850 (tp)
  outliers start: 20
  outliers final: 11
  residues processed: 192
  average time/residue: 0.1494
  time to fit residues: 47.2537
Evaluate side-chains
  170 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 159
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1344 ASP
Chi-restraints excluded: chain A residue 1688 THR
Chi-restraints excluded: chain A residue 2536 ASP
Chi-restraints excluded: chain A residue 2581 LEU
Chi-restraints excluded: chain A residue 2976 LEU
Chi-restraints excluded: chain A residue 3044 LEU
Chi-restraints excluded: chain A residue 3154 LEU
Chi-restraints excluded: chain A residue 3495 THR
Chi-restraints excluded: chain A residue 3514 ILE
Chi-restraints excluded: chain A residue 4572 ASN
Chi-restraints excluded: chain A residue 4597 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 303
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 66 optimal weight:    7.9990
   chunk 274 optimal weight:    1.9990
   chunk 199 optimal weight:    0.9990
   chunk 296 optimal weight:    0.4980
   chunk 190 optimal weight:    5.9990
   chunk 212 optimal weight:    0.7980
   chunk 128 optimal weight:    0.7980
   chunk 151 optimal weight:    0.8980
   chunk 69 optimal weight:    0.0040
   chunk 210 optimal weight:    0.4980
   overall best weight:    0.4992

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

Flipped N/Q/H residues before XYZ refinement:
A1500 HIS
** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2698 GLN
** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3202 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.075517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.060329 restraints weight = 88275.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.062055 restraints weight = 42501.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 68)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.063192 restraints weight = 26830.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.063908 restraints weight = 19978.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.064383 restraints weight = 16634.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  25113  Z= 0.099
  Angle     :  0.501   8.566  34052  Z= 0.250
  Chirality :  0.038   0.178   3816
  Planarity :  0.004   0.053   4362
  Dihedral  :  6.237  96.240   3391
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  9.51 %
    Favored  : 89.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.16), residues: 3028
  helix:  2.04 (0.12), residues: 1776
  sheet: -0.64 (0.32), residues: 260
  loop : -0.09 (0.21), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A2729 
 TYR   0.018   0.001   TYR A3026 
 PHE   0.037   0.001   PHE A4410 
 TRP   0.015   0.001   TRP A2234 
 HIS   0.005   0.001   HIS A2918 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 (25113)
  covalent geometry    : angle       0.50141 (34052)
  hydrogen bonds       : bond        0.03574 ( 1456)
  hydrogen bonds       : angle       4.15421 ( 4224)

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

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

  6056 Ramachandran restraints generated.
    3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6056 Ramachandran restraints generated.
    3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 189
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1457 MET cc_start: 0.8802 (ttt) cc_final: 0.8559 (mtp)
REVERT: A 2863 ARG cc_start: 0.8500 (ptp90) cc_final: 0.7410 (tmm160)
REVERT: A 3030 MET cc_start: 0.7051 (mmt) cc_final: 0.6545 (mmt)
REVERT: A 3506 ASP cc_start: 0.8909 (t0) cc_final: 0.8603 (t0)
REVERT: A 3788 ASP cc_start: 0.8017 (t0) cc_final: 0.7365 (t0)
REVERT: A 3792 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8518 (pm20)
REVERT: A 4063 ASN cc_start: 0.8868 (m-40) cc_final: 0.8636 (m-40)
REVERT: A 4192 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7875 (mm-30)
REVERT: A 4344 LEU cc_start: 0.9164 (tp) cc_final: 0.8887 (tp)
  outliers start: 26
  outliers final: 13
  residues processed: 207
  average time/residue: 0.1536
  time to fit residues: 52.4970
Evaluate side-chains
  177 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 163
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1344 ASP
Chi-restraints excluded: chain A residue 1688 THR
Chi-restraints excluded: chain A residue 1719 GLU
Chi-restraints excluded: chain A residue 2307 VAL
Chi-restraints excluded: chain A residue 2581 LEU
Chi-restraints excluded: chain A residue 2976 LEU
Chi-restraints excluded: chain A residue 3044 LEU
Chi-restraints excluded: chain A residue 3154 LEU
Chi-restraints excluded: chain A residue 3478 LEU
Chi-restraints excluded: chain A residue 3495 THR
Chi-restraints excluded: chain A residue 3514 ILE
Chi-restraints excluded: chain A residue 3792 GLN
Chi-restraints excluded: chain A residue 4291 HIS
Chi-restraints excluded: chain A residue 4597 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 303
   random chunks:
   chunk 206 optimal weight:    0.9990
   chunk 72 optimal weight:    0.5980
   chunk 119 optimal weight:    0.1980
   chunk 17 optimal weight:    7.9990
   chunk 9 optimal weight:    0.0980
   chunk 246 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 99 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 124 optimal weight:    5.9990
   chunk 189 optimal weight:    8.9990
   overall best weight:    0.4982

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

Flipped N/Q/H residues before XYZ refinement:
** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.075721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.060589 restraints weight = 88241.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.062337 restraints weight = 42675.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.063473 restraints weight = 26914.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.064194 restraints weight = 20039.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.064653 restraints weight = 16650.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  25113  Z= 0.097
  Angle     :  0.498  11.334  34052  Z= 0.247
  Chirality :  0.038   0.257   3816
  Planarity :  0.004   0.057   4362
  Dihedral  :  6.041  93.532   3391
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 10.80 %
    Favored  : 88.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.75 (0.16), residues: 3028
  helix:  2.11 (0.12), residues: 1778
  sheet: -0.60 (0.32), residues: 260
  loop : -0.04 (0.21), residues: 990

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2729 
 TYR   0.018   0.001   TYR A1480 
 PHE   0.016   0.001   PHE A1836 
 TRP   0.015   0.001   TRP A2234 
 HIS   0.004   0.001   HIS A2918 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 (25113)
  covalent geometry    : angle       0.49756 (34052)
  hydrogen bonds       : bond        0.03468 ( 1456)
  hydrogen bonds       : angle       4.07041 ( 4224)

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

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

  6056 Ramachandran restraints generated.
    3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6056 Ramachandran restraints generated.
    3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 190
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1417 MET cc_start: 0.6432 (ptp) cc_final: 0.5920 (ptp)
REVERT: A 1769 MET cc_start: 0.8637 (mmm) cc_final: 0.8406 (mmm)
REVERT: A 2755 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8268 (tpp)
REVERT: A 2863 ARG cc_start: 0.8494 (ptp90) cc_final: 0.7418 (tmm160)
REVERT: A 3030 MET cc_start: 0.6957 (mmt) cc_final: 0.6386 (mmt)
REVERT: A 3176 TYR cc_start: 0.9313 (t80) cc_final: 0.8943 (t80)
REVERT: A 3506 ASP cc_start: 0.8905 (t0) cc_final: 0.8592 (t0)
REVERT: A 3788 ASP cc_start: 0.8013 (t0) cc_final: 0.7364 (t0)
REVERT: A 3792 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8542 (pm20)
REVERT: A 4063 ASN cc_start: 0.8877 (m-40) cc_final: 0.8646 (m-40)
REVERT: A 4192 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7882 (mm-30)
REVERT: A 4344 LEU cc_start: 0.9149 (tp) cc_final: 0.8867 (tp)
  outliers start: 24
  outliers final: 16
  residues processed: 208
  average time/residue: 0.1600
  time to fit residues: 54.7099
Evaluate side-chains
  185 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 167
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1344 ASP
Chi-restraints excluded: chain A residue 1531 MET
Chi-restraints excluded: chain A residue 1688 THR
Chi-restraints excluded: chain A residue 1719 GLU
Chi-restraints excluded: chain A residue 2307 VAL
Chi-restraints excluded: chain A residue 2627 THR
Chi-restraints excluded: chain A residue 2755 MET
Chi-restraints excluded: chain A residue 2976 LEU
Chi-restraints excluded: chain A residue 3044 LEU
Chi-restraints excluded: chain A residue 3154 LEU
Chi-restraints excluded: chain A residue 3478 LEU
Chi-restraints excluded: chain A residue 3495 THR
Chi-restraints excluded: chain A residue 3792 GLN
Chi-restraints excluded: chain A residue 3846 LEU
Chi-restraints excluded: chain A residue 4291 HIS
Chi-restraints excluded: chain A residue 4435 VAL
Chi-restraints excluded: chain A residue 4462 ARG
Chi-restraints excluded: chain A residue 4597 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 303
   random chunks:
   chunk 148 optimal weight:    3.9990
   chunk 130 optimal weight:    4.9990
   chunk 121 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 243 optimal weight:    8.9990
   chunk 181 optimal weight:    0.9990
   chunk 108 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   chunk 67 optimal weight:    0.8980
   chunk 255 optimal weight:    3.9990
   chunk 297 optimal weight:    2.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A1495 ASN
A1500 HIS
** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.075323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.060189 restraints weight = 88909.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.061914 restraints weight = 42926.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.063045 restraints weight = 27102.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.063762 restraints weight = 20227.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.064213 restraints weight = 16828.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.055  25113  Z= 0.108
  Angle     :  0.501  10.657  34052  Z= 0.248
  Chirality :  0.038   0.211   3816
  Planarity :  0.004   0.076   4362
  Dihedral  :  5.882  91.033   3391
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 11.95 %
    Favored  : 87.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.82 (0.16), residues: 3028
  helix:  2.17 (0.12), residues: 1772
  sheet: -0.49 (0.32), residues: 259
  loop : -0.01 (0.20), residues: 997

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2729 
 TYR   0.017   0.001   TYR A1480 
 PHE   0.034   0.001   PHE A4410 
 TRP   0.014   0.001   TRP A2234 
 HIS   0.006   0.001   HIS A2918 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (25113)
  covalent geometry    : angle       0.50090 (34052)
  hydrogen bonds       : bond        0.03445 ( 1456)
  hydrogen bonds       : angle       4.04312 ( 4224)

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

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

  6056 Ramachandran restraints generated.
    3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6056 Ramachandran restraints generated.
    3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 180
  time to evaluate  : 1.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1417 MET cc_start: 0.6426 (ptp) cc_final: 0.5910 (ptp)
REVERT: A 2222 MET cc_start: 0.8774 (mtm) cc_final: 0.8544 (mtm)
REVERT: A 2510 MET cc_start: 0.8300 (tpp) cc_final: 0.8048 (mmt)
REVERT: A 2755 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8536 (ttm)
REVERT: A 2799 MET cc_start: 0.9162 (mmm) cc_final: 0.8576 (mmm)
REVERT: A 2863 ARG cc_start: 0.8494 (ptp90) cc_final: 0.7509 (tmm160)
REVERT: A 3030 MET cc_start: 0.7105 (mmt) cc_final: 0.6524 (mmt)
REVERT: A 3176 TYR cc_start: 0.9332 (t80) cc_final: 0.8962 (t80)
REVERT: A 3506 ASP cc_start: 0.8913 (t0) cc_final: 0.8598 (t0)
REVERT: A 3788 ASP cc_start: 0.8048 (t0) cc_final: 0.7305 (t0)
REVERT: A 3792 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8534 (pm20)
REVERT: A 4063 ASN cc_start: 0.8877 (m-40) cc_final: 0.8651 (m-40)
REVERT: A 4344 LEU cc_start: 0.9183 (tp) cc_final: 0.8882 (tp)
  outliers start: 25
  outliers final: 17
  residues processed: 199
  average time/residue: 0.1695
  time to fit residues: 56.2232
Evaluate side-chains
  184 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 165
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1344 ASP
Chi-restraints excluded: chain A residue 1531 MET
Chi-restraints excluded: chain A residue 1688 THR
Chi-restraints excluded: chain A residue 1719 GLU
Chi-restraints excluded: chain A residue 2307 VAL
Chi-restraints excluded: chain A residue 2581 LEU
Chi-restraints excluded: chain A residue 2627 THR
Chi-restraints excluded: chain A residue 2755 MET
Chi-restraints excluded: chain A residue 2793 ILE
Chi-restraints excluded: chain A residue 2976 LEU
Chi-restraints excluded: chain A residue 3044 LEU
Chi-restraints excluded: chain A residue 3154 LEU
Chi-restraints excluded: chain A residue 3478 LEU
Chi-restraints excluded: chain A residue 3495 THR
Chi-restraints excluded: chain A residue 3792 GLN
Chi-restraints excluded: chain A residue 3846 LEU
Chi-restraints excluded: chain A residue 4291 HIS
Chi-restraints excluded: chain A residue 4462 ARG
Chi-restraints excluded: chain A residue 4597 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 303
   random chunks:
   chunk 129 optimal weight:    0.5980
   chunk 58 optimal weight:    3.9990
   chunk 294 optimal weight:    9.9990
   chunk 161 optimal weight:    0.7980
   chunk 230 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 213 optimal weight:    0.6980
   chunk 114 optimal weight:    3.9990
   chunk 147 optimal weight:    2.9990
   chunk 130 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2752 ASN
A4347 GLN
A4595 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.074834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.059832 restraints weight = 89015.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.061506 restraints weight = 44516.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.062565 restraints weight = 28540.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 69)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.063264 restraints weight = 21655.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.063657 restraints weight = 18109.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  25113  Z= 0.124
  Angle     :  0.512  10.555  34052  Z= 0.253
  Chirality :  0.039   0.257   3816
  Planarity :  0.004   0.073   4362
  Dihedral  :  5.796  88.601   3391
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 12.47 %
    Favored  : 86.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.88 (0.16), residues: 3028
  helix:  2.20 (0.12), residues: 1770
  sheet: -0.46 (0.32), residues: 259
  loop :  0.06 (0.21), residues: 999

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG A1388 
 TYR   0.016   0.001   TYR A1480 
 PHE   0.022   0.001   PHE A3957 
 TRP   0.014   0.001   TRP A1701 
 HIS   0.007   0.001   HIS A2918 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (25113)
  covalent geometry    : angle       0.51203 (34052)
  hydrogen bonds       : bond        0.03467 ( 1456)
  hydrogen bonds       : angle       4.04914 ( 4224)

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

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

  6056 Ramachandran restraints generated.
    3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6056 Ramachandran restraints generated.
    3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 168
  time to evaluate  : 1.074 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1769 MET cc_start: 0.8657 (mmm) cc_final: 0.8421 (mmm)
REVERT: A 2423 MET cc_start: 0.8377 (mtp) cc_final: 0.8071 (mtm)
REVERT: A 2510 MET cc_start: 0.8299 (tpp) cc_final: 0.8024 (mmt)
REVERT: A 2755 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8594 (ttm)
REVERT: A 2799 MET cc_start: 0.9198 (mmm) cc_final: 0.8883 (mmm)
REVERT: A 3030 MET cc_start: 0.7166 (mmt) cc_final: 0.6574 (mmt)
REVERT: A 3506 ASP cc_start: 0.8922 (t0) cc_final: 0.8686 (t0)
REVERT: A 3788 ASP cc_start: 0.8069 (t0) cc_final: 0.7309 (t0)
REVERT: A 3792 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8535 (pm20)
REVERT: A 4063 ASN cc_start: 0.8889 (m-40) cc_final: 0.8662 (m-40)
REVERT: A 4344 LEU cc_start: 0.9138 (tp) cc_final: 0.8854 (tp)
  outliers start: 32
  outliers final: 21
  residues processed: 190
  average time/residue: 0.1596
  time to fit residues: 49.5793
Evaluate side-chains
  184 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 161
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1344 ASP
Chi-restraints excluded: chain A residue 1531 MET
Chi-restraints excluded: chain A residue 1688 THR
Chi-restraints excluded: chain A residue 1719 GLU
Chi-restraints excluded: chain A residue 2307 VAL
Chi-restraints excluded: chain A residue 2581 LEU
Chi-restraints excluded: chain A residue 2627 THR
Chi-restraints excluded: chain A residue 2755 MET
Chi-restraints excluded: chain A residue 2793 ILE
Chi-restraints excluded: chain A residue 2946 LEU
Chi-restraints excluded: chain A residue 2976 LEU
Chi-restraints excluded: chain A residue 3044 LEU
Chi-restraints excluded: chain A residue 3154 LEU
Chi-restraints excluded: chain A residue 3478 LEU
Chi-restraints excluded: chain A residue 3495 THR
Chi-restraints excluded: chain A residue 3708 LEU
Chi-restraints excluded: chain A residue 3792 GLN
Chi-restraints excluded: chain A residue 3829 LEU
Chi-restraints excluded: chain A residue 3846 LEU
Chi-restraints excluded: chain A residue 4291 HIS
Chi-restraints excluded: chain A residue 4462 ARG
Chi-restraints excluded: chain A residue 4572 ASN
Chi-restraints excluded: chain A residue 4597 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 303
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 188 optimal weight:    0.6980
   chunk 258 optimal weight:    4.9990
   chunk 289 optimal weight:    3.9990
   chunk 79 optimal weight:    7.9990
   chunk 175 optimal weight:    0.0570
   chunk 145 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 4 optimal weight:    9.9990
   chunk 210 optimal weight:    0.0470
   chunk 6 optimal weight:    5.9990
   overall best weight:    0.7398

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

Flipped N/Q/H residues before XYZ refinement:
** A1397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3735 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.075327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.060188 restraints weight = 89027.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.061917 restraints weight = 42939.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.063026 restraints weight = 27112.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.063779 restraints weight = 20310.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.064209 restraints weight = 16787.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  25113  Z= 0.104
  Angle     :  0.515  11.836  34052  Z= 0.253
  Chirality :  0.038   0.185   3816
  Planarity :  0.004   0.106   4362
  Dihedral  :  5.712  89.672   3391
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 12.73 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.94 (0.16), residues: 3028
  helix:  2.24 (0.12), residues: 1767
  sheet: -0.43 (0.32), residues: 266
  loop :  0.09 (0.20), residues: 995

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.000   ARG A1388 
 TYR   0.015   0.001   TYR A1480 
 PHE   0.017   0.001   PHE A3957 
 TRP   0.015   0.001   TRP A2234 
 HIS   0.005   0.000   HIS A2918 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (25113)
  covalent geometry    : angle       0.51457 (34052)
  hydrogen bonds       : bond        0.03400 ( 1456)
  hydrogen bonds       : angle       4.00668 ( 4224)

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

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

  6056 Ramachandran restraints generated.
    3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6056 Ramachandran restraints generated.
    3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 172
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1769 MET cc_start: 0.8652 (mmm) cc_final: 0.8451 (mmm)
REVERT: A 2423 MET cc_start: 0.8307 (mtp) cc_final: 0.7994 (mtm)
REVERT: A 2755 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8261 (tpp)
REVERT: A 2799 MET cc_start: 0.9205 (mmm) cc_final: 0.8891 (mmm)
REVERT: A 3030 MET cc_start: 0.7064 (mmt) cc_final: 0.6459 (mmt)
REVERT: A 3176 TYR cc_start: 0.9325 (t80) cc_final: 0.8969 (t80)
REVERT: A 3199 MET cc_start: 0.8795 (ppp) cc_final: 0.8524 (ppp)
REVERT: A 3788 ASP cc_start: 0.8055 (t0) cc_final: 0.7303 (t0)
REVERT: A 3792 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8525 (pm20)
REVERT: A 4007 MET cc_start: 0.8239 (ttp) cc_final: 0.7964 (ttp)
REVERT: A 4063 ASN cc_start: 0.8875 (m-40) cc_final: 0.8650 (m-40)
REVERT: A 4344 LEU cc_start: 0.9134 (tp) cc_final: 0.8835 (tp)
  outliers start: 27
  outliers final: 20
  residues processed: 193
  average time/residue: 0.1452
  time to fit residues: 46.6976
Evaluate side-chains
  189 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 167
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1344 ASP
Chi-restraints excluded: chain A residue 1531 MET
Chi-restraints excluded: chain A residue 1688 THR
Chi-restraints excluded: chain A residue 1719 GLU
Chi-restraints excluded: chain A residue 1982 LEU
Chi-restraints excluded: chain A residue 2307 VAL
Chi-restraints excluded: chain A residue 2581 LEU
Chi-restraints excluded: chain A residue 2627 THR
Chi-restraints excluded: chain A residue 2755 MET
Chi-restraints excluded: chain A residue 2793 ILE
Chi-restraints excluded: chain A residue 2976 LEU
Chi-restraints excluded: chain A residue 3044 LEU
Chi-restraints excluded: chain A residue 3154 LEU
Chi-restraints excluded: chain A residue 3478 LEU
Chi-restraints excluded: chain A residue 3495 THR
Chi-restraints excluded: chain A residue 3708 LEU
Chi-restraints excluded: chain A residue 3792 GLN
Chi-restraints excluded: chain A residue 3829 LEU
Chi-restraints excluded: chain A residue 3846 LEU
Chi-restraints excluded: chain A residue 4291 HIS
Chi-restraints excluded: chain A residue 4462 ARG
Chi-restraints excluded: chain A residue 4597 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 303
   random chunks:
   chunk 105 optimal weight:    4.9990
   chunk 239 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   chunk 191 optimal weight:    0.9990
   chunk 214 optimal weight:    6.9990
   chunk 266 optimal weight:    2.9990
   chunk 290 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 302 optimal weight:    0.7980
   chunk 165 optimal weight:   10.0000
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A4526 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.074561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.059333 restraints weight = 89548.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.061064 restraints weight = 43541.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.062168 restraints weight = 27470.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.062880 restraints weight = 20599.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.063318 restraints weight = 17165.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  25113  Z= 0.134
  Angle     :  0.535  11.238  34052  Z= 0.265
  Chirality :  0.039   0.199   3816
  Planarity :  0.004   0.135   4362
  Dihedral  :  5.672  88.558   3391
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 13.10 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.96 (0.16), residues: 3028
  helix:  2.25 (0.12), residues: 1767
  sheet: -0.41 (0.32), residues: 260
  loop :  0.12 (0.21), residues: 1001

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.000   ARG A1388 
 TYR   0.016   0.001   TYR A1480 
 PHE   0.020   0.001   PHE A1836 
 TRP   0.022   0.001   TRP A4105 
 HIS   0.005   0.001   HIS A2918 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (25113)
  covalent geometry    : angle       0.53530 (34052)
  hydrogen bonds       : bond        0.03499 ( 1456)
  hydrogen bonds       : angle       4.05260 ( 4224)

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

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

  6056 Ramachandran restraints generated.
    3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6056 Ramachandran restraints generated.
    3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 167
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1769 MET cc_start: 0.8664 (mmm) cc_final: 0.8447 (mmm)
REVERT: A 2423 MET cc_start: 0.8379 (mtp) cc_final: 0.8083 (mtm)
REVERT: A 2755 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8599 (ttm)
REVERT: A 2799 MET cc_start: 0.9227 (mmm) cc_final: 0.8934 (mmm)
REVERT: A 3030 MET cc_start: 0.7077 (mmt) cc_final: 0.6472 (mmt)
REVERT: A 3199 MET cc_start: 0.8793 (ppp) cc_final: 0.8516 (ppp)
REVERT: A 3776 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7671 (tm-30)
REVERT: A 3788 ASP cc_start: 0.8067 (t0) cc_final: 0.7283 (t0)
REVERT: A 3792 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8492 (pm20)
REVERT: A 4007 MET cc_start: 0.8270 (ttp) cc_final: 0.8007 (ttp)
REVERT: A 4063 ASN cc_start: 0.8889 (m-40) cc_final: 0.8662 (m-40)
REVERT: A 4344 LEU cc_start: 0.9190 (tp) cc_final: 0.8888 (tp)
  outliers start: 27
  outliers final: 21
  residues processed: 187
  average time/residue: 0.1627
  time to fit residues: 50.1832
Evaluate side-chains
  186 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 163
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1344 ASP
Chi-restraints excluded: chain A residue 1531 MET
Chi-restraints excluded: chain A residue 1688 THR
Chi-restraints excluded: chain A residue 1719 GLU
Chi-restraints excluded: chain A residue 2307 VAL
Chi-restraints excluded: chain A residue 2581 LEU
Chi-restraints excluded: chain A residue 2627 THR
Chi-restraints excluded: chain A residue 2755 MET
Chi-restraints excluded: chain A residue 2793 ILE
Chi-restraints excluded: chain A residue 2976 LEU
Chi-restraints excluded: chain A residue 3044 LEU
Chi-restraints excluded: chain A residue 3154 LEU
Chi-restraints excluded: chain A residue 3478 LEU
Chi-restraints excluded: chain A residue 3495 THR
Chi-restraints excluded: chain A residue 3579 MET
Chi-restraints excluded: chain A residue 3708 LEU
Chi-restraints excluded: chain A residue 3792 GLN
Chi-restraints excluded: chain A residue 3829 LEU
Chi-restraints excluded: chain A residue 3846 LEU
Chi-restraints excluded: chain A residue 3928 THR
Chi-restraints excluded: chain A residue 4291 HIS
Chi-restraints excluded: chain A residue 4462 ARG
Chi-restraints excluded: chain A residue 4597 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 303
   random chunks:
   chunk 14 optimal weight:    0.4980
   chunk 198 optimal weight:    0.3980
   chunk 23 optimal weight:    5.9990
   chunk 98 optimal weight:    0.0770
   chunk 93 optimal weight:    0.9980
   chunk 162 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0470
   chunk 115 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.3236

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

Flipped N/Q/H residues before XYZ refinement:
** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A4131 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.076106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.061209 restraints weight = 88346.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.062877 restraints weight = 43870.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.063967 restraints weight = 28151.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.064639 restraints weight = 21208.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 67)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.065103 restraints weight = 17817.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  25113  Z= 0.096
  Angle     :  0.532  12.499  34052  Z= 0.260
  Chirality :  0.038   0.212   3816
  Planarity :  0.004   0.065   4362
  Dihedral  :  5.541  89.613   3391
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 13.39 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.00 (0.16), residues: 3028
  helix:  2.29 (0.12), residues: 1764
  sheet: -0.41 (0.32), residues: 266
  loop :  0.13 (0.21), residues: 998

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG A1388 
 TYR   0.013   0.001   TYR A2496 
 PHE   0.014   0.001   PHE A1836 
 TRP   0.034   0.001   TRP A4105 
 HIS   0.003   0.000   HIS A3200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 (25113)
  covalent geometry    : angle       0.53207 (34052)
  hydrogen bonds       : bond        0.03312 ( 1456)
  hydrogen bonds       : angle       3.99423 ( 4224)

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

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

  6056 Ramachandran restraints generated.
    3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6056 Ramachandran restraints generated.
    3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 190
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2755 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8165 (tpp)
REVERT: A 2799 MET cc_start: 0.9207 (mmm) cc_final: 0.8909 (mmm)
REVERT: A 3030 MET cc_start: 0.7142 (mmt) cc_final: 0.6488 (mmt)
REVERT: A 3176 TYR cc_start: 0.9299 (t80) cc_final: 0.8970 (t80)
REVERT: A 3199 MET cc_start: 0.8785 (ppp) cc_final: 0.8511 (ppp)
REVERT: A 3788 ASP cc_start: 0.8047 (t0) cc_final: 0.7275 (t0)
REVERT: A 3792 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8528 (pm20)
REVERT: A 4007 MET cc_start: 0.8201 (ttp) cc_final: 0.7999 (ttp)
REVERT: A 4063 ASN cc_start: 0.8882 (m-40) cc_final: 0.8647 (m-40)
REVERT: A 4344 LEU cc_start: 0.9131 (tp) cc_final: 0.8848 (tp)
  outliers start: 23
  outliers final: 19
  residues processed: 205
  average time/residue: 0.1604
  time to fit residues: 54.6235
Evaluate side-chains
  194 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 173
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1344 ASP
Chi-restraints excluded: chain A residue 1531 MET
Chi-restraints excluded: chain A residue 1688 THR
Chi-restraints excluded: chain A residue 1719 GLU
Chi-restraints excluded: chain A residue 2307 VAL
Chi-restraints excluded: chain A residue 2581 LEU
Chi-restraints excluded: chain A residue 2627 THR
Chi-restraints excluded: chain A residue 2755 MET
Chi-restraints excluded: chain A residue 2793 ILE
Chi-restraints excluded: chain A residue 2976 LEU
Chi-restraints excluded: chain A residue 3044 LEU
Chi-restraints excluded: chain A residue 3154 LEU
Chi-restraints excluded: chain A residue 3478 LEU
Chi-restraints excluded: chain A residue 3495 THR
Chi-restraints excluded: chain A residue 3708 LEU
Chi-restraints excluded: chain A residue 3792 GLN
Chi-restraints excluded: chain A residue 3829 LEU
Chi-restraints excluded: chain A residue 3846 LEU
Chi-restraints excluded: chain A residue 4291 HIS
Chi-restraints excluded: chain A residue 4462 ARG
Chi-restraints excluded: chain A residue 4597 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 303
   random chunks:
   chunk 249 optimal weight:    1.9990
   chunk 191 optimal weight:   10.0000
   chunk 92 optimal weight:    4.9990
   chunk 150 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 254 optimal weight:    0.9990
   chunk 217 optimal weight:    8.9990
   chunk 118 optimal weight:    0.8980
   chunk 295 optimal weight:    0.7980
   chunk 132 optimal weight:    5.9990
   chunk 119 optimal weight:    5.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A1500 HIS
** A1985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2637 HIS
A3057 GLN
A4549 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.073976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.058717 restraints weight = 89988.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.060444 restraints weight = 43872.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.061520 restraints weight = 27776.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 62)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.062218 restraints weight = 20905.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.062655 restraints weight = 17488.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  25113  Z= 0.169
  Angle     :  0.572  11.957  34052  Z= 0.284
  Chirality :  0.040   0.191   3816
  Planarity :  0.004   0.080   4362
  Dihedral  :  5.567  87.914   3391
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 13.65 %
    Favored  : 85.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.97 (0.16), residues: 3028
  helix:  2.24 (0.12), residues: 1768
  sheet: -0.42 (0.33), residues: 260
  loop :  0.16 (0.21), residues: 1000

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG A1388 
 TYR   0.015   0.001   TYR A3812 
 PHE   0.023   0.001   PHE A1836 
 TRP   0.053   0.001   TRP A4105 
 HIS   0.011   0.001   HIS A2637 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (25113)
  covalent geometry    : angle       0.57216 (34052)
  hydrogen bonds       : bond        0.03565 ( 1456)
  hydrogen bonds       : angle       4.11682 ( 4224)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4167.05 seconds
wall clock time: 72 minutes 56.11 seconds (4376.11 seconds total)