Starting phenix.real_space_refine
on Fri Sep 19 05:33:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bm6_44689/09_2025/9bm6_44689.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bm6_44689/09_2025/9bm6_44689.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.22
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bm6_44689/09_2025/9bm6_44689.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bm6_44689/09_2025/9bm6_44689.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bm6_44689/09_2025/9bm6_44689.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bm6_44689/09_2025/9bm6_44689.map"
  }
  resolution = 3.22
  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=   0.025
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     115      5.16       5
     C   14703      2.51       5
     N    3987      2.21       5
     O    4295      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 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: 23111
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 22994
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2858, 22994
          Classifications: {'peptide': 2858}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 129, 'TRANS': 2728}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 117
          Unusual residues: {' MG': 1, 'ADP': 2, 'ATP': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 5.36, per 1000 atoms: 0.23
  Number of scatterers: 23111
  At special positions: 0
  Unit cell: (150.592, 148.928, 124.8, 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     115     16.00
     P      10     15.00
     Mg      1     11.99
     O    4295      8.00
     N    3987      7.00
     C   14703      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: 2.18
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  5688 Ramachandran restraints generated.
    2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5440

  Finding SS restraints...
    Secondary structure from input PDB file:
      128 helices and 20 sheets defined
      61.9% alpha, 8.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1460 through 1472
    Processing helix  chain 'A' and resid 1489 through 1510
    Processing helix  chain 'A' and resid 1512 through 1552
      removed outlier: 4.236A  pdb=" N   PHE A1516 " --> pdb=" O   TYR A1512 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   GLU A1518 " --> pdb=" O   LYS A1514 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   ASP A1519 " --> pdb=" O   VAL A1515 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   VAL A1536 " --> pdb=" O   ALA A1532 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ASP A1539 " --> pdb=" O   ASP A1535 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   TRP A1544 " --> pdb=" O   VAL A1540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1556 through 1561
    Processing helix  chain 'A' and resid 1561 through 1584
    Processing helix  chain 'A' and resid 1587 through 1593
    Processing helix  chain 'A' and resid 1596 through 1626
    Processing helix  chain 'A' and resid 1627 through 1631
    Processing helix  chain 'A' and resid 1633 through 1643
    Processing helix  chain 'A' and resid 1646 through 1650
      removed outlier: 3.652A  pdb=" N   LYS A1649 " --> pdb=" O   ASN A1646 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1653 through 1658
      removed outlier: 3.815A  pdb=" N   MET A1657 " --> pdb=" O   HIS A1653 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   PHE A1658 " --> pdb=" O   PHE A1654 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1653 through 1658'
    Processing helix  chain 'A' and resid 1697 through 1729
      removed outlier: 3.718A  pdb=" N   ILE A1726 " --> pdb=" O   THR A1722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1734 through 1745
    Processing helix  chain 'A' and resid 1746 through 1769
    Processing helix  chain 'A' and resid 1777 through 1797
      removed outlier: 3.641A  pdb=" N   LEU A1797 " --> pdb=" O   ALA A1793 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1801 through 1824
      removed outlier: 3.535A  pdb=" N   SER A1824 " --> pdb=" O   ASP A1820 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1835 through 1840
    Processing helix  chain 'A' and resid 1852 through 1855
    Processing helix  chain 'A' and resid 1882 through 1898
    Processing helix  chain 'A' and resid 1911 through 1923
    Processing helix  chain 'A' and resid 1937 through 1952
      removed outlier: 4.498A  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
    Processing helix  chain 'A' and resid 2045 through 2057
    Processing helix  chain 'A' and resid 2061 through 2079
      Proline residue:  A2071  - end of helix
    Processing helix  chain 'A' and resid 2089 through 2113
    Processing helix  chain 'A' and resid 2132 through 2146
    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 2152 through 2165
      removed outlier: 4.227A  pdb=" N   LEU A2156 " --> pdb=" O   GLU A2152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2175 through 2189
      removed outlier: 3.742A  pdb=" N   GLU A2181 " --> pdb=" O   ALA A2177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2200 through 2217
    Processing helix  chain 'A' and resid 2230 through 2246
    Processing helix  chain 'A' and resid 2260 through 2265
    Processing helix  chain 'A' and resid 2278 through 2290
    Processing helix  chain 'A' and resid 2315 through 2320
      removed outlier: 3.542A  pdb=" N   ASP A2320 " --> pdb=" O   ASN A2316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2352 through 2358
    Processing helix  chain 'A' and resid 2365 through 2369
    Processing helix  chain 'A' and resid 2370 through 2385
    Processing helix  chain 'A' and resid 2411 through 2424
    Processing helix  chain 'A' and resid 2425 through 2427
      No H-bonds generated for 'chain 'A' and resid 2425 through 2427'
    Processing helix  chain 'A' and resid 2431 through 2443
      removed outlier: 3.616A  pdb=" N   GLN A2442 " --> pdb=" O   GLU A2438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2450 through 2476
    Processing helix  chain 'A' and resid 2482 through 2502
      removed outlier: 3.652A  pdb=" N   VAL A2495 " --> pdb=" O   GLN A2491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2507 through 2522
    Processing helix  chain 'A' and resid 2533 through 2535
      No H-bonds generated for 'chain 'A' and resid 2533 through 2535'
    Processing helix  chain 'A' and resid 2549 through 2552
    Processing helix  chain 'A' and resid 2558 through 2562
    Processing helix  chain 'A' and resid 2571 through 2586
    Processing helix  chain 'A' and resid 2600 through 2612
      removed outlier: 3.631A  pdb=" N   THR A2604 " --> pdb=" O   GLY A2600 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU A2612 " --> pdb=" O   ALA A2608 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2627 through 2638
      removed outlier: 4.105A  pdb=" N   LEU A2631 " --> pdb=" O   THR A2627 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2677 through 2689
    Processing helix  chain 'A' and resid 2724 through 2729
    Processing helix  chain 'A' and resid 2740 through 2757
      removed outlier: 3.543A  pdb=" N   ARG A2757 " --> pdb=" O   ARG A2753 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2758 through 2764
      removed outlier: 6.629A  pdb=" N   SER A2761 " --> pdb=" O   LEU A2758 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   THR A2764 " --> pdb=" O   SER A2761 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2765 through 2783
    Processing helix  chain 'A' and resid 2795 through 2811
      removed outlier: 3.743A  pdb=" N   MET A2799 " --> pdb=" O   SER A2795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2817 through 2834
    Processing helix  chain 'A' and resid 2839 through 2858
      removed outlier: 3.501A  pdb=" N   ARG A2843 " --> pdb=" O   GLU A2839 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2885 through 2904
      removed outlier: 3.529A  pdb=" N   LEU A2889 " --> pdb=" O   ASP A2885 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2912 through 2928
    Processing helix  chain 'A' and resid 2942 through 2955
    Processing helix  chain 'A' and resid 2968 through 2985
    Processing helix  chain 'A' and resid 3001 through 3015
      removed outlier: 3.828A  pdb=" N   LEU A3005 " --> pdb=" O   ASP A3001 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3023 through 3041
    Processing helix  chain 'A' and resid 3046 through 3061
    Processing helix  chain 'A' and resid 3083 through 3087
    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 3220
      removed outlier: 4.126A  pdb=" N   ARG A3220 " --> pdb=" O   GLU A3216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3472 through 3502
    Processing helix  chain 'A' and resid 3503 through 3516
    Processing helix  chain 'A' and resid 3521 through 3539
    Processing helix  chain 'A' and resid 3548 through 3553
      removed outlier: 3.998A  pdb=" N   TYR A3552 " --> pdb=" O   ALA A3548 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU A3553 " --> pdb=" O   ARG A3549 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 3548 through 3553'
    Processing helix  chain 'A' and resid 3555 through 3565
    Processing helix  chain 'A' and resid 3570 through 3582
    Processing helix  chain 'A' and resid 3594 through 3604
    Processing helix  chain 'A' and resid 3618 through 3627
    Processing helix  chain 'A' and resid 3637 through 3641
    Processing helix  chain 'A' and resid 3642 through 3644
      No H-bonds generated for 'chain 'A' and resid 3642 through 3644'
    Processing helix  chain 'A' and resid 3645 through 3650
    Processing helix  chain 'A' and resid 3689 through 3694
    Processing helix  chain 'A' and resid 3704 through 3721
    Processing helix  chain 'A' and resid 3721 through 3735
      removed outlier: 4.016A  pdb=" N   GLN A3735 " --> pdb=" O   LEU A3731 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3736 through 3757
    Processing helix  chain 'A' and resid 3762 through 3786
      removed outlier: 3.759A  pdb=" N   THR A3769 " --> pdb=" O   THR A3765 " (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
      removed outlier: 3.595A  pdb=" N   PHE A3832 " --> pdb=" O   SER A3828 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3843 through 3847
      removed outlier: 3.837A  pdb=" N   LYS A3847 " --> pdb=" O   PRO A3844 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3851 through 3874
      removed outlier: 4.221A  pdb=" N   GLY A3874 " --> pdb=" O   ARG A3870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3875 through 3878
      removed outlier: 5.970A  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 3910
    Processing helix  chain 'A' and resid 3928 through 3940
    Processing helix  chain 'A' and resid 3941 through 3945
      removed outlier: 3.577A  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
      removed outlier: 3.548A  pdb=" N   ASP A3962 " --> pdb=" O   GLY A3958 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3981 through 3996
    Processing helix  chain 'A' and resid 3997 through 3999
      No H-bonds generated for 'chain 'A' and resid 3997 through 3999'
    Processing helix  chain 'A' and resid 4000 through 4013
    Processing helix  chain 'A' and resid 4018 through 4023
      removed outlier: 3.530A  pdb=" N   GLN A4023 " --> pdb=" O   SER A4019 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4027 through 4033
    Processing helix  chain 'A' and resid 4051 through 4062
      removed outlier: 3.929A  pdb=" N   VAL A4055 " --> pdb=" O   ALA A4051 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4074 through 4091
      removed outlier: 4.028A  pdb=" N   ASN A4078 " --> pdb=" O   ALA A4074 " (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 4114
    Processing helix  chain 'A' and resid 4135 through 4142
    Processing helix  chain 'A' and resid 4152 through 4164
    Processing helix  chain 'A' and resid 4165 through 4170
      removed outlier: 3.636A  pdb=" N   ILE A4169 " --> pdb=" O   PRO A4165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4174 through 4196
      removed outlier: 3.876A  pdb=" N   ARG A4178 " --> pdb=" O   ASN A4174 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   LEU A4194 " --> pdb=" O   ILE A4190 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ARG A4195 " --> pdb=" O   GLN A4191 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   TYR A4196 " --> pdb=" O   GLU A4192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4197 through 4202
      removed outlier: 3.510A  pdb=" N   TRP A4201 " --> pdb=" O   ALA A4197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4208 through 4227
      removed outlier: 3.609A  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 4249
    Processing helix  chain 'A' and resid 4250 through 4255
      removed outlier: 3.997A  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 4301 through 4311
      removed outlier: 3.581A  pdb=" N   PHE A4305 " --> pdb=" O   ARG A4301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4317 through 4322
    Processing helix  chain 'A' and resid 4325 through 4346
      removed outlier: 4.412A  pdb=" N   ARG A4329 " --> pdb=" O   ASN A4325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4376 through 4391
    Processing helix  chain 'A' and resid 4407 through 4439
    Processing helix  chain 'A' and resid 4445 through 4458
      removed outlier: 3.640A  pdb=" N   LYS A4457 " --> pdb=" O   ASN A4453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4474 through 4500
    Processing helix  chain 'A' and resid 4516 through 4531
    Processing helix  chain 'A' and resid 4532 through 4534
      No H-bonds generated for 'chain 'A' and resid 4532 through 4534'
    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
      removed outlier: 3.525A  pdb=" N   PHE A4635 " --> pdb=" O   ASP A4631 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1477 through 1480
      removed outlier: 3.777A  pdb=" N   CYS A1484 " --> pdb=" O   TYR A1480 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1661 through 1666
      removed outlier: 6.741A  pdb=" N   SER A1677 " --> pdb=" O   SER A1662 " (cutoff:3.500A)
      removed outlier: 4.769A  pdb=" N   ILE A1664 " --> pdb=" O   GLY A1675 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   GLY A1675 " --> pdb=" O   ILE A1664 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   LEU A1666 " --> pdb=" O   VAL A1673 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   VAL A1673 " --> pdb=" O   LEU A1666 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   VAL A1690 " --> pdb=" O   VAL A1673 " (cutoff:3.500A)
      removed outlier: 7.874A  pdb=" N   GLY A1675 " --> pdb=" O   THR A1688 " (cutoff:3.500A)
      removed outlier: 10.900A  pdb=" N   THR A1688 " --> pdb=" O   GLY A1675 " (cutoff:3.500A)
      removed outlier: 11.572A  pdb=" N   SER A1677 " --> pdb=" O   PHE A1686 " (cutoff:3.500A)
      removed outlier: 11.555A  pdb=" N   PHE A1686 " --> pdb=" O   SER A1677 " (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 1903
      removed outlier: 6.267A  pdb=" N   GLY A1901 " --> pdb=" O   ARG A2037 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1930
      removed outlier: 6.108A  pdb=" N   LEU A1928 " --> pdb=" O   CYS A1956 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   GLY A1955 " --> pdb=" O   PHE A2015 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    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 2253
      removed outlier: 6.282A  pdb=" N   MET A2221 " --> pdb=" O   VAL A2362 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 2266 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 2621
      removed outlier: 5.995A  pdb=" N   LEU A2659 " --> pdb=" O   GLN A2707 " (cutoff:3.500A)
      removed outlier: 7.171A  pdb=" N   VAL A2709 " --> pdb=" O   LEU A2659 " (cutoff:3.500A)
      removed outlier: 5.675A  pdb=" N   LEU A2661 " --> pdb=" O   VAL A2709 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   ALA A2711 " --> pdb=" O   LEU A2661 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   CYS A2663 " --> pdb=" O   ALA A2711 " (cutoff:3.500A)
      removed outlier: 5.854A  pdb=" N   LEU A2593 " --> pdb=" O   CYS A2712 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   VAL A2592 " --> pdb=" O   VAL A2734 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2642
      removed outlier: 3.602A  pdb=" N   THR A2699 " --> pdb=" O   ARG A2694 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 2873 through 2874
      removed outlier: 3.646A  pdb=" N   SER A2874 " --> pdb=" O   ILE A2882 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 2957 through 2960
      removed outlier: 6.601A  pdb=" N   SER A2957 " --> pdb=" O   ALA A2991 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   ILE A2993 " --> pdb=" O   SER A2957 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   TYR A2959 " --> pdb=" O   ILE A2993 " (cutoff:3.500A)
      removed outlier: 8.365A  pdb=" N   ASP A2995 " --> pdb=" O   TYR A2959 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 3610 through 3613
      removed outlier: 6.159A  pdb=" N   THR A3610 " --> pdb=" O   LEU A3634 " (cutoff:3.500A)
      removed outlier: 7.555A  pdb=" N   GLN A3636 " --> pdb=" O   THR A3610 " (cutoff:3.500A)
      removed outlier: 7.312A  pdb=" N   THR A3612 " --> pdb=" O   GLN A3636 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LEU A3633 " --> pdb=" O   PHE A3678 " (cutoff:3.500A)
      removed outlier: 7.642A  pdb=" N   SER A3680 " --> pdb=" O   LEU A3633 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   VAL A3635 " --> pdb=" O   SER A3680 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 3661 through 3664
    Processing sheet with id=AB8, first strand: chain 'A' and resid 4066 through 4070
      removed outlier: 5.792A  pdb=" N   THR A4067 " --> pdb=" O   MET A4095 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   LYS A4097 " --> pdb=" O   THR A4067 " (cutoff:3.500A)
      removed outlier: 6.655A  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: 7.587A  pdb=" N   THR A4127 " --> pdb=" O   VAL A4094 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   LEU A4096 " --> pdb=" O   THR A4127 " (cutoff:3.500A)
      removed outlier: 8.385A  pdb=" N   GLU A4129 " --> pdb=" O   LEU A4096 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   LEU A4042 " --> pdb=" O   PHE A4145 " (cutoff:3.500A)
      removed outlier: 7.597A  pdb=" N   PHE A4147 " --> pdb=" O   LEU A4042 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   CYS A4044 " --> pdb=" O   PHE A4147 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 4283 through 4288
      removed outlier: 6.585A  pdb=" N   ILE A4294 " --> pdb=" O   LEU A4284 " (cutoff:3.500A)
      removed outlier: 5.527A  pdb=" N   CYS A4286 " --> pdb=" O   LYS A4292 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   LYS A4292 " --> pdb=" O   CYS A4286 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 4509 through 4510
      removed outlier: 9.992A  pdb=" N   VAL A4509 " --> pdb=" O   SER A4557 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   GLY A4559 " --> pdb=" O   VAL A4509 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 4568 through 4571
      removed outlier: 3.811A  pdb=" N   PHE A4620 " --> pdb=" O   VAL A4609 " (cutoff:3.500A)
      removed outlier: 8.331A  pdb=" N   VAL A4642 " --> pdb=" O   THR A4606 " (cutoff:3.500A)

    1325 hydrogen bonds defined for protein.
    3852 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: 6.86

  Time building geometry restraints manager: 2.88 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 7595
        1.34 -     1.46: 5278
        1.46 -     1.58: 10533
        1.58 -     1.70: 13
        1.70 -     1.82: 192
  Bond restraints: 23611
  Sorted by residual:
  bond pdb=" N   LEU A2387 "
       pdb=" CA  LEU A2387 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.21e-02 6.83e+03 5.35e+00
  bond pdb=" C   SER A4172 "
       pdb=" N   PRO A4173 "
    ideal  model  delta    sigma   weight residual
    1.331  1.360 -0.029 1.27e-02 6.20e+03 5.15e+00
  bond pdb=" CB  CYS A2454 "
       pdb=" SG  CYS A2454 "
    ideal  model  delta    sigma   weight residual
    1.808  1.753  0.055 3.30e-02 9.18e+02 2.83e+00
  bond pdb=" N   ASP A2388 "
       pdb=" CA  ASP A2388 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.63e+00
  bond pdb=" CA  GLY A3165 "
       pdb=" C   GLY A3165 "
    ideal  model  delta    sigma   weight residual
    1.530  1.516  0.015 1.04e-02 9.25e+03 2.00e+00
  ... (remaining 23606 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.35: 31913
        3.35 -     6.70: 104
        6.70 -    10.05: 11
       10.05 -    13.40: 0
       13.40 -    16.75: 1
  Bond angle restraints: 32029
  Sorted by residual:
  angle pdb=" C   ASP A3045 "
        pdb=" CA  ASP A3045 "
        pdb=" CB  ASP A3045 "
      ideal   model   delta    sigma   weight residual
     116.63  109.98    6.65 1.16e+00 7.43e-01 3.29e+01
  angle pdb=" CA  LEU A4451 "
        pdb=" CB  LEU A4451 "
        pdb=" CG  LEU A4451 "
      ideal   model   delta    sigma   weight residual
     116.30  133.05  -16.75 3.50e+00 8.16e-02 2.29e+01
  angle pdb=" CA  MET A1507 "
        pdb=" CB  MET A1507 "
        pdb=" CG  MET A1507 "
      ideal   model   delta    sigma   weight residual
     114.10  120.81   -6.71 2.00e+00 2.50e-01 1.13e+01
  angle pdb=" CA  ASP A3045 "
        pdb=" C   ASP A3045 "
        pdb=" N   SER A3046 "
      ideal   model   delta    sigma   weight residual
     119.63  116.96    2.67 8.10e-01 1.52e+00 1.09e+01
  angle pdb=" CB  MET A3043 "
        pdb=" CG  MET A3043 "
        pdb=" SD  MET A3043 "
      ideal   model   delta    sigma   weight residual
     112.70  122.43   -9.73 3.00e+00 1.11e-01 1.05e+01
  ... (remaining 32024 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.03: 12311
       18.03 -    36.06: 1498
       36.06 -    54.09: 399
       54.09 -    72.12: 88
       72.12 -    90.15: 29
  Dihedral angle restraints: 14325
    sinusoidal: 5954
      harmonic: 8371
  Sorted by residual:
  dihedral pdb=" CA  LEU A1533 "
           pdb=" C   LEU A1533 "
           pdb=" N   PHE A1534 "
           pdb=" CA  PHE A1534 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.26  -20.74     0      5.00e+00 4.00e-02 1.72e+01
  dihedral pdb=" C5' ADP A4701 "
           pdb=" O5' ADP A4701 "
           pdb=" PA  ADP A4701 "
           pdb=" O2A ADP A4701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   13.54  -73.54     1      2.00e+01 2.50e-03 1.72e+01
  dihedral pdb=" CA  LYS A2865 "
           pdb=" C   LYS A2865 "
           pdb=" N   ALA A2866 "
           pdb=" CA  ALA A2866 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.50  -18.50     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 14322 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 2764
       0.042 -    0.083: 608
       0.083 -    0.125: 218
       0.125 -    0.166: 12
       0.166 -    0.208: 1
  Chirality restraints: 3603
  Sorted by residual:
  chirality pdb=" CB  THR A3502 "
            pdb=" CA  THR A3502 "
            pdb=" OG1 THR A3502 "
            pdb=" CG2 THR A3502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CB  ILE A2138 "
            pdb=" CA  ILE A2138 "
            pdb=" CG1 ILE A2138 "
            pdb=" CG2 ILE A2138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 5.03e-01
  chirality pdb=" CA  ILE A2882 "
            pdb=" N   ILE A2882 "
            pdb=" C   ILE A2882 "
            pdb=" CB  ILE A2882 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 5.01e-01
  ... (remaining 3600 not shown)

  Planarity restraints: 4094
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A1531 "    0.010 2.00e-02 2.50e+03   1.98e-02 3.92e+00
        pdb=" C   MET A1531 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   MET A1531 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ALA A1532 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A2773 "    0.010 2.00e-02 2.50e+03   1.93e-02 3.74e+00
        pdb=" C   MET A2773 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   MET A2773 "    0.012 2.00e-02 2.50e+03
        pdb=" N   VAL A2774 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A4172 "    0.032 5.00e-02 4.00e+02   4.79e-02 3.66e+00
        pdb=" N   PRO A4173 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A4173 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A4173 "    0.027 5.00e-02 4.00e+02
  ... (remaining 4091 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 209
        2.60 -     3.17: 19915
        3.17 -     3.75: 37640
        3.75 -     4.32: 50038
        4.32 -     4.90: 84246
  Nonbonded interactions: 192048
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A2602 "
            pdb="MG    MG A4705 "
     model   vdw
     2.020 2.170
  nonbonded pdb=" O2G ATP A4703 "
            pdb="MG    MG A4705 "
     model   vdw
     2.032 2.170
  nonbonded pdb=" O   TYR A4447 "
            pdb=" OG1 THR A4450 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" O   ALA A2497 "
            pdb=" OG  SER A2501 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OG  SER A2231 "
            pdb=" O1B ATP A4702 "
     model   vdw
     2.198 3.040
  ... (remaining 192043 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.480
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
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   0.055  23611  Z= 0.127
  Angle     :  0.570  16.751  32029  Z= 0.294
  Chirality :  0.039   0.208   3603
  Planarity :  0.004   0.048   4094
  Dihedral  : 17.272  90.147   8885
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.64 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  : 21.50 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.16), residues: 2844
  helix:  1.79 (0.13), residues: 1585
  sheet: -0.61 (0.35), residues: 233
  loop : -0.03 (0.21), residues: 1026

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A3682 
 TYR   0.024   0.001   TYR A2170 
 PHE   0.014   0.001   PHE A3813 
 TRP   0.019   0.001   TRP A4376 
 HIS   0.004   0.000   HIS A1817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (23611)
  covalent geometry    : angle       0.56993 (32029)
  hydrogen bonds       : bond        0.12805 ( 1325)
  hydrogen bonds       : angle       5.49293 ( 3852)

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

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

  5688 Ramachandran restraints generated.
    2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5688 Ramachandran restraints generated.
    2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 235
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1967 MET cc_start: 0.8257 (mmp) cc_final: 0.7880 (tpt)
  outliers start: 9
  outliers final: 4
  residues processed: 240
  average time/residue: 0.1484
  time to fit residues: 56.0524
Evaluate side-chains
  230 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 226
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1589 MET
Chi-restraints excluded: chain A residue 1854 LEU
Chi-restraints excluded: chain A residue 2031 ASN
Chi-restraints excluded: chain A residue 3710 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 285
   random chunks:
   chunk 197 optimal weight:    4.9990
   chunk 215 optimal weight:   10.0000
   chunk 20 optimal weight:    8.9990
   chunk 132 optimal weight:    3.9990
   chunk 261 optimal weight:    6.9990
   chunk 248 optimal weight:    4.9990
   chunk 207 optimal weight:    3.9990
   chunk 155 optimal weight:    3.9990
   chunk 244 optimal weight:    3.9990
   chunk 183 optimal weight:    0.2980
   chunk 111 optimal weight:    0.8980
   overall best weight:    2.6386

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

Flipped N/Q/H residues before XYZ refinement:
A1748 GLN
** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2296 GLN
A2752 ASN
A3202 ASN
A3622 ASN
A4038 ASN
A4381 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.134669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.094707 restraints weight = 36652.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 2.90
r_work: 0.3008 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.0858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055  23611  Z= 0.248
  Angle     :  0.599  10.390  32029  Z= 0.301
  Chirality :  0.042   0.157   3603
  Planarity :  0.004   0.046   4094
  Dihedral  :  6.997  87.994   3204
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.81 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 19.54 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.16), residues: 2844
  helix:  1.98 (0.13), residues: 1617
  sheet: -0.87 (0.36), residues: 226
  loop : -0.11 (0.21), residues: 1001

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1962 
 TYR   0.019   0.002   TYR A2748 
 PHE   0.021   0.002   PHE A3813 
 TRP   0.017   0.001   TRP A2234 
 HIS   0.005   0.001   HIS A4119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00597 (23611)
  covalent geometry    : angle       0.59931 (32029)
  hydrogen bonds       : bond        0.04728 ( 1325)
  hydrogen bonds       : angle       4.34889 ( 3852)

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

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

  5688 Ramachandran restraints generated.
    2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5688 Ramachandran restraints generated.
    2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 240
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
REVERT: A 1679 ARG cc_start: 0.8595 (ttp80) cc_final: 0.8250 (ttp80)
REVERT: A 1941 MET cc_start: 0.8006 (ttm) cc_final: 0.7737 (ttm)
REVERT: A 1967 MET cc_start: 0.7954 (mmp) cc_final: 0.7654 (tpt)
REVERT: A 2286 LYS cc_start: 0.8385 (mttt) cc_final: 0.8152 (ttmm)
REVERT: A 2614 ASP cc_start: 0.8672 (p0) cc_final: 0.8358 (p0)
REVERT: A 2855 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8415 (mm)
REVERT: A 2881 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.8014 (m-80)
REVERT: A 3001 ASP cc_start: 0.8674 (p0) cc_final: 0.8365 (p0)
REVERT: A 3068 MET cc_start: 0.8807 (ptm) cc_final: 0.8329 (ptp)
REVERT: A 3169 MET cc_start: 0.8470 (mmt) cc_final: 0.8244 (mmm)
REVERT: A 3611 ARG cc_start: 0.8565 (mtp85) cc_final: 0.8267 (mtt-85)
REVERT: A 3910 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7590 (ptp-110)
REVERT: A 4018 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.6661 (mmm)
  outliers start: 64
  outliers final: 33
  residues processed: 285
  average time/residue: 0.1639
  time to fit residues: 73.0929
Evaluate side-chains
  258 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 221
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1510 SER
Chi-restraints excluded: chain A residue 1634 ASP
Chi-restraints excluded: chain A residue 1749 LEU
Chi-restraints excluded: chain A residue 1851 THR
Chi-restraints excluded: chain A residue 2157 LEU
Chi-restraints excluded: chain A residue 2171 HIS
Chi-restraints excluded: chain A residue 2204 VAL
Chi-restraints excluded: chain A residue 2226 SER
Chi-restraints excluded: chain A residue 2247 VAL
Chi-restraints excluded: chain A residue 2352 THR
Chi-restraints excluded: chain A residue 2371 THR
Chi-restraints excluded: chain A residue 2607 SER
Chi-restraints excluded: chain A residue 2623 SER
Chi-restraints excluded: chain A residue 2813 LEU
Chi-restraints excluded: chain A residue 2855 LEU
Chi-restraints excluded: chain A residue 2881 TYR
Chi-restraints excluded: chain A residue 2905 LEU
Chi-restraints excluded: chain A residue 2925 ILE
Chi-restraints excluded: chain A residue 3087 ASN
Chi-restraints excluded: chain A residue 3154 LEU
Chi-restraints excluded: chain A residue 3629 PHE
Chi-restraints excluded: chain A residue 3677 ILE
Chi-restraints excluded: chain A residue 3685 THR
Chi-restraints excluded: chain A residue 3704 THR
Chi-restraints excluded: chain A residue 3910 ARG
Chi-restraints excluded: chain A residue 3915 VAL
Chi-restraints excluded: chain A residue 3921 THR
Chi-restraints excluded: chain A residue 3961 LEU
Chi-restraints excluded: chain A residue 4018 MET
Chi-restraints excluded: chain A residue 4084 ILE
Chi-restraints excluded: chain A residue 4163 SER
Chi-restraints excluded: chain A residue 4199 LEU
Chi-restraints excluded: chain A residue 4291 HIS
Chi-restraints excluded: chain A residue 4380 LEU
Chi-restraints excluded: chain A residue 4438 CYS
Chi-restraints excluded: chain A residue 4463 SER
Chi-restraints excluded: chain A residue 4509 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 285
   random chunks:
   chunk 125 optimal weight:    0.7980
   chunk 178 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 215 optimal weight:    8.9990
   chunk 9 optimal weight:    8.9990
   chunk 166 optimal weight:    0.0970
   chunk 120 optimal weight:    1.9990
   chunk 164 optimal weight:    1.9990
   chunk 124 optimal weight:    0.6980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A2998 ASN
A4326 ASN
A4526 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.137295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.097480 restraints weight = 36214.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 2.92
r_work: 0.3050 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.0952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  23611  Z= 0.123
  Angle     :  0.508   7.791  32029  Z= 0.254
  Chirality :  0.039   0.152   3603
  Planarity :  0.004   0.055   4094
  Dihedral  :  6.713  88.958   3196
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.46 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 19.85 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.76 (0.16), residues: 2844
  helix:  2.27 (0.13), residues: 1608
  sheet: -0.74 (0.36), residues: 220
  loop : -0.14 (0.20), residues: 1016

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1962 
 TYR   0.017   0.001   TYR A2748 
 PHE   0.018   0.001   PHE A3813 
 TRP   0.016   0.001   TRP A1701 
 HIS   0.003   0.001   HIS A1817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (23611)
  covalent geometry    : angle       0.50758 (32029)
  hydrogen bonds       : bond        0.04026 ( 1325)
  hydrogen bonds       : angle       4.08909 ( 3852)

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

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

  5688 Ramachandran restraints generated.
    2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5688 Ramachandran restraints generated.
    2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 244
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
REVERT: A 1892 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8449 (mmp)
REVERT: A 1931 ASN cc_start: 0.8004 (p0) cc_final: 0.7457 (p0)
REVERT: A 1941 MET cc_start: 0.7982 (ttm) cc_final: 0.7763 (ttm)
REVERT: A 1967 MET cc_start: 0.7912 (mmp) cc_final: 0.7691 (tpt)
REVERT: A 1973 GLN cc_start: 0.7955 (mm110) cc_final: 0.7576 (mm-40)
REVERT: A 2286 LYS cc_start: 0.8401 (mttt) cc_final: 0.8168 (ttmm)
REVERT: A 2614 ASP cc_start: 0.8602 (p0) cc_final: 0.8335 (p0)
REVERT: A 2632 LEU cc_start: 0.8407 (mm) cc_final: 0.8205 (mm)
REVERT: A 2855 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8443 (mm)
REVERT: A 2867 MET cc_start: 0.5501 (pmm) cc_final: 0.4772 (pmm)
REVERT: A 2881 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.8085 (m-80)
REVERT: A 3001 ASP cc_start: 0.8701 (p0) cc_final: 0.8437 (p0)
REVERT: A 3610 THR cc_start: 0.7255 (m) cc_final: 0.6811 (p)
REVERT: A 4018 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.6070 (mmm)
  outliers start: 67
  outliers final: 32
  residues processed: 290
  average time/residue: 0.1572
  time to fit residues: 71.7520
Evaluate side-chains
  264 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 228
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1510 SER
Chi-restraints excluded: chain A residue 1634 ASP
Chi-restraints excluded: chain A residue 1749 LEU
Chi-restraints excluded: chain A residue 1854 LEU
Chi-restraints excluded: chain A residue 1892 MET
Chi-restraints excluded: chain A residue 2031 ASN
Chi-restraints excluded: chain A residue 2157 LEU
Chi-restraints excluded: chain A residue 2171 HIS
Chi-restraints excluded: chain A residue 2175 MET
Chi-restraints excluded: chain A residue 2204 VAL
Chi-restraints excluded: chain A residue 2226 SER
Chi-restraints excluded: chain A residue 2247 VAL
Chi-restraints excluded: chain A residue 2291 VAL
Chi-restraints excluded: chain A residue 2352 THR
Chi-restraints excluded: chain A residue 2371 THR
Chi-restraints excluded: chain A residue 2813 LEU
Chi-restraints excluded: chain A residue 2855 LEU
Chi-restraints excluded: chain A residue 2881 TYR
Chi-restraints excluded: chain A residue 2925 ILE
Chi-restraints excluded: chain A residue 3087 ASN
Chi-restraints excluded: chain A residue 3154 LEU
Chi-restraints excluded: chain A residue 3198 GLN
Chi-restraints excluded: chain A residue 3549 ARG
Chi-restraints excluded: chain A residue 3629 PHE
Chi-restraints excluded: chain A residue 3639 GLU
Chi-restraints excluded: chain A residue 3677 ILE
Chi-restraints excluded: chain A residue 3771 GLU
Chi-restraints excluded: chain A residue 3833 LEU
Chi-restraints excluded: chain A residue 3915 VAL
Chi-restraints excluded: chain A residue 3929 VAL
Chi-restraints excluded: chain A residue 3961 LEU
Chi-restraints excluded: chain A residue 4018 MET
Chi-restraints excluded: chain A residue 4084 ILE
Chi-restraints excluded: chain A residue 4291 HIS
Chi-restraints excluded: chain A residue 4376 TRP
Chi-restraints excluded: chain A residue 4380 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 285
   random chunks:
   chunk 169 optimal weight:    7.9990
   chunk 4 optimal weight:   20.0000
   chunk 16 optimal weight:    6.9990
   chunk 172 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 202 optimal weight:    4.9990
   chunk 105 optimal weight:    3.9990
   chunk 152 optimal weight:    4.9990
   chunk 224 optimal weight:    3.9990
   chunk 276 optimal weight:    9.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A1922 GLN
** A2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A4526 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.134630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.095359 restraints weight = 36451.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 2.76
r_work: 0.3018 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.1261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  23611  Z= 0.214
  Angle     :  0.561   8.424  32029  Z= 0.280
  Chirality :  0.041   0.154   3603
  Planarity :  0.004   0.049   4094
  Dihedral  :  6.669  87.443   3196
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.88 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 19.97 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.63 (0.16), residues: 2844
  helix:  2.18 (0.13), residues: 1608
  sheet: -0.97 (0.35), residues: 225
  loop : -0.19 (0.20), residues: 1011

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1679 
 TYR   0.019   0.001   TYR A2748 
 PHE   0.020   0.001   PHE A3813 
 TRP   0.018   0.001   TRP A1701 
 HIS   0.005   0.001   HIS A2085 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 (23611)
  covalent geometry    : angle       0.56150 (32029)
  hydrogen bonds       : bond        0.04270 ( 1325)
  hydrogen bonds       : angle       4.13475 ( 3852)

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

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

  5688 Ramachandran restraints generated.
    2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5688 Ramachandran restraints generated.
    2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 230
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
REVERT: A 1892 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8438 (mmp)
REVERT: A 1931 ASN cc_start: 0.8084 (p0) cc_final: 0.7480 (p0)
REVERT: A 1941 MET cc_start: 0.8102 (ttm) cc_final: 0.7778 (ttm)
REVERT: A 2286 LYS cc_start: 0.8408 (mttt) cc_final: 0.8188 (ttmm)
REVERT: A 2614 ASP cc_start: 0.8624 (p0) cc_final: 0.8406 (p0)
REVERT: A 2855 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8466 (mm)
REVERT: A 2867 MET cc_start: 0.5640 (pmm) cc_final: 0.5279 (pmm)
REVERT: A 2881 TYR cc_start: 0.8841 (OUTLIER) cc_final: 0.8031 (m-80)
REVERT: A 3001 ASP cc_start: 0.8633 (p0) cc_final: 0.8421 (p0)
REVERT: A 3610 THR cc_start: 0.7180 (m) cc_final: 0.6585 (p)
REVERT: A 4018 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.6608 (mmm)
REVERT: A 4466 HIS cc_start: 0.8064 (m90) cc_final: 0.7824 (m-70)
  outliers start: 77
  outliers final: 49
  residues processed: 284
  average time/residue: 0.1539
  time to fit residues: 70.0897
Evaluate side-chains
  274 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 221
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1510 SER
Chi-restraints excluded: chain A residue 1634 ASP
Chi-restraints excluded: chain A residue 1650 LEU
Chi-restraints excluded: chain A residue 1851 THR
Chi-restraints excluded: chain A residue 1854 LEU
Chi-restraints excluded: chain A residue 1892 MET
Chi-restraints excluded: chain A residue 2031 ASN
Chi-restraints excluded: chain A residue 2157 LEU
Chi-restraints excluded: chain A residue 2171 HIS
Chi-restraints excluded: chain A residue 2175 MET
Chi-restraints excluded: chain A residue 2204 VAL
Chi-restraints excluded: chain A residue 2226 SER
Chi-restraints excluded: chain A residue 2247 VAL
Chi-restraints excluded: chain A residue 2291 VAL
Chi-restraints excluded: chain A residue 2352 THR
Chi-restraints excluded: chain A residue 2371 THR
Chi-restraints excluded: chain A residue 2454 CYS
Chi-restraints excluded: chain A residue 2800 THR
Chi-restraints excluded: chain A residue 2855 LEU
Chi-restraints excluded: chain A residue 2881 TYR
Chi-restraints excluded: chain A residue 2905 LEU
Chi-restraints excluded: chain A residue 2925 ILE
Chi-restraints excluded: chain A residue 3056 SER
Chi-restraints excluded: chain A residue 3087 ASN
Chi-restraints excluded: chain A residue 3154 LEU
Chi-restraints excluded: chain A residue 3495 THR
Chi-restraints excluded: chain A residue 3629 PHE
Chi-restraints excluded: chain A residue 3639 GLU
Chi-restraints excluded: chain A residue 3677 ILE
Chi-restraints excluded: chain A residue 3704 THR
Chi-restraints excluded: chain A residue 3771 GLU
Chi-restraints excluded: chain A residue 3833 LEU
Chi-restraints excluded: chain A residue 3915 VAL
Chi-restraints excluded: chain A residue 3921 THR
Chi-restraints excluded: chain A residue 3929 VAL
Chi-restraints excluded: chain A residue 3961 LEU
Chi-restraints excluded: chain A residue 4018 MET
Chi-restraints excluded: chain A residue 4027 LEU
Chi-restraints excluded: chain A residue 4042 LEU
Chi-restraints excluded: chain A residue 4066 ILE
Chi-restraints excluded: chain A residue 4084 ILE
Chi-restraints excluded: chain A residue 4163 SER
Chi-restraints excluded: chain A residue 4270 GLU
Chi-restraints excluded: chain A residue 4274 THR
Chi-restraints excluded: chain A residue 4291 HIS
Chi-restraints excluded: chain A residue 4306 VAL
Chi-restraints excluded: chain A residue 4315 THR
Chi-restraints excluded: chain A residue 4346 MET
Chi-restraints excluded: chain A residue 4376 TRP
Chi-restraints excluded: chain A residue 4380 LEU
Chi-restraints excluded: chain A residue 4463 SER
Chi-restraints excluded: chain A residue 4509 VAL
Chi-restraints excluded: chain A residue 4537 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 285
   random chunks:
   chunk 232 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   chunk 210 optimal weight:    2.9990
   chunk 128 optimal weight:    0.7980
   chunk 161 optimal weight:    5.9990
   chunk 156 optimal weight:    0.7980
   chunk 235 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 168 optimal weight:    7.9990
   chunk 77 optimal weight:    0.6980
   chunk 53 optimal weight:   10.0000
   overall best weight:    1.2584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.136040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.096949 restraints weight = 36265.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 2.77
r_work: 0.3042 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.1305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  23611  Z= 0.141
  Angle     :  0.516   8.291  32029  Z= 0.256
  Chirality :  0.040   0.162   3603
  Planarity :  0.004   0.055   4094
  Dihedral  :  6.595  85.619   3196
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.60 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 20.28 %
    Favored  : 76.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.76 (0.16), residues: 2844
  helix:  2.31 (0.13), residues: 1606
  sheet: -0.97 (0.35), residues: 225
  loop : -0.14 (0.20), residues: 1013

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1679 
 TYR   0.015   0.001   TYR A2748 
 PHE   0.018   0.001   PHE A3813 
 TRP   0.017   0.001   TRP A1701 
 HIS   0.003   0.001   HIS A4119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (23611)
  covalent geometry    : angle       0.51581 (32029)
  hydrogen bonds       : bond        0.03950 ( 1325)
  hydrogen bonds       : angle       4.02281 ( 3852)

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

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

  5688 Ramachandran restraints generated.
    2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5688 Ramachandran restraints generated.
    2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 237
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
REVERT: A 1892 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8388 (mmp)
REVERT: A 1931 ASN cc_start: 0.8047 (p0) cc_final: 0.7515 (p0)
REVERT: A 1941 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7535 (tpp)
REVERT: A 1973 GLN cc_start: 0.7938 (mm110) cc_final: 0.7582 (mm-40)
REVERT: A 2205 GLU cc_start: 0.8383 (tp30) cc_final: 0.8146 (tp30)
REVERT: A 2286 LYS cc_start: 0.8397 (mttt) cc_final: 0.8180 (ttmm)
REVERT: A 2881 TYR cc_start: 0.8853 (OUTLIER) cc_final: 0.8053 (m-80)
REVERT: A 3001 ASP cc_start: 0.8641 (p0) cc_final: 0.8425 (p0)
REVERT: A 3029 LEU cc_start: 0.9012 (tp) cc_final: 0.8746 (tt)
REVERT: A 3610 THR cc_start: 0.7134 (m) cc_final: 0.6478 (p)
REVERT: A 4018 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.6338 (mmm)
REVERT: A 4433 ASP cc_start: 0.6729 (t0) cc_final: 0.6446 (t0)
REVERT: A 4466 HIS cc_start: 0.8110 (m90) cc_final: 0.7835 (m-70)
  outliers start: 73
  outliers final: 53
  residues processed: 286
  average time/residue: 0.1619
  time to fit residues: 73.9325
Evaluate side-chains
  283 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 226
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1510 SER
Chi-restraints excluded: chain A residue 1634 ASP
Chi-restraints excluded: chain A residue 1650 LEU
Chi-restraints excluded: chain A residue 1851 THR
Chi-restraints excluded: chain A residue 1854 LEU
Chi-restraints excluded: chain A residue 1892 MET
Chi-restraints excluded: chain A residue 1941 MET
Chi-restraints excluded: chain A residue 2031 ASN
Chi-restraints excluded: chain A residue 2053 MET
Chi-restraints excluded: chain A residue 2157 LEU
Chi-restraints excluded: chain A residue 2171 HIS
Chi-restraints excluded: chain A residue 2175 MET
Chi-restraints excluded: chain A residue 2204 VAL
Chi-restraints excluded: chain A residue 2226 SER
Chi-restraints excluded: chain A residue 2247 VAL
Chi-restraints excluded: chain A residue 2291 VAL
Chi-restraints excluded: chain A residue 2352 THR
Chi-restraints excluded: chain A residue 2371 THR
Chi-restraints excluded: chain A residue 2534 ILE
Chi-restraints excluded: chain A residue 2607 SER
Chi-restraints excluded: chain A residue 2800 THR
Chi-restraints excluded: chain A residue 2881 TYR
Chi-restraints excluded: chain A residue 2905 LEU
Chi-restraints excluded: chain A residue 2925 ILE
Chi-restraints excluded: chain A residue 3087 ASN
Chi-restraints excluded: chain A residue 3154 LEU
Chi-restraints excluded: chain A residue 3495 THR
Chi-restraints excluded: chain A residue 3549 ARG
Chi-restraints excluded: chain A residue 3629 PHE
Chi-restraints excluded: chain A residue 3639 GLU
Chi-restraints excluded: chain A residue 3677 ILE
Chi-restraints excluded: chain A residue 3704 THR
Chi-restraints excluded: chain A residue 3771 GLU
Chi-restraints excluded: chain A residue 3833 LEU
Chi-restraints excluded: chain A residue 3915 VAL
Chi-restraints excluded: chain A residue 3921 THR
Chi-restraints excluded: chain A residue 3929 VAL
Chi-restraints excluded: chain A residue 3961 LEU
Chi-restraints excluded: chain A residue 4018 MET
Chi-restraints excluded: chain A residue 4027 LEU
Chi-restraints excluded: chain A residue 4042 LEU
Chi-restraints excluded: chain A residue 4066 ILE
Chi-restraints excluded: chain A residue 4094 VAL
Chi-restraints excluded: chain A residue 4163 SER
Chi-restraints excluded: chain A residue 4199 LEU
Chi-restraints excluded: chain A residue 4270 GLU
Chi-restraints excluded: chain A residue 4274 THR
Chi-restraints excluded: chain A residue 4275 THR
Chi-restraints excluded: chain A residue 4291 HIS
Chi-restraints excluded: chain A residue 4315 THR
Chi-restraints excluded: chain A residue 4346 MET
Chi-restraints excluded: chain A residue 4376 TRP
Chi-restraints excluded: chain A residue 4380 LEU
Chi-restraints excluded: chain A residue 4435 VAL
Chi-restraints excluded: chain A residue 4438 CYS
Chi-restraints excluded: chain A residue 4509 VAL
Chi-restraints excluded: chain A residue 4537 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 285
   random chunks:
   chunk 198 optimal weight:    6.9990
   chunk 154 optimal weight:   10.0000
   chunk 203 optimal weight:    1.9990
   chunk 233 optimal weight:    6.9990
   chunk 280 optimal weight:    2.9990
   chunk 52 optimal weight:    0.3980
   chunk 159 optimal weight:    0.9990
   chunk 104 optimal weight:    1.9990
   chunk 212 optimal weight:    2.9990
   chunk 134 optimal weight:    5.9990
   chunk 249 optimal weight:    1.9990
   overall best weight:    1.4788

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

Flipped N/Q/H residues before XYZ refinement:
** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.135548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.096370 restraints weight = 36571.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 2.78
r_work: 0.3035 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.1429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  23611  Z= 0.158
  Angle     :  0.527   8.764  32029  Z= 0.262
  Chirality :  0.040   0.159   3603
  Planarity :  0.004   0.054   4094
  Dihedral  :  6.503  88.842   3196
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.06 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 20.20 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.75 (0.16), residues: 2844
  helix:  2.32 (0.13), residues: 1605
  sheet: -1.00 (0.35), residues: 225
  loop : -0.17 (0.20), residues: 1014

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1679 
 TYR   0.017   0.001   TYR A2748 
 PHE   0.019   0.001   PHE A3813 
 TRP   0.030   0.001   TRP A4478 
 HIS   0.003   0.001   HIS A4119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (23611)
  covalent geometry    : angle       0.52737 (32029)
  hydrogen bonds       : bond        0.03945 ( 1325)
  hydrogen bonds       : angle       4.00050 ( 3852)

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

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

  5688 Ramachandran restraints generated.
    2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5688 Ramachandran restraints generated.
    2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 240
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
REVERT: A 1892 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8426 (mmp)
REVERT: A 1931 ASN cc_start: 0.8052 (p0) cc_final: 0.7520 (p0)
REVERT: A 1973 GLN cc_start: 0.7948 (mm110) cc_final: 0.7593 (mm-40)
REVERT: A 2205 GLU cc_start: 0.8421 (tp30) cc_final: 0.8186 (tp30)
REVERT: A 2286 LYS cc_start: 0.8393 (mttt) cc_final: 0.8179 (ttmm)
REVERT: A 2855 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8331 (mm)
REVERT: A 2881 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.8080 (m-80)
REVERT: A 3001 ASP cc_start: 0.8661 (p0) cc_final: 0.8442 (p0)
REVERT: A 3029 LEU cc_start: 0.8997 (tp) cc_final: 0.8765 (tt)
REVERT: A 3610 THR cc_start: 0.7153 (m) cc_final: 0.6483 (p)
REVERT: A 3682 ARG cc_start: 0.8693 (mmm160) cc_final: 0.8424 (mmm160)
REVERT: A 4018 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.6430 (mmm)
REVERT: A 4466 HIS cc_start: 0.8088 (m90) cc_final: 0.7834 (m-70)
  outliers start: 80
  outliers final: 63
  residues processed: 295
  average time/residue: 0.1670
  time to fit residues: 78.0869
Evaluate side-chains
  295 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 228
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1510 SER
Chi-restraints excluded: chain A residue 1632 VAL
Chi-restraints excluded: chain A residue 1634 ASP
Chi-restraints excluded: chain A residue 1650 LEU
Chi-restraints excluded: chain A residue 1851 THR
Chi-restraints excluded: chain A residue 1854 LEU
Chi-restraints excluded: chain A residue 1892 MET
Chi-restraints excluded: chain A residue 1941 MET
Chi-restraints excluded: chain A residue 2031 ASN
Chi-restraints excluded: chain A residue 2053 MET
Chi-restraints excluded: chain A residue 2157 LEU
Chi-restraints excluded: chain A residue 2171 HIS
Chi-restraints excluded: chain A residue 2175 MET
Chi-restraints excluded: chain A residue 2204 VAL
Chi-restraints excluded: chain A residue 2226 SER
Chi-restraints excluded: chain A residue 2247 VAL
Chi-restraints excluded: chain A residue 2291 VAL
Chi-restraints excluded: chain A residue 2371 THR
Chi-restraints excluded: chain A residue 2490 ILE
Chi-restraints excluded: chain A residue 2534 ILE
Chi-restraints excluded: chain A residue 2607 SER
Chi-restraints excluded: chain A residue 2800 THR
Chi-restraints excluded: chain A residue 2855 LEU
Chi-restraints excluded: chain A residue 2881 TYR
Chi-restraints excluded: chain A residue 2905 LEU
Chi-restraints excluded: chain A residue 2925 ILE
Chi-restraints excluded: chain A residue 2961 ILE
Chi-restraints excluded: chain A residue 3056 SER
Chi-restraints excluded: chain A residue 3087 ASN
Chi-restraints excluded: chain A residue 3154 LEU
Chi-restraints excluded: chain A residue 3201 LEU
Chi-restraints excluded: chain A residue 3495 THR
Chi-restraints excluded: chain A residue 3549 ARG
Chi-restraints excluded: chain A residue 3612 THR
Chi-restraints excluded: chain A residue 3629 PHE
Chi-restraints excluded: chain A residue 3639 GLU
Chi-restraints excluded: chain A residue 3677 ILE
Chi-restraints excluded: chain A residue 3704 THR
Chi-restraints excluded: chain A residue 3767 ILE
Chi-restraints excluded: chain A residue 3771 GLU
Chi-restraints excluded: chain A residue 3833 LEU
Chi-restraints excluded: chain A residue 3915 VAL
Chi-restraints excluded: chain A residue 3921 THR
Chi-restraints excluded: chain A residue 3929 VAL
Chi-restraints excluded: chain A residue 3961 LEU
Chi-restraints excluded: chain A residue 4018 MET
Chi-restraints excluded: chain A residue 4027 LEU
Chi-restraints excluded: chain A residue 4042 LEU
Chi-restraints excluded: chain A residue 4046 VAL
Chi-restraints excluded: chain A residue 4058 LEU
Chi-restraints excluded: chain A residue 4066 ILE
Chi-restraints excluded: chain A residue 4094 VAL
Chi-restraints excluded: chain A residue 4163 SER
Chi-restraints excluded: chain A residue 4199 LEU
Chi-restraints excluded: chain A residue 4270 GLU
Chi-restraints excluded: chain A residue 4274 THR
Chi-restraints excluded: chain A residue 4275 THR
Chi-restraints excluded: chain A residue 4291 HIS
Chi-restraints excluded: chain A residue 4306 VAL
Chi-restraints excluded: chain A residue 4346 MET
Chi-restraints excluded: chain A residue 4376 TRP
Chi-restraints excluded: chain A residue 4380 LEU
Chi-restraints excluded: chain A residue 4435 VAL
Chi-restraints excluded: chain A residue 4438 CYS
Chi-restraints excluded: chain A residue 4463 SER
Chi-restraints excluded: chain A residue 4509 VAL
Chi-restraints excluded: chain A residue 4537 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 285
   random chunks:
   chunk 284 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 234 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 210 optimal weight:    1.9990
   chunk 130 optimal weight:    2.9990
   chunk 268 optimal weight:    0.9980
   chunk 76 optimal weight:    3.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A1841 GLN
** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.135919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.098005 restraints weight = 36311.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 2.88
r_work: 0.3043 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.1481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  23611  Z= 0.147
  Angle     :  0.525   9.242  32029  Z= 0.260
  Chirality :  0.040   0.158   3603
  Planarity :  0.004   0.055   4094
  Dihedral  :  6.322  83.096   3196
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.81 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 20.40 %
    Favored  : 76.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.77 (0.16), residues: 2844
  helix:  2.34 (0.13), residues: 1605
  sheet: -0.99 (0.35), residues: 225
  loop : -0.17 (0.20), residues: 1014

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2844 
 TYR   0.015   0.001   TYR A2901 
 PHE   0.018   0.001   PHE A3813 
 TRP   0.022   0.001   TRP A4478 
 HIS   0.003   0.001   HIS A1817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (23611)
  covalent geometry    : angle       0.52526 (32029)
  hydrogen bonds       : bond        0.03877 ( 1325)
  hydrogen bonds       : angle       3.96485 ( 3852)

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

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

  5688 Ramachandran restraints generated.
    2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5688 Ramachandran restraints generated.
    2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 236
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
REVERT: A 1892 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8405 (mmp)
REVERT: A 1931 ASN cc_start: 0.8029 (p0) cc_final: 0.7526 (p0)
REVERT: A 1941 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7462 (tpp)
REVERT: A 1973 GLN cc_start: 0.7946 (mm110) cc_final: 0.7584 (mm-40)
REVERT: A 2205 GLU cc_start: 0.8379 (tp30) cc_final: 0.8120 (tp30)
REVERT: A 2286 LYS cc_start: 0.8374 (mttt) cc_final: 0.8165 (ttmm)
REVERT: A 2816 LEU cc_start: 0.9006 (tp) cc_final: 0.8800 (tp)
REVERT: A 2855 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8290 (mm)
REVERT: A 2881 TYR cc_start: 0.8847 (OUTLIER) cc_final: 0.8189 (m-80)
REVERT: A 3001 ASP cc_start: 0.8630 (p0) cc_final: 0.8405 (p0)
REVERT: A 3029 LEU cc_start: 0.8977 (tp) cc_final: 0.8745 (tt)
REVERT: A 3610 THR cc_start: 0.7105 (m) cc_final: 0.6390 (p)
REVERT: A 3682 ARG cc_start: 0.8717 (mmm160) cc_final: 0.8385 (mmm-85)
REVERT: A 4018 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.6412 (mmm)
REVERT: A 4131 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8460 (t0)
REVERT: A 4466 HIS cc_start: 0.8046 (m90) cc_final: 0.7774 (m-70)
  outliers start: 81
  outliers final: 65
  residues processed: 290
  average time/residue: 0.1648
  time to fit residues: 76.3117
Evaluate side-chains
  300 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 229
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1510 SER
Chi-restraints excluded: chain A residue 1632 VAL
Chi-restraints excluded: chain A residue 1634 ASP
Chi-restraints excluded: chain A residue 1650 LEU
Chi-restraints excluded: chain A residue 1851 THR
Chi-restraints excluded: chain A residue 1854 LEU
Chi-restraints excluded: chain A residue 1892 MET
Chi-restraints excluded: chain A residue 1941 MET
Chi-restraints excluded: chain A residue 2031 ASN
Chi-restraints excluded: chain A residue 2053 MET
Chi-restraints excluded: chain A residue 2157 LEU
Chi-restraints excluded: chain A residue 2171 HIS
Chi-restraints excluded: chain A residue 2175 MET
Chi-restraints excluded: chain A residue 2204 VAL
Chi-restraints excluded: chain A residue 2226 SER
Chi-restraints excluded: chain A residue 2247 VAL
Chi-restraints excluded: chain A residue 2291 VAL
Chi-restraints excluded: chain A residue 2352 THR
Chi-restraints excluded: chain A residue 2371 THR
Chi-restraints excluded: chain A residue 2490 ILE
Chi-restraints excluded: chain A residue 2534 ILE
Chi-restraints excluded: chain A residue 2607 SER
Chi-restraints excluded: chain A residue 2800 THR
Chi-restraints excluded: chain A residue 2813 LEU
Chi-restraints excluded: chain A residue 2855 LEU
Chi-restraints excluded: chain A residue 2881 TYR
Chi-restraints excluded: chain A residue 2905 LEU
Chi-restraints excluded: chain A residue 2925 ILE
Chi-restraints excluded: chain A residue 2961 ILE
Chi-restraints excluded: chain A residue 3056 SER
Chi-restraints excluded: chain A residue 3087 ASN
Chi-restraints excluded: chain A residue 3154 LEU
Chi-restraints excluded: chain A residue 3495 THR
Chi-restraints excluded: chain A residue 3549 ARG
Chi-restraints excluded: chain A residue 3612 THR
Chi-restraints excluded: chain A residue 3629 PHE
Chi-restraints excluded: chain A residue 3639 GLU
Chi-restraints excluded: chain A residue 3677 ILE
Chi-restraints excluded: chain A residue 3704 THR
Chi-restraints excluded: chain A residue 3767 ILE
Chi-restraints excluded: chain A residue 3771 GLU
Chi-restraints excluded: chain A residue 3833 LEU
Chi-restraints excluded: chain A residue 3915 VAL
Chi-restraints excluded: chain A residue 3921 THR
Chi-restraints excluded: chain A residue 3929 VAL
Chi-restraints excluded: chain A residue 3961 LEU
Chi-restraints excluded: chain A residue 4018 MET
Chi-restraints excluded: chain A residue 4027 LEU
Chi-restraints excluded: chain A residue 4042 LEU
Chi-restraints excluded: chain A residue 4046 VAL
Chi-restraints excluded: chain A residue 4058 LEU
Chi-restraints excluded: chain A residue 4066 ILE
Chi-restraints excluded: chain A residue 4073 SER
Chi-restraints excluded: chain A residue 4094 VAL
Chi-restraints excluded: chain A residue 4131 ASN
Chi-restraints excluded: chain A residue 4163 SER
Chi-restraints excluded: chain A residue 4199 LEU
Chi-restraints excluded: chain A residue 4270 GLU
Chi-restraints excluded: chain A residue 4274 THR
Chi-restraints excluded: chain A residue 4275 THR
Chi-restraints excluded: chain A residue 4291 HIS
Chi-restraints excluded: chain A residue 4306 VAL
Chi-restraints excluded: chain A residue 4346 MET
Chi-restraints excluded: chain A residue 4376 TRP
Chi-restraints excluded: chain A residue 4380 LEU
Chi-restraints excluded: chain A residue 4435 VAL
Chi-restraints excluded: chain A residue 4438 CYS
Chi-restraints excluded: chain A residue 4451 LEU
Chi-restraints excluded: chain A residue 4463 SER
Chi-restraints excluded: chain A residue 4509 VAL
Chi-restraints excluded: chain A residue 4537 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 285
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 251 optimal weight:    4.9990
   chunk 147 optimal weight:    0.9990
   chunk 259 optimal weight:    6.9990
   chunk 261 optimal weight:    0.5980
   chunk 119 optimal weight:    3.9990
   chunk 120 optimal weight:    4.9990
   chunk 138 optimal weight:    0.0170
   chunk 139 optimal weight:    3.9990
   chunk 168 optimal weight:    6.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    1.3022

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

Flipped N/Q/H residues before XYZ refinement:
** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.135529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.096188 restraints weight = 35981.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 2.86
r_work: 0.3027 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.1566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  23611  Z= 0.145
  Angle     :  0.529  10.318  32029  Z= 0.262
  Chirality :  0.040   0.156   3603
  Planarity :  0.004   0.056   4094
  Dihedral  :  6.124  79.214   3196
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.06 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 20.64 %
    Favored  : 76.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.81 (0.16), residues: 2844
  helix:  2.37 (0.13), residues: 1603
  sheet: -1.05 (0.36), residues: 201
  loop : -0.16 (0.20), residues: 1040

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2844 
 TYR   0.017   0.001   TYR A3120 
 PHE   0.018   0.001   PHE A3813 
 TRP   0.026   0.001   TRP A4478 
 HIS   0.003   0.001   HIS A1985 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (23611)
  covalent geometry    : angle       0.52883 (32029)
  hydrogen bonds       : bond        0.03837 ( 1325)
  hydrogen bonds       : angle       3.94519 ( 3852)

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

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

  5688 Ramachandran restraints generated.
    2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5688 Ramachandran restraints generated.
    2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 239
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1892 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8446 (mmp)
REVERT: A 1931 ASN cc_start: 0.8038 (p0) cc_final: 0.7547 (p0)
REVERT: A 1941 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7896 (tpp)
REVERT: A 1973 GLN cc_start: 0.7965 (mm110) cc_final: 0.7609 (mm-40)
REVERT: A 2018 MET cc_start: 0.8320 (mtp) cc_final: 0.7973 (mtp)
REVERT: A 2205 GLU cc_start: 0.8437 (tp30) cc_final: 0.8183 (tp30)
REVERT: A 2286 LYS cc_start: 0.8408 (mttt) cc_final: 0.8188 (ttmm)
REVERT: A 2371 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.8068 (m)
REVERT: A 2855 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8361 (mm)
REVERT: A 2881 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.8228 (m-80)
REVERT: A 3001 ASP cc_start: 0.8657 (p0) cc_final: 0.8424 (p0)
REVERT: A 3610 THR cc_start: 0.7159 (m) cc_final: 0.6489 (p)
REVERT: A 3611 ARG cc_start: 0.8294 (tpp80) cc_final: 0.8039 (mtt-85)
REVERT: A 3682 ARG cc_start: 0.8783 (mmm160) cc_final: 0.8440 (mmm-85)
REVERT: A 4018 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.6424 (mmm)
REVERT: A 4043 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7334 (mtt)
REVERT: A 4279 ASP cc_start: 0.8723 (m-30) cc_final: 0.8436 (m-30)
REVERT: A 4460 LEU cc_start: 0.8276 (pt) cc_final: 0.8061 (tp)
REVERT: A 4466 HIS cc_start: 0.8086 (m90) cc_final: 0.7825 (m-70)
  outliers start: 76
  outliers final: 64
  residues processed: 290
  average time/residue: 0.1646
  time to fit residues: 76.2222
Evaluate side-chains
  301 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 230
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1510 SER
Chi-restraints excluded: chain A residue 1632 VAL
Chi-restraints excluded: chain A residue 1634 ASP
Chi-restraints excluded: chain A residue 1650 LEU
Chi-restraints excluded: chain A residue 1851 THR
Chi-restraints excluded: chain A residue 1854 LEU
Chi-restraints excluded: chain A residue 1892 MET
Chi-restraints excluded: chain A residue 1941 MET
Chi-restraints excluded: chain A residue 2031 ASN
Chi-restraints excluded: chain A residue 2053 MET
Chi-restraints excluded: chain A residue 2157 LEU
Chi-restraints excluded: chain A residue 2171 HIS
Chi-restraints excluded: chain A residue 2175 MET
Chi-restraints excluded: chain A residue 2204 VAL
Chi-restraints excluded: chain A residue 2226 SER
Chi-restraints excluded: chain A residue 2247 VAL
Chi-restraints excluded: chain A residue 2291 VAL
Chi-restraints excluded: chain A residue 2352 THR
Chi-restraints excluded: chain A residue 2371 THR
Chi-restraints excluded: chain A residue 2490 ILE
Chi-restraints excluded: chain A residue 2534 ILE
Chi-restraints excluded: chain A residue 2607 SER
Chi-restraints excluded: chain A residue 2800 THR
Chi-restraints excluded: chain A residue 2813 LEU
Chi-restraints excluded: chain A residue 2855 LEU
Chi-restraints excluded: chain A residue 2881 TYR
Chi-restraints excluded: chain A residue 2905 LEU
Chi-restraints excluded: chain A residue 2925 ILE
Chi-restraints excluded: chain A residue 2961 ILE
Chi-restraints excluded: chain A residue 3056 SER
Chi-restraints excluded: chain A residue 3087 ASN
Chi-restraints excluded: chain A residue 3154 LEU
Chi-restraints excluded: chain A residue 3495 THR
Chi-restraints excluded: chain A residue 3549 ARG
Chi-restraints excluded: chain A residue 3612 THR
Chi-restraints excluded: chain A residue 3629 PHE
Chi-restraints excluded: chain A residue 3639 GLU
Chi-restraints excluded: chain A residue 3677 ILE
Chi-restraints excluded: chain A residue 3704 THR
Chi-restraints excluded: chain A residue 3767 ILE
Chi-restraints excluded: chain A residue 3771 GLU
Chi-restraints excluded: chain A residue 3833 LEU
Chi-restraints excluded: chain A residue 3915 VAL
Chi-restraints excluded: chain A residue 3921 THR
Chi-restraints excluded: chain A residue 3929 VAL
Chi-restraints excluded: chain A residue 3961 LEU
Chi-restraints excluded: chain A residue 4018 MET
Chi-restraints excluded: chain A residue 4027 LEU
Chi-restraints excluded: chain A residue 4042 LEU
Chi-restraints excluded: chain A residue 4043 MET
Chi-restraints excluded: chain A residue 4046 VAL
Chi-restraints excluded: chain A residue 4058 LEU
Chi-restraints excluded: chain A residue 4066 ILE
Chi-restraints excluded: chain A residue 4073 SER
Chi-restraints excluded: chain A residue 4094 VAL
Chi-restraints excluded: chain A residue 4163 SER
Chi-restraints excluded: chain A residue 4199 LEU
Chi-restraints excluded: chain A residue 4218 THR
Chi-restraints excluded: chain A residue 4270 GLU
Chi-restraints excluded: chain A residue 4274 THR
Chi-restraints excluded: chain A residue 4275 THR
Chi-restraints excluded: chain A residue 4291 HIS
Chi-restraints excluded: chain A residue 4306 VAL
Chi-restraints excluded: chain A residue 4346 MET
Chi-restraints excluded: chain A residue 4376 TRP
Chi-restraints excluded: chain A residue 4380 LEU
Chi-restraints excluded: chain A residue 4435 VAL
Chi-restraints excluded: chain A residue 4438 CYS
Chi-restraints excluded: chain A residue 4463 SER
Chi-restraints excluded: chain A residue 4509 VAL
Chi-restraints excluded: chain A residue 4537 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 285
   random chunks:
   chunk 109 optimal weight:    0.5980
   chunk 165 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 175 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 117 optimal weight:    0.8980
   chunk 126 optimal weight:    1.9990
   chunk 233 optimal weight:    6.9990
   chunk 2 optimal weight:    7.9990
   chunk 140 optimal weight:    0.8980
   chunk 8 optimal weight:   10.0000
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.136171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.097023 restraints weight = 36200.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 2.88
r_work: 0.3046 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.1586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  23611  Z= 0.127
  Angle     :  0.523  11.025  32029  Z= 0.258
  Chirality :  0.039   0.163   3603
  Planarity :  0.003   0.057   4094
  Dihedral  :  5.986  76.821   3196
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.53 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 20.87 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.88 (0.16), residues: 2844
  helix:  2.42 (0.13), residues: 1603
  sheet: -1.09 (0.36), residues: 212
  loop : -0.10 (0.20), residues: 1029

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2844 
 TYR   0.015   0.001   TYR A2748 
 PHE   0.017   0.001   PHE A3813 
 TRP   0.024   0.001   TRP A4478 
 HIS   0.004   0.001   HIS A1985 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (23611)
  covalent geometry    : angle       0.52332 (32029)
  hydrogen bonds       : bond        0.03707 ( 1325)
  hydrogen bonds       : angle       3.90521 ( 3852)

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

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

  5688 Ramachandran restraints generated.
    2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5688 Ramachandran restraints generated.
    2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 237
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1892 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8449 (mmp)
REVERT: A 1931 ASN cc_start: 0.7982 (p0) cc_final: 0.7500 (p0)
REVERT: A 1941 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7780 (ttm)
REVERT: A 1973 GLN cc_start: 0.7944 (mm110) cc_final: 0.7578 (mm-40)
REVERT: A 2018 MET cc_start: 0.8289 (mtp) cc_final: 0.7951 (mtp)
REVERT: A 2205 GLU cc_start: 0.8428 (tp30) cc_final: 0.8165 (tp30)
REVERT: A 2286 LYS cc_start: 0.8411 (mttt) cc_final: 0.8195 (ttmm)
REVERT: A 2371 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.8021 (m)
REVERT: A 2438 GLU cc_start: 0.8478 (tp30) cc_final: 0.8050 (mt-10)
REVERT: A 2855 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8351 (mm)
REVERT: A 2881 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.8221 (m-80)
REVERT: A 3001 ASP cc_start: 0.8661 (p0) cc_final: 0.8421 (p0)
REVERT: A 3610 THR cc_start: 0.7155 (m) cc_final: 0.6514 (p)
REVERT: A 3664 LEU cc_start: 0.8107 (tp) cc_final: 0.7708 (tt)
REVERT: A 3682 ARG cc_start: 0.8763 (mmm160) cc_final: 0.8410 (mmm-85)
REVERT: A 4018 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.6314 (mmm)
REVERT: A 4043 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7304 (mmt)
REVERT: A 4131 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8440 (t0)
REVERT: A 4279 ASP cc_start: 0.8708 (m-30) cc_final: 0.8440 (m-30)
REVERT: A 4389 HIS cc_start: 0.7469 (m90) cc_final: 0.7219 (m90)
REVERT: A 4466 HIS cc_start: 0.8081 (m90) cc_final: 0.7823 (m-70)
  outliers start: 72
  outliers final: 58
  residues processed: 283
  average time/residue: 0.1526
  time to fit residues: 68.4781
Evaluate side-chains
  296 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 230
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1510 SER
Chi-restraints excluded: chain A residue 1632 VAL
Chi-restraints excluded: chain A residue 1634 ASP
Chi-restraints excluded: chain A residue 1650 LEU
Chi-restraints excluded: chain A residue 1851 THR
Chi-restraints excluded: chain A residue 1854 LEU
Chi-restraints excluded: chain A residue 1892 MET
Chi-restraints excluded: chain A residue 1941 MET
Chi-restraints excluded: chain A residue 2031 ASN
Chi-restraints excluded: chain A residue 2053 MET
Chi-restraints excluded: chain A residue 2157 LEU
Chi-restraints excluded: chain A residue 2171 HIS
Chi-restraints excluded: chain A residue 2175 MET
Chi-restraints excluded: chain A residue 2204 VAL
Chi-restraints excluded: chain A residue 2226 SER
Chi-restraints excluded: chain A residue 2247 VAL
Chi-restraints excluded: chain A residue 2291 VAL
Chi-restraints excluded: chain A residue 2371 THR
Chi-restraints excluded: chain A residue 2528 THR
Chi-restraints excluded: chain A residue 2534 ILE
Chi-restraints excluded: chain A residue 2607 SER
Chi-restraints excluded: chain A residue 2800 THR
Chi-restraints excluded: chain A residue 2855 LEU
Chi-restraints excluded: chain A residue 2881 TYR
Chi-restraints excluded: chain A residue 2905 LEU
Chi-restraints excluded: chain A residue 2925 ILE
Chi-restraints excluded: chain A residue 2961 ILE
Chi-restraints excluded: chain A residue 3056 SER
Chi-restraints excluded: chain A residue 3087 ASN
Chi-restraints excluded: chain A residue 3154 LEU
Chi-restraints excluded: chain A residue 3495 THR
Chi-restraints excluded: chain A residue 3549 ARG
Chi-restraints excluded: chain A residue 3612 THR
Chi-restraints excluded: chain A residue 3629 PHE
Chi-restraints excluded: chain A residue 3639 GLU
Chi-restraints excluded: chain A residue 3677 ILE
Chi-restraints excluded: chain A residue 3704 THR
Chi-restraints excluded: chain A residue 3771 GLU
Chi-restraints excluded: chain A residue 3833 LEU
Chi-restraints excluded: chain A residue 3915 VAL
Chi-restraints excluded: chain A residue 3921 THR
Chi-restraints excluded: chain A residue 3929 VAL
Chi-restraints excluded: chain A residue 3961 LEU
Chi-restraints excluded: chain A residue 4018 MET
Chi-restraints excluded: chain A residue 4027 LEU
Chi-restraints excluded: chain A residue 4042 LEU
Chi-restraints excluded: chain A residue 4043 MET
Chi-restraints excluded: chain A residue 4058 LEU
Chi-restraints excluded: chain A residue 4066 ILE
Chi-restraints excluded: chain A residue 4073 SER
Chi-restraints excluded: chain A residue 4094 VAL
Chi-restraints excluded: chain A residue 4131 ASN
Chi-restraints excluded: chain A residue 4163 SER
Chi-restraints excluded: chain A residue 4218 THR
Chi-restraints excluded: chain A residue 4270 GLU
Chi-restraints excluded: chain A residue 4275 THR
Chi-restraints excluded: chain A residue 4291 HIS
Chi-restraints excluded: chain A residue 4306 VAL
Chi-restraints excluded: chain A residue 4346 MET
Chi-restraints excluded: chain A residue 4376 TRP
Chi-restraints excluded: chain A residue 4380 LEU
Chi-restraints excluded: chain A residue 4435 VAL
Chi-restraints excluded: chain A residue 4438 CYS
Chi-restraints excluded: chain A residue 4463 SER
Chi-restraints excluded: chain A residue 4509 VAL
Chi-restraints excluded: chain A residue 4537 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 285
   random chunks:
   chunk 273 optimal weight:    0.6980
   chunk 123 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9990
   chunk 122 optimal weight:    0.7980
   chunk 108 optimal weight:    3.9990
   chunk 184 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 31 optimal weight:    7.9990
   chunk 143 optimal weight:    1.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.136465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.097431 restraints weight = 36219.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 2.87
r_work: 0.3051 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.1652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  23611  Z= 0.122
  Angle     :  0.534  11.637  32029  Z= 0.263
  Chirality :  0.039   0.166   3603
  Planarity :  0.003   0.057   4094
  Dihedral  :  5.917  75.168   3196
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.71 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 21.19 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.93 (0.16), residues: 2844
  helix:  2.47 (0.13), residues: 1603
  sheet: -1.04 (0.36), residues: 212
  loop : -0.07 (0.20), residues: 1029

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2844 
 TYR   0.018   0.001   TYR A3120 
 PHE   0.018   0.001   PHE A4410 
 TRP   0.032   0.001   TRP A4478 
 HIS   0.004   0.001   HIS A1985 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (23611)
  covalent geometry    : angle       0.53411 (32029)
  hydrogen bonds       : bond        0.03651 ( 1325)
  hydrogen bonds       : angle       3.87398 ( 3852)

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

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

  5688 Ramachandran restraints generated.
    2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5688 Ramachandran restraints generated.
    2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 245
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1892 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8520 (mmp)
REVERT: A 1931 ASN cc_start: 0.7952 (p0) cc_final: 0.7451 (p0)
REVERT: A 1966 ARG cc_start: 0.8459 (ptm-80) cc_final: 0.8186 (ptt90)
REVERT: A 1973 GLN cc_start: 0.7942 (mm110) cc_final: 0.7573 (mm-40)
REVERT: A 2018 MET cc_start: 0.8303 (mtp) cc_final: 0.7951 (mtp)
REVERT: A 2205 GLU cc_start: 0.8401 (tp30) cc_final: 0.8141 (tp30)
REVERT: A 2286 LYS cc_start: 0.8405 (mttt) cc_final: 0.8184 (ttmm)
REVERT: A 2292 ARG cc_start: 0.7729 (mtp180) cc_final: 0.7401 (tpt-90)
REVERT: A 2371 THR cc_start: 0.8281 (OUTLIER) cc_final: 0.8026 (m)
REVERT: A 2855 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8373 (mm)
REVERT: A 2881 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.8179 (m-80)
REVERT: A 3001 ASP cc_start: 0.8666 (p0) cc_final: 0.8422 (p0)
REVERT: A 3029 LEU cc_start: 0.9024 (tp) cc_final: 0.8798 (tt)
REVERT: A 3030 MET cc_start: 0.8437 (mmm) cc_final: 0.7967 (mmm)
REVERT: A 3610 THR cc_start: 0.7244 (m) cc_final: 0.6630 (p)
REVERT: A 3682 ARG cc_start: 0.8782 (mmm160) cc_final: 0.8443 (mmm-85)
REVERT: A 3813 PHE cc_start: 0.8673 (m-80) cc_final: 0.8342 (m-80)
REVERT: A 4018 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.6288 (mmm)
REVERT: A 4043 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7316 (mmt)
REVERT: A 4131 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8452 (t0)
REVERT: A 4279 ASP cc_start: 0.8712 (m-30) cc_final: 0.8415 (m-30)
REVERT: A 4389 HIS cc_start: 0.7470 (m90) cc_final: 0.7213 (m90)
REVERT: A 4466 HIS cc_start: 0.8081 (m90) cc_final: 0.7836 (m-70)
  outliers start: 67
  outliers final: 54
  residues processed: 288
  average time/residue: 0.1590
  time to fit residues: 73.1045
Evaluate side-chains
  293 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 232
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1510 SER
Chi-restraints excluded: chain A residue 1632 VAL
Chi-restraints excluded: chain A residue 1634 ASP
Chi-restraints excluded: chain A residue 1650 LEU
Chi-restraints excluded: chain A residue 1851 THR
Chi-restraints excluded: chain A residue 1854 LEU
Chi-restraints excluded: chain A residue 1892 MET
Chi-restraints excluded: chain A residue 2031 ASN
Chi-restraints excluded: chain A residue 2053 MET
Chi-restraints excluded: chain A residue 2157 LEU
Chi-restraints excluded: chain A residue 2171 HIS
Chi-restraints excluded: chain A residue 2175 MET
Chi-restraints excluded: chain A residue 2204 VAL
Chi-restraints excluded: chain A residue 2226 SER
Chi-restraints excluded: chain A residue 2247 VAL
Chi-restraints excluded: chain A residue 2291 VAL
Chi-restraints excluded: chain A residue 2352 THR
Chi-restraints excluded: chain A residue 2371 THR
Chi-restraints excluded: chain A residue 2534 ILE
Chi-restraints excluded: chain A residue 2607 SER
Chi-restraints excluded: chain A residue 2800 THR
Chi-restraints excluded: chain A residue 2855 LEU
Chi-restraints excluded: chain A residue 2881 TYR
Chi-restraints excluded: chain A residue 2905 LEU
Chi-restraints excluded: chain A residue 2925 ILE
Chi-restraints excluded: chain A residue 2961 ILE
Chi-restraints excluded: chain A residue 3056 SER
Chi-restraints excluded: chain A residue 3087 ASN
Chi-restraints excluded: chain A residue 3154 LEU
Chi-restraints excluded: chain A residue 3495 THR
Chi-restraints excluded: chain A residue 3549 ARG
Chi-restraints excluded: chain A residue 3612 THR
Chi-restraints excluded: chain A residue 3629 PHE
Chi-restraints excluded: chain A residue 3639 GLU
Chi-restraints excluded: chain A residue 3677 ILE
Chi-restraints excluded: chain A residue 3704 THR
Chi-restraints excluded: chain A residue 3771 GLU
Chi-restraints excluded: chain A residue 3833 LEU
Chi-restraints excluded: chain A residue 3915 VAL
Chi-restraints excluded: chain A residue 3921 THR
Chi-restraints excluded: chain A residue 3929 VAL
Chi-restraints excluded: chain A residue 3961 LEU
Chi-restraints excluded: chain A residue 4018 MET
Chi-restraints excluded: chain A residue 4027 LEU
Chi-restraints excluded: chain A residue 4042 LEU
Chi-restraints excluded: chain A residue 4043 MET
Chi-restraints excluded: chain A residue 4046 VAL
Chi-restraints excluded: chain A residue 4058 LEU
Chi-restraints excluded: chain A residue 4094 VAL
Chi-restraints excluded: chain A residue 4131 ASN
Chi-restraints excluded: chain A residue 4163 SER
Chi-restraints excluded: chain A residue 4291 HIS
Chi-restraints excluded: chain A residue 4306 VAL
Chi-restraints excluded: chain A residue 4346 MET
Chi-restraints excluded: chain A residue 4376 TRP
Chi-restraints excluded: chain A residue 4380 LEU
Chi-restraints excluded: chain A residue 4435 VAL
Chi-restraints excluded: chain A residue 4438 CYS
Chi-restraints excluded: chain A residue 4463 SER
Chi-restraints excluded: chain A residue 4509 VAL
Chi-restraints excluded: chain A residue 4537 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 285
   random chunks:
   chunk 122 optimal weight:    2.9990
   chunk 174 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 259 optimal weight:    0.9980
   chunk 177 optimal weight:    0.6980
   chunk 192 optimal weight:    0.0270
   chunk 225 optimal weight:    0.1980
   chunk 76 optimal weight:    0.2980
   chunk 74 optimal weight:    3.9990
   chunk 248 optimal weight:    0.9990
   chunk 7 optimal weight:    8.9990
   overall best weight:    0.4438

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

Flipped N/Q/H residues before XYZ refinement:
A1985 HIS
** A2857 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.138308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.099119 restraints weight = 36079.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 2.91
r_work: 0.3081 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051  23611  Z= 0.104
  Angle     :  0.529  13.290  32029  Z= 0.258
  Chirality :  0.039   0.350   3603
  Planarity :  0.003   0.058   4094
  Dihedral  :  5.784  71.277   3196
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.60 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 21.78 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.04 (0.16), residues: 2844
  helix:  2.56 (0.13), residues: 1602
  sheet: -0.90 (0.37), residues: 201
  loop : -0.07 (0.20), residues: 1041

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2844 
 TYR   0.019   0.001   TYR A3516 
 PHE   0.018   0.001   PHE A3957 
 TRP   0.030   0.001   TRP A4478 
 HIS   0.005   0.001   HIS A1985 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (23611)
  covalent geometry    : angle       0.52878 (32029)
  hydrogen bonds       : bond        0.03465 ( 1325)
  hydrogen bonds       : angle       3.80479 ( 3852)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5980.70 seconds
wall clock time: 103 minutes 4.83 seconds (6184.83 seconds total)