Starting phenix.real_space_refine
on Fri Sep 19 10:20:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bmb_44694/09_2025/9bmb_44694.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bmb_44694/09_2025/9bmb_44694.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bmb_44694/09_2025/9bmb_44694.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bmb_44694/09_2025/9bmb_44694.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bmb_44694/09_2025/9bmb_44694.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bmb_44694/09_2025/9bmb_44694.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.003 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       9      5.49       5
     Mg      2      5.21       5
     S     122      5.16       5
     C   15646      2.51       5
     N    4254      2.21       5
     O    4584      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 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: 24617
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 24503
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3043, 24503
          Classifications: {'peptide': 3043}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 130, 'TRANS': 2909}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 114
          Unusual residues: {' MG': 2, 'ADP': 3, 'ATP': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
  Time building chain proxies: 5.84, per 1000 atoms: 0.24
  Number of scatterers: 24617
  At special positions: 0
  Unit cell: (126.146, 170.123, 177.067, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S     122     16.00
     P       9     15.00
     Mg      2     11.99
     O    4584      8.00
     N    4254      7.00
     C   15646      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: 2.61
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  6070 Ramachandran restraints generated.
    3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5788

  Finding SS restraints...
    Secondary structure from input PDB file:
      140 helices and 19 sheets defined
      63.6% alpha, 7.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1327 through 1348
    Processing helix  chain 'A' and resid 1350 through 1354
    Processing helix  chain 'A' and resid 1355 through 1372
    Processing helix  chain 'A' and resid 1374 through 1379
    Processing helix  chain 'A' and resid 1380 through 1396
    Processing helix  chain 'A' and resid 1396 through 1404
    Processing helix  chain 'A' and resid 1410 through 1421
    Processing helix  chain 'A' and resid 1430 through 1437
      removed outlier: 4.163A  pdb=" N   ILE A1434 " --> pdb=" O   THR A1430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1442 through 1473
    Processing helix  chain 'A' and resid 1489 through 1507
    Processing helix  chain 'A' and resid 1508 through 1509
      No H-bonds generated for 'chain 'A' and resid 1508 through 1509'
    Processing helix  chain 'A' and resid 1510 through 1515
    Processing helix  chain 'A' and resid 1517 through 1554
      removed outlier: 3.644A  pdb=" N   ASP A1539 " --> pdb=" O   ASP A1535 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   SER A1554 " --> pdb=" O   ILE A1550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1555 through 1561
      removed outlier: 4.056A  pdb=" N   HIS A1559 " --> pdb=" O   ALA A1555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1563 through 1585
      removed outlier: 3.778A  pdb=" N   SER A1585 " --> pdb=" O   LYS A1581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1587 through 1593
    Processing helix  chain 'A' and resid 1596 through 1626
    Processing helix  chain 'A' and resid 1627 through 1632
    Processing helix  chain 'A' and resid 1634 through 1643
    Processing helix  chain 'A' and resid 1646 through 1652
      removed outlier: 3.820A  pdb=" N   LYS A1649 " --> pdb=" O   ASN A1646 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLN A1651 " --> pdb=" O   ALA A1648 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   LYS A1652 " --> pdb=" O   LYS A1649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1653 through 1658
    Processing helix  chain 'A' and resid 1697 through 1729
      removed outlier: 3.645A  pdb=" N   ILE A1726 " --> pdb=" O   THR A1722 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LYS A1729 " --> pdb=" O   GLU A1725 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1734 through 1745
      removed outlier: 3.528A  pdb=" N   TYR A1745 " --> pdb=" O   TRP A1741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1746 through 1772
      removed outlier: 3.583A  pdb=" N   GLY A1771 " --> pdb=" O   SER A1767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1775 through 1798
      removed outlier: 3.575A  pdb=" N   MET A1798 " --> pdb=" O   ASP A1794 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1801 through 1829
      removed outlier: 3.865A  pdb=" N   HIS A1817 " --> pdb=" O   THR A1813 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1835 through 1840
    Processing helix  chain 'A' and resid 1852 through 1855
    Processing helix  chain 'A' and resid 1882 through 1898
    Processing helix  chain 'A' and resid 1911 through 1923
    Processing helix  chain 'A' and resid 1937 through 1952
      removed outlier: 4.107A  pdb=" N   GLY A1942 " --> pdb=" O   PHE A1938 " (cutoff:3.500A)
      removed outlier: 5.314A  pdb=" N   ARG A1943 " --> pdb=" O   GLN A1939 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1959 through 1963
      removed outlier: 3.537A  pdb=" N   LEU A1963 " --> pdb=" O   PHE A1960 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1964 through 1984
    Processing helix  chain 'A' and resid 2045 through 2057
    Processing helix  chain 'A' and resid 2061 through 2080
      Proline residue:  A2071  - end of helix
      removed outlier: 3.583A  pdb=" N   LEU A2080 " --> pdb=" O   CYS A2076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2089 through 2118
      removed outlier: 3.805A  pdb=" N   VAL A2098 " --> pdb=" O   LYS A2094 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2123 through 2130
    Processing helix  chain 'A' and resid 2132 through 2146
      removed outlier: 3.545A  pdb=" N   ILE A2136 " --> pdb=" O   PRO A2132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2147 through 2149
      No H-bonds generated for 'chain 'A' and resid 2147 through 2149'
    Processing helix  chain 'A' and resid 2152 through 2165
      removed outlier: 4.382A  pdb=" N   LEU A2156 " --> pdb=" O   GLU A2152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2175 through 2189
    Processing helix  chain 'A' and resid 2200 through 2217
    Processing helix  chain 'A' and resid 2229 through 2246
    Processing helix  chain 'A' and resid 2260 through 2266
    Processing helix  chain 'A' and resid 2278 through 2290
    Processing helix  chain 'A' and resid 2293 through 2297
    Processing helix  chain 'A' and resid 2314 through 2320
      removed outlier: 4.241A  pdb=" N   VAL A2318 " --> pdb=" O   ASN A2314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2352 through 2359
    Processing helix  chain 'A' and resid 2365 through 2369
      removed outlier: 3.522A  pdb=" N   LEU A2369 " --> pdb=" O   GLU A2366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2370 through 2385
      removed outlier: 3.622A  pdb=" N   ILE A2374 " --> pdb=" O   SER A2370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2394 through 2400
      removed outlier: 3.979A  pdb=" N   ARG A2398 " --> pdb=" O   ALA A2394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2410 through 2424
    Processing helix  chain 'A' and resid 2425 through 2428
      removed outlier: 3.908A  pdb=" N   THR A2428 " --> pdb=" O   PRO A2425 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2425 through 2428'
    Processing helix  chain 'A' and resid 2431 through 2443
      removed outlier: 3.643A  pdb=" N   GLN A2442 " --> pdb=" O   GLU A2438 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU A2443 " --> pdb=" O   HIS A2439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2450 through 2476
      removed outlier: 3.560A  pdb=" N   CYS A2454 " --> pdb=" O   THR A2450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2482 through 2503
      removed outlier: 3.527A  pdb=" N   SER A2503 " --> pdb=" O   LEU A2499 " (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 2571 through 2587
      removed outlier: 3.577A  pdb=" N   GLU A2587 " --> pdb=" O   THR A2583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2600 through 2611
    Processing helix  chain 'A' and resid 2627 through 2638
      removed outlier: 3.778A  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 2756
      removed outlier: 4.049A  pdb=" N   PHE A2751 " --> pdb=" O   ILE A2747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2762 through 2764
      No H-bonds generated for 'chain 'A' and resid 2762 through 2764'
    Processing helix  chain 'A' and resid 2765 through 2784
    Processing helix  chain 'A' and resid 2795 through 2811
      removed outlier: 4.051A  pdb=" N   MET A2799 " --> pdb=" O   SER A2795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2817 through 2833
    Processing helix  chain 'A' and resid 2834 through 2837
      removed outlier: 3.592A  pdb=" N   LEU A2837 " --> pdb=" O   GLN A2834 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2834 through 2837'
    Processing helix  chain 'A' and resid 2839 through 2858
      removed outlier: 3.663A  pdb=" N   ASP A2851 " --> pdb=" O   ASP A2847 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2862 through 2867
    Processing helix  chain 'A' and resid 2885 through 2904
    Processing helix  chain 'A' and resid 2912 through 2927
    Processing helix  chain 'A' and resid 2942 through 2954
      removed outlier: 3.554A  pdb=" N   LEU A2946 " --> pdb=" O   GLY A2942 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2968 through 2985
      removed outlier: 3.559A  pdb=" N   PHE A2972 " --> pdb=" O   THR A2968 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3001 through 3015
      removed outlier: 4.021A  pdb=" N   LEU A3005 " --> pdb=" O   ASP A3001 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   GLU A3006 " --> pdb=" O   SER A3002 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ARG A3007 " --> pdb=" O   GLY A3003 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3023 through 3041
      removed outlier: 3.559A  pdb=" N   GLU A3035 " --> pdb=" O   THR A3031 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3046 through 3061
    Processing helix  chain 'A' and resid 3071 through 3082
    Processing helix  chain 'A' and resid 3083 through 3088
    Processing helix  chain 'A' and resid 3098 through 3110
    Processing helix  chain 'A' and resid 3138 through 3165
    Processing helix  chain 'A' and resid 3172 through 3221
      removed outlier: 3.832A  pdb=" N   ASP A3221 " --> pdb=" O   GLU A3217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3471 through 3516
      removed outlier: 5.013A  pdb=" N   ALA A3504 " --> pdb=" O   MET A3500 " (cutoff:3.500A)
      removed outlier: 5.299A  pdb=" N   GLY A3505 " --> pdb=" O   SER A3501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3521 through 3539
    Processing helix  chain 'A' and resid 3548 through 3553
    Processing helix  chain 'A' and resid 3555 through 3565
      removed outlier: 3.538A  pdb=" N   ARG A3559 " --> pdb=" O   ASN A3555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3570 through 3582
    Processing helix  chain 'A' and resid 3594 through 3604
      removed outlier: 3.694A  pdb=" N   GLU A3598 " --> pdb=" O   GLY A3594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3605 through 3608
    Processing helix  chain 'A' and resid 3618 through 3629
    Processing helix  chain 'A' and resid 3637 through 3641
      removed outlier: 3.778A  pdb=" N   SER A3640 " --> pdb=" O   ASP A3637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3642 through 3644
      No H-bonds generated for 'chain 'A' and resid 3642 through 3644'
    Processing helix  chain 'A' and resid 3645 through 3651
    Processing helix  chain 'A' and resid 3689 through 3694
    Processing helix  chain 'A' and resid 3706 through 3721
    Processing helix  chain 'A' and resid 3721 through 3734
    Processing helix  chain 'A' and resid 3736 through 3755
      removed outlier: 3.790A  pdb=" N   GLU A3755 " --> pdb=" O   GLN A3751 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3758 through 3762
    Processing helix  chain 'A' and resid 3766 through 3786
      removed outlier: 4.203A  pdb=" N   LEU A3770 " --> pdb=" O   ILE A3766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3786 through 3818
      Proline residue:  A3803  - end of helix
    Processing helix  chain 'A' and resid 3819 through 3821
      No H-bonds generated for 'chain 'A' and resid 3819 through 3821'
    Processing helix  chain 'A' and resid 3828 through 3841
    Processing helix  chain 'A' and resid 3851 through 3874
      removed outlier: 3.562A  pdb=" N   ARG A3873 " --> pdb=" O   ASN A3869 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLY A3874 " --> pdb=" O   ARG A3870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3879 through 3895
    Processing helix  chain 'A' and resid 3901 through 3910
    Processing helix  chain 'A' and resid 3911 through 3913
      No H-bonds generated for 'chain 'A' and resid 3911 through 3913'
    Processing helix  chain 'A' and resid 3928 through 3940
      removed outlier: 3.539A  pdb=" N   CYS A3940 " --> pdb=" O   VAL A3936 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3941 through 3945
      removed outlier: 3.568A  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 3963
      removed outlier: 4.255A  pdb=" N   TRP A3960 " --> pdb=" O   GLN A3956 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3965 through 3969
    Processing helix  chain 'A' and resid 3981 through 3997
    Processing helix  chain 'A' and resid 4000 through 4013
    Processing helix  chain 'A' and resid 4014 through 4017
      removed outlier: 3.539A  pdb=" N   PHE A4017 " --> pdb=" O   GLY A4014 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 4014 through 4017'
    Processing helix  chain 'A' and resid 4018 through 4023
      removed outlier: 3.563A  pdb=" N   GLU A4022 " --> pdb=" O   MET A4018 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4026 through 4033
      removed outlier: 3.613A  pdb=" N   ILE A4030 " --> pdb=" O   ASP A4026 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4051 through 4062
      removed outlier: 4.012A  pdb=" N   VAL A4055 " --> pdb=" O   ALA A4051 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4073 through 4091
    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 4115
    Processing helix  chain 'A' and resid 4135 through 4141
    Processing helix  chain 'A' and resid 4152 through 4164
    Processing helix  chain 'A' and resid 4165 through 4170
      removed outlier: 3.576A  pdb=" N   ILE A4169 " --> pdb=" O   PRO A4165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4174 through 4194
      removed outlier: 3.961A  pdb=" N   ARG A4178 " --> pdb=" O   ASN A4174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4208 through 4228
    Processing helix  chain 'A' and resid 4239 through 4250
    Processing helix  chain 'A' and resid 4258 through 4273
    Processing helix  chain 'A' and resid 4274 through 4279
    Processing helix  chain 'A' and resid 4301 through 4311
    Processing helix  chain 'A' and resid 4317 through 4321
    Processing helix  chain 'A' and resid 4326 through 4348
    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
    Processing helix  chain 'A' and resid 4474 through 4500
    Processing helix  chain 'A' and resid 4501 through 4506
      removed outlier: 4.092A  pdb=" N   LYS A4505 " --> pdb=" O   ALA A4501 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ASN A4506 " --> pdb=" O   LYS A4502 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 4501 through 4506'
    Processing helix  chain 'A' and resid 4516 through 4532
      removed outlier: 3.505A  pdb=" N   TYR A4520 " --> pdb=" O   VAL A4516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4631 through 4638
      removed outlier: 3.509A  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
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1663 through 1666
      removed outlier: 3.538A  pdb=" N   VAL A1690 " --> pdb=" O   VAL A1673 " (cutoff:3.500A)
      removed outlier: 7.523A  pdb=" N   GLY A1675 " --> pdb=" O   THR A1688 " (cutoff:3.500A)
      removed outlier: 11.029A  pdb=" N   THR A1688 " --> pdb=" O   GLY A1675 " (cutoff:3.500A)
      removed outlier: 11.593A  pdb=" N   SER A1677 " --> pdb=" O   PHE A1686 " (cutoff:3.500A)
      removed outlier: 11.532A  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 1905
      removed outlier: 3.705A  pdb=" N   LEU A2039 " --> pdb=" O   SER A1903 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1927 through 1930
      removed outlier: 6.198A  pdb=" N   LEU A1928 " --> pdb=" O   CYS A1956 " (cutoff:3.500A)
      removed outlier: 6.449A  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 2251
      removed outlier: 6.586A  pdb=" N   VAL A2250 " --> pdb=" O   TRP A2300 " (cutoff:3.500A)
      removed outlier: 7.312A  pdb=" N   VAL A2302 " --> pdb=" O   VAL A2250 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   GLN A2299 " --> pdb=" O   ARG A2340 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   MET A2342 " --> pdb=" O   GLN A2299 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   ILE A2301 " --> pdb=" O   MET A2342 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   GLU A2344 " --> pdb=" O   ILE A2301 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 2324 through 2326
    Processing sheet with id=AA9, first strand: chain 'A' and resid 2537 through 2539
    Processing sheet with id=AB1, first strand: chain 'A' and resid 2710 through 2712
    Processing sheet with id=AB2, first strand: chain 'A' and resid 2615 through 2617
      removed outlier: 5.969A  pdb=" N   GLU A2616 " --> pdb=" O   VAL A2660 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   LEU A2659 " --> pdb=" O   GLN A2707 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'A' and resid 2639 through 2643
      removed outlier: 4.212A  pdb=" N   VAL A2648 " --> pdb=" O   TRP A2700 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 2957 through 2960
      removed outlier: 5.972A  pdb=" N   ILE A2990 " --> pdb=" O   HIS A3063 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   VAL A3065 " --> pdb=" O   ILE A2990 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   PHE A2992 " --> pdb=" O   VAL A3065 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   THR A3067 " --> pdb=" O   PHE A2992 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   MET A2994 " --> pdb=" O   THR A3067 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 3610 through 3613
      removed outlier: 6.146A  pdb=" N   THR A3610 " --> pdb=" O   LEU A3634 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   GLN A3636 " --> pdb=" O   THR A3610 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   THR A3612 " --> pdb=" O   GLN A3636 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   PHE A3678 " --> pdb=" O   LEU A3633 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 3654 through 3656
    Processing sheet with id=AB7, first strand: chain 'A' and resid 4066 through 4070
      removed outlier: 6.727A  pdb=" N   VAL A4094 " --> pdb=" O   PHE A4125 " (cutoff:3.500A)
      removed outlier: 7.717A  pdb=" N   THR A4127 " --> pdb=" O   VAL A4094 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   LEU A4096 " --> pdb=" O   THR A4127 " (cutoff:3.500A)
      removed outlier: 8.459A  pdb=" N   GLU A4129 " --> pdb=" O   LEU A4096 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   MET A4128 " --> pdb=" O   MET A4043 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   LEU A4042 " --> pdb=" O   PHE A4145 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   PHE A4147 " --> pdb=" O   LEU A4042 " (cutoff:3.500A)
      removed outlier: 7.446A  pdb=" N   CYS A4044 " --> pdb=" O   PHE A4147 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 4283 through 4285
      removed outlier: 7.193A  pdb=" N   ILE A4294 " --> pdb=" O   LEU A4284 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 4509 through 4510
      removed outlier: 6.217A  pdb=" N   VAL A4509 " --> pdb=" O   THR A4561 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 4564 through 4570
      removed outlier: 3.639A  pdb=" N   GLY A4567 " --> pdb=" O   ILE A4581 " (cutoff:3.500A)
      removed outlier: 7.981A  pdb=" N   ILE A4581 " --> pdb=" O   GLY A4567 " (cutoff:3.500A)
      removed outlier: 9.865A  pdb=" N   THR A4569 " --> pdb=" O   ASN A4579 " (cutoff:3.500A)
      removed outlier: 9.812A  pdb=" N   ASN A4579 " --> pdb=" O   THR A4569 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   PHE A4620 " --> pdb=" O   VAL A4609 " (cutoff:3.500A)
      removed outlier: 8.314A  pdb=" N   VAL A4642 " --> pdb=" O   THR A4606 " (cutoff:3.500A)

    1434 hydrogen bonds defined for protein.
    4182 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 7.54

  Time building geometry restraints manager: 3.39 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 8121
        1.34 -     1.46: 5219
        1.46 -     1.58: 11584
        1.58 -     1.70: 12
        1.70 -     1.81: 206
  Bond restraints: 25142
  Sorted by residual:
  bond pdb=" N   ILE A1611 "
       pdb=" CA  ILE A1611 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.17e-02 7.31e+03 8.21e+00
  bond pdb=" N   ASP A1606 "
       pdb=" CA  ASP A1606 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.17e-02 7.31e+03 6.18e+00
  bond pdb=" N   PHE A1568 "
       pdb=" CA  PHE A1568 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.21e-02 6.83e+03 6.16e+00
  bond pdb=" N   LEU A1607 "
       pdb=" CA  LEU A1607 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.028 1.19e-02 7.06e+03 5.71e+00
  bond pdb=" N   LEU A1608 "
       pdb=" CA  LEU A1608 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.19e-02 7.06e+03 5.53e+00
  ... (remaining 25137 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 33176
        1.56 -     3.12: 742
        3.12 -     4.68: 122
        4.68 -     6.24: 43
        6.24 -     7.81: 6
  Bond angle restraints: 34089
  Sorted by residual:
  angle pdb=" N   ASP A1410 "
        pdb=" CA  ASP A1410 "
        pdb=" C   ASP A1410 "
      ideal   model   delta    sigma   weight residual
     114.56  108.19    6.37 1.27e+00 6.20e-01 2.51e+01
  angle pdb=" N   GLU A1406 "
        pdb=" CA  GLU A1406 "
        pdb=" C   GLU A1406 "
      ideal   model   delta    sigma   weight residual
     113.30  109.02    4.28 1.34e+00 5.57e-01 1.02e+01
  angle pdb=" CA  THR A1565 "
        pdb=" CB  THR A1565 "
        pdb=" OG1 THR A1565 "
      ideal   model   delta    sigma   weight residual
     109.60  104.89    4.71 1.50e+00 4.44e-01 9.86e+00
  angle pdb=" CA  THR A1565 "
        pdb=" C   THR A1565 "
        pdb=" O   THR A1565 "
      ideal   model   delta    sigma   weight residual
     120.82  117.91    2.91 1.05e+00 9.07e-01 7.67e+00
  angle pdb=" CA  ASP A1606 "
        pdb=" C   ASP A1606 "
        pdb=" O   ASP A1606 "
      ideal   model   delta    sigma   weight residual
     121.00  118.11    2.89 1.05e+00 9.07e-01 7.56e+00
  ... (remaining 34084 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.51: 13581
       17.51 -    35.02: 1374
       35.02 -    52.52: 209
       52.52 -    70.03: 66
       70.03 -    87.54: 28
  Dihedral angle restraints: 15258
    sinusoidal: 6348
      harmonic: 8910
  Sorted by residual:
  dihedral pdb=" CA  SER A1510 "
           pdb=" C   SER A1510 "
           pdb=" N   PRO A1511 "
           pdb=" CA  PRO A1511 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.16  -20.84     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" O2A ADP A4701 "
           pdb=" O3A ADP A4701 "
           pdb=" PA  ADP A4701 "
           pdb=" PB  ADP A4701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   13.45  -73.44     1      2.00e+01 2.50e-03 1.72e+01
  dihedral pdb=" C5' ADP A4703 "
           pdb=" O5' ADP A4703 "
           pdb=" PA  ADP A4703 "
           pdb=" O2A ADP A4703 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -131.09   71.10     1      2.00e+01 2.50e-03 1.62e+01
  ... (remaining 15255 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 3034
       0.047 -    0.095: 640
       0.095 -    0.142: 139
       0.142 -    0.190: 7
       0.190 -    0.237: 1
  Chirality restraints: 3821
  Sorted by residual:
  chirality pdb=" CB  ILE A3171 "
            pdb=" CA  ILE A3171 "
            pdb=" CG1 ILE A3171 "
            pdb=" CG2 ILE A3171 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CB  ILE A3662 "
            pdb=" CA  ILE A3662 "
            pdb=" CG1 ILE A3662 "
            pdb=" CG2 ILE A3662 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.75e-01
  chirality pdb=" CA  ILE A1611 "
            pdb=" N   ILE A1611 "
            pdb=" C   ILE A1611 "
            pdb=" CB  ILE A1611 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.18 2.00e-01 2.50e+01 8.32e-01
  ... (remaining 3818 not shown)

  Planarity restraints: 4367
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A4482 "    0.024 2.00e-02 2.50e+03   2.19e-02 8.37e+00
        pdb=" CG  PHE A4482 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD1 PHE A4482 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE A4482 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE A4482 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 PHE A4482 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A4482 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A2529 "    0.038 5.00e-02 4.00e+02   5.73e-02 5.25e+00
        pdb=" N   PRO A2530 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A2530 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A2530 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A3552 "    0.010 2.00e-02 2.50e+03   1.49e-02 4.41e+00
        pdb=" CG  TYR A3552 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 TYR A3552 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR A3552 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 TYR A3552 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A3552 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A3552 "    0.012 2.00e-02 2.50e+03
        pdb=" OH  TYR A3552 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 4364 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 149
        2.53 -     3.12: 19234
        3.12 -     3.71: 39608
        3.71 -     4.31: 51739
        4.31 -     4.90: 87358
  Nonbonded interactions: 198088
  Sorted by model distance:
  nonbonded pdb=" O3B ATP A4702 "
            pdb="MG    MG A4706 "
     model   vdw
     1.937 2.170
  nonbonded pdb=" O2G ATP A4702 "
            pdb="MG    MG A4706 "
     model   vdw
     2.018 2.170
  nonbonded pdb=" O1A ADP A4701 "
            pdb="MG    MG A4705 "
     model   vdw
     2.026 2.170
  nonbonded pdb=" O1B ATP A4702 "
            pdb="MG    MG A4706 "
     model   vdw
     2.047 2.170
  nonbonded pdb=" OH  TYR A3103 "
            pdb=" OE1 GLU A3141 "
     model   vdw
     2.065 3.040
  ... (remaining 198083 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     27.850
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
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   0.040  25142  Z= 0.154
  Angle     :  0.588   7.806  34089  Z= 0.314
  Chirality :  0.041   0.237   3821
  Planarity :  0.004   0.057   4367
  Dihedral  : 14.556  87.538   9470
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.16), residues: 3035
  helix:  1.74 (0.13), residues: 1751
  sheet: -0.90 (0.32), residues: 268
  loop :  0.24 (0.21), residues: 1016

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A2642 
 TYR   0.035   0.001   TYR A3552 
 PHE   0.049   0.002   PHE A4482 
 TRP   0.024   0.002   TRP A1435 
 HIS   0.008   0.001   HIS A2463 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (25142)
  covalent geometry    : angle       0.58818 (34089)
  hydrogen bonds       : bond        0.12560 ( 1434)
  hydrogen bonds       : angle       5.27208 ( 4182)

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

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

  6070 Ramachandran restraints generated.
    3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6070 Ramachandran restraints generated.
    3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 316
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1417 MET cc_start: 0.7918 (tmm) cc_final: 0.7663 (tmm)
REVERT: A 1531 MET cc_start: 0.7813 (tpt) cc_final: 0.7581 (tpp)
REVERT: A 1798 MET cc_start: 0.8017 (mtp) cc_final: 0.7674 (mtp)
REVERT: A 2324 LEU cc_start: 0.8037 (tt) cc_final: 0.7138 (tt)
REVERT: A 2461 MET cc_start: 0.7695 (ttm) cc_final: 0.7450 (ttm)
REVERT: A 3043 MET cc_start: 0.6571 (mmp) cc_final: 0.5668 (mmp)
REVERT: A 3962 ASP cc_start: 0.8205 (t70) cc_final: 0.7795 (t0)
REVERT: A 4339 MET cc_start: 0.8016 (tmm) cc_final: 0.7668 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 316
  average time/residue: 0.1668
  time to fit residues: 84.6152
Evaluate side-chains
  235 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 197 optimal weight:    0.9980
   chunk 215 optimal weight:    0.9980
   chunk 20 optimal weight:    6.9990
   chunk 132 optimal weight:    2.9990
   chunk 261 optimal weight:    0.9990
   chunk 248 optimal weight:    8.9990
   chunk 207 optimal weight:    4.9990
   chunk 155 optimal weight:    1.9990
   chunk 244 optimal weight:    0.0070
   chunk 183 optimal weight:    0.8980
   chunk 298 optimal weight:    2.9990
   overall best weight:    0.7800

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

Flipped N/Q/H residues before XYZ refinement:
A1495 ASN
A1653 HIS
** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2752 ASN
A3069 ASN
** A3175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A3709 GLN
** A3865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A4063 ASN
A4156 ASN
A4466 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.133324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.098317 restraints weight = 45416.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.101975 restraints weight = 24194.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.104375 restraints weight = 16239.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.105947 restraints weight = 12610.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.106871 restraints weight = 10709.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.0899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  25142  Z= 0.136
  Angle     :  0.563   9.502  34089  Z= 0.282
  Chirality :  0.040   0.181   3821
  Planarity :  0.004   0.050   4367
  Dihedral  :  5.916  85.895   3377
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  6.95 %
    Favored  : 92.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.76 (0.16), residues: 3035
  helix:  2.03 (0.12), residues: 1775
  sheet: -0.97 (0.32), residues: 264
  loop :  0.33 (0.21), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A4123 
 TYR   0.020   0.001   TYR A2748 
 PHE   0.020   0.002   PHE A1960 
 TRP   0.015   0.001   TRP A2234 
 HIS   0.007   0.001   HIS A2463 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (25142)
  covalent geometry    : angle       0.56283 (34089)
  hydrogen bonds       : bond        0.04256 ( 1434)
  hydrogen bonds       : angle       4.21377 ( 4182)

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

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

  6070 Ramachandran restraints generated.
    3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6070 Ramachandran restraints generated.
    3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 269
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1417 MET cc_start: 0.7840 (tmm) cc_final: 0.7503 (tmm)
REVERT: A 1512 TYR cc_start: 0.7195 (OUTLIER) cc_final: 0.6797 (m-80)
REVERT: A 1589 MET cc_start: 0.8521 (mmm) cc_final: 0.8310 (mmm)
REVERT: A 1892 MET cc_start: 0.8305 (mmp) cc_final: 0.8044 (mmp)
REVERT: A 2192 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8304 (p)
REVERT: A 2464 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8539 (tm-30)
REVERT: A 2481 MET cc_start: 0.6586 (pmm) cc_final: 0.6326 (pmm)
REVERT: A 3043 MET cc_start: 0.6762 (mmp) cc_final: 0.5777 (mmp)
REVERT: A 3962 ASP cc_start: 0.8139 (t70) cc_final: 0.7693 (t0)
REVERT: A 4339 MET cc_start: 0.8114 (tmm) cc_final: 0.7688 (tmm)
  outliers start: 23
  outliers final: 15
  residues processed: 280
  average time/residue: 0.1523
  time to fit residues: 68.3457
Evaluate side-chains
  249 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 232
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1512 TYR
Chi-restraints excluded: chain A residue 1674 LEU
Chi-restraints excluded: chain A residue 2192 THR
Chi-restraints excluded: chain A residue 2226 SER
Chi-restraints excluded: chain A residue 2232 MET
Chi-restraints excluded: chain A residue 2327 LEU
Chi-restraints excluded: chain A residue 2733 VAL
Chi-restraints excluded: chain A residue 3155 HIS
Chi-restraints excluded: chain A residue 3168 THR
Chi-restraints excluded: chain A residue 3489 TRP
Chi-restraints excluded: chain A residue 3676 VAL
Chi-restraints excluded: chain A residue 3772 ASN
Chi-restraints excluded: chain A residue 4011 THR
Chi-restraints excluded: chain A residue 4055 VAL
Chi-restraints excluded: chain A residue 4113 LEU
Chi-restraints excluded: chain A residue 4340 ILE
Chi-restraints excluded: chain A residue 4390 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 215 optimal weight:    1.9990
   chunk 190 optimal weight:    0.6980
   chunk 178 optimal weight:    0.0070
   chunk 5 optimal weight:    7.9990
   chunk 207 optimal weight:    5.9990
   chunk 47 optimal weight:    0.0770
   chunk 147 optimal weight:    1.9990
   chunk 213 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 144 optimal weight:    1.9990
   chunk 206 optimal weight:    1.9990
   overall best weight:    0.9560

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

Flipped N/Q/H residues before XYZ refinement:
A1755 GLN
A1922 GLN
A2322 ASN
** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3087 ASN
A3197 GLN
A3534 HIS
A3602 ASN
A3865 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.134833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.099590 restraints weight = 44135.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.103515 restraints weight = 22622.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.106133 restraints weight = 14837.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 64)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.107844 restraints weight = 11343.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.108918 restraints weight = 9527.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  25142  Z= 0.144
  Angle     :  0.549   9.072  34089  Z= 0.273
  Chirality :  0.039   0.171   3821
  Planarity :  0.004   0.046   4367
  Dihedral  :  5.776  79.078   3377
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  9.28 %
    Favored  : 89.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.16), residues: 3035
  helix:  2.08 (0.12), residues: 1778
  sheet: -0.99 (0.32), residues: 264
  loop :  0.31 (0.21), residues: 993

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A2332 
 TYR   0.030   0.001   TYR A1513 
 PHE   0.018   0.002   PHE A2635 
 TRP   0.015   0.001   TRP A2234 
 HIS   0.006   0.001   HIS A3155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (25142)
  covalent geometry    : angle       0.54937 (34089)
  hydrogen bonds       : bond        0.03987 ( 1434)
  hydrogen bonds       : angle       4.08259 ( 4182)

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

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

  6070 Ramachandran restraints generated.
    3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6070 Ramachandran restraints generated.
    3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 253
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1417 MET cc_start: 0.7614 (tmm) cc_final: 0.7281 (tmm)
REVERT: A 1512 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6861 (m-80)
REVERT: A 1892 MET cc_start: 0.8234 (mmp) cc_final: 0.8033 (mmp)
REVERT: A 2192 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8215 (p)
REVERT: A 2296 GLN cc_start: 0.8743 (mp10) cc_final: 0.8470 (mp10)
REVERT: A 2327 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7456 (mm)
REVERT: A 2332 ARG cc_start: 0.7227 (mmp-170) cc_final: 0.6866 (mmp-170)
REVERT: A 2412 MET cc_start: 0.7329 (mmm) cc_final: 0.6870 (tpt)
REVERT: A 2461 MET cc_start: 0.7705 (ttm) cc_final: 0.7150 (ttm)
REVERT: A 2464 GLN cc_start: 0.8796 (tm-30) cc_final: 0.8410 (tm-30)
REVERT: A 3043 MET cc_start: 0.6895 (mmp) cc_final: 0.6224 (mmp)
REVERT: A 3799 GLN cc_start: 0.7611 (tm-30) cc_final: 0.7307 (tm-30)
REVERT: A 4484 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8360 (mp0)
  outliers start: 35
  outliers final: 24
  residues processed: 274
  average time/residue: 0.1606
  time to fit residues: 71.1093
Evaluate side-chains
  257 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 229
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1459 LEU
Chi-restraints excluded: chain A residue 1512 TYR
Chi-restraints excluded: chain A residue 1674 LEU
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain A residue 1797 LEU
Chi-restraints excluded: chain A residue 2192 THR
Chi-restraints excluded: chain A residue 2226 SER
Chi-restraints excluded: chain A residue 2232 MET
Chi-restraints excluded: chain A residue 2327 LEU
Chi-restraints excluded: chain A residue 2733 VAL
Chi-restraints excluded: chain A residue 2910 VAL
Chi-restraints excluded: chain A residue 3005 LEU
Chi-restraints excluded: chain A residue 3047 HIS
Chi-restraints excluded: chain A residue 3087 ASN
Chi-restraints excluded: chain A residue 3155 HIS
Chi-restraints excluded: chain A residue 3168 THR
Chi-restraints excluded: chain A residue 3489 TRP
Chi-restraints excluded: chain A residue 3676 VAL
Chi-restraints excluded: chain A residue 3772 ASN
Chi-restraints excluded: chain A residue 3981 THR
Chi-restraints excluded: chain A residue 4011 THR
Chi-restraints excluded: chain A residue 4043 MET
Chi-restraints excluded: chain A residue 4055 VAL
Chi-restraints excluded: chain A residue 4113 LEU
Chi-restraints excluded: chain A residue 4340 ILE
Chi-restraints excluded: chain A residue 4447 TYR
Chi-restraints excluded: chain A residue 4484 GLU
Chi-restraints excluded: chain A residue 4516 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 96 optimal weight:    6.9990
   chunk 9 optimal weight:    0.2980
   chunk 88 optimal weight:    1.9990
   chunk 263 optimal weight:    0.6980
   chunk 128 optimal weight:    0.0980
   chunk 236 optimal weight:    0.2980
   chunk 159 optimal weight:    0.8980
   chunk 115 optimal weight:    1.9990
   chunk 211 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A1961 ASN
** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2577 HIS
A3087 ASN
** A3175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A3197 GLN
A3534 HIS
A3880 HIS
A4386 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.136484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.101644 restraints weight = 43573.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.105590 restraints weight = 22533.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.108204 restraints weight = 14798.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.109906 restraints weight = 11307.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.110973 restraints weight = 9504.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.1352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  25142  Z= 0.109
  Angle     :  0.520  10.035  34089  Z= 0.257
  Chirality :  0.038   0.175   3821
  Planarity :  0.004   0.045   4367
  Dihedral  :  5.683  79.646   3377
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 10.53 %
    Favored  : 88.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.94 (0.16), residues: 3035
  helix:  2.22 (0.12), residues: 1774
  sheet: -0.91 (0.32), residues: 264
  loop :  0.31 (0.22), residues: 997

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A3088 
 TYR   0.031   0.001   TYR A1513 
 PHE   0.018   0.001   PHE A2635 
 TRP   0.015   0.001   TRP A2234 
 HIS   0.005   0.001   HIS A3155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (25142)
  covalent geometry    : angle       0.52006 (34089)
  hydrogen bonds       : bond        0.03690 ( 1434)
  hydrogen bonds       : angle       3.94995 ( 4182)

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

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

  6070 Ramachandran restraints generated.
    3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6070 Ramachandran restraints generated.
    3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 255
  time to evaluate  : 1.058 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1417 MET cc_start: 0.7475 (tmm) cc_final: 0.7113 (tmm)
REVERT: A 2296 GLN cc_start: 0.8795 (mp10) cc_final: 0.8581 (mp10)
REVERT: A 2412 MET cc_start: 0.7486 (mmm) cc_final: 0.6991 (tpt)
REVERT: A 2461 MET cc_start: 0.7623 (ttm) cc_final: 0.6778 (mtp)
REVERT: A 2464 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8386 (tm-30)
REVERT: A 2642 ARG cc_start: 0.6996 (ttp-110) cc_final: 0.6627 (ptp-110)
REVERT: A 2752 ASN cc_start: 0.6973 (m-40) cc_final: 0.6623 (m110)
REVERT: A 2792 TYR cc_start: 0.8157 (m-80) cc_final: 0.7952 (m-80)
REVERT: A 2901 TYR cc_start: 0.7060 (m-10) cc_final: 0.6735 (m-10)
REVERT: A 3043 MET cc_start: 0.6779 (mmp) cc_final: 0.6363 (mmp)
REVERT: A 3552 TYR cc_start: 0.8190 (t80) cc_final: 0.7785 (t80)
REVERT: A 3799 GLN cc_start: 0.7519 (tm-30) cc_final: 0.7216 (tm-30)
REVERT: A 4484 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8301 (mp0)
  outliers start: 34
  outliers final: 21
  residues processed: 275
  average time/residue: 0.1624
  time to fit residues: 72.3950
Evaluate side-chains
  248 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 226
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1674 LEU
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain A residue 1797 LEU
Chi-restraints excluded: chain A residue 2189 MET
Chi-restraints excluded: chain A residue 2226 SER
Chi-restraints excluded: chain A residue 2232 MET
Chi-restraints excluded: chain A residue 3005 LEU
Chi-restraints excluded: chain A residue 3047 HIS
Chi-restraints excluded: chain A residue 3155 HIS
Chi-restraints excluded: chain A residue 3168 THR
Chi-restraints excluded: chain A residue 3489 TRP
Chi-restraints excluded: chain A residue 3633 LEU
Chi-restraints excluded: chain A residue 3676 VAL
Chi-restraints excluded: chain A residue 3772 ASN
Chi-restraints excluded: chain A residue 3835 ILE
Chi-restraints excluded: chain A residue 3836 TYR
Chi-restraints excluded: chain A residue 4011 THR
Chi-restraints excluded: chain A residue 4055 VAL
Chi-restraints excluded: chain A residue 4113 LEU
Chi-restraints excluded: chain A residue 4340 ILE
Chi-restraints excluded: chain A residue 4484 GLU
Chi-restraints excluded: chain A residue 4516 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 240 optimal weight:    0.0370
   chunk 6 optimal weight:    5.9990
   chunk 187 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 265 optimal weight:    0.4980
   chunk 126 optimal weight:    0.9990
   chunk 209 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9990
   chunk 164 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A3534 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.136318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.101281 restraints weight = 43550.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.105248 restraints weight = 22247.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.107902 restraints weight = 14548.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.109573 restraints weight = 11087.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 55)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.110705 restraints weight = 9337.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.1524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  25142  Z= 0.113
  Angle     :  0.526  10.444  34089  Z= 0.258
  Chirality :  0.038   0.178   3821
  Planarity :  0.004   0.046   4367
  Dihedral  :  5.565  79.907   3377
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 11.60 %
    Favored  : 87.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.03 (0.16), residues: 3035
  helix:  2.28 (0.12), residues: 1778
  sheet: -0.88 (0.32), residues: 265
  loop :  0.36 (0.22), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A3655 
 TYR   0.021   0.001   TYR A1513 
 PHE   0.017   0.001   PHE A2635 
 TRP   0.015   0.001   TRP A2234 
 HIS   0.004   0.001   HIS A3155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (25142)
  covalent geometry    : angle       0.52556 (34089)
  hydrogen bonds       : bond        0.03588 ( 1434)
  hydrogen bonds       : angle       3.88956 ( 4182)

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

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

  6070 Ramachandran restraints generated.
    3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6070 Ramachandran restraints generated.
    3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 256
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1417 MET cc_start: 0.7581 (tmm) cc_final: 0.7204 (tmm)
REVERT: A 2145 MET cc_start: 0.8007 (tpp) cc_final: 0.7770 (tpp)
REVERT: A 2192 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8211 (p)
REVERT: A 2296 GLN cc_start: 0.8864 (mp10) cc_final: 0.8647 (mp10)
REVERT: A 2412 MET cc_start: 0.7308 (mmm) cc_final: 0.6895 (tpt)
REVERT: A 2461 MET cc_start: 0.7590 (ttm) cc_final: 0.6923 (mtp)
REVERT: A 2464 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8569 (tm-30)
REVERT: A 2752 ASN cc_start: 0.7048 (m-40) cc_final: 0.6645 (m110)
REVERT: A 2792 TYR cc_start: 0.8188 (m-80) cc_final: 0.7949 (m-80)
REVERT: A 2839 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7860 (tm-30)
REVERT: A 3043 MET cc_start: 0.6800 (mmp) cc_final: 0.6574 (mmp)
REVERT: A 3552 TYR cc_start: 0.8297 (t80) cc_final: 0.7860 (t80)
REVERT: A 3799 GLN cc_start: 0.7531 (tm-30) cc_final: 0.7224 (tm-30)
REVERT: A 4404 ASN cc_start: 0.6874 (m110) cc_final: 0.6657 (m110)
REVERT: A 4484 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8303 (mp0)
  outliers start: 34
  outliers final: 27
  residues processed: 278
  average time/residue: 0.1649
  time to fit residues: 74.0806
Evaluate side-chains
  260 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 231
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1674 LEU
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain A residue 1797 LEU
Chi-restraints excluded: chain A residue 2189 MET
Chi-restraints excluded: chain A residue 2192 THR
Chi-restraints excluded: chain A residue 2226 SER
Chi-restraints excluded: chain A residue 2232 MET
Chi-restraints excluded: chain A residue 2623 SER
Chi-restraints excluded: chain A residue 2871 ILE
Chi-restraints excluded: chain A residue 3005 LEU
Chi-restraints excluded: chain A residue 3047 HIS
Chi-restraints excluded: chain A residue 3155 HIS
Chi-restraints excluded: chain A residue 3168 THR
Chi-restraints excluded: chain A residue 3489 TRP
Chi-restraints excluded: chain A residue 3633 LEU
Chi-restraints excluded: chain A residue 3676 VAL
Chi-restraints excluded: chain A residue 3716 VAL
Chi-restraints excluded: chain A residue 3772 ASN
Chi-restraints excluded: chain A residue 3835 ILE
Chi-restraints excluded: chain A residue 3836 TYR
Chi-restraints excluded: chain A residue 4009 VAL
Chi-restraints excluded: chain A residue 4011 THR
Chi-restraints excluded: chain A residue 4043 MET
Chi-restraints excluded: chain A residue 4055 VAL
Chi-restraints excluded: chain A residue 4113 LEU
Chi-restraints excluded: chain A residue 4250 SER
Chi-restraints excluded: chain A residue 4340 ILE
Chi-restraints excluded: chain A residue 4484 GLU
Chi-restraints excluded: chain A residue 4516 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 88 optimal weight:    0.8980
   chunk 188 optimal weight:    0.8980
   chunk 225 optimal weight:    1.9990
   chunk 170 optimal weight:    4.9990
   chunk 297 optimal weight:    0.9980
   chunk 257 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 114 optimal weight:    0.0060
   chunk 191 optimal weight:    0.7980
   chunk 199 optimal weight:    0.1980
   chunk 255 optimal weight:    2.9990
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3057 GLN
** A3175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A3197 GLN
** A3534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.136079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.101235 restraints weight = 43677.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.105240 restraints weight = 22246.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.107890 restraints weight = 14488.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 68)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.109586 restraints weight = 11028.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.110535 restraints weight = 9271.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  25142  Z= 0.114
  Angle     :  0.533  10.430  34089  Z= 0.261
  Chirality :  0.038   0.178   3821
  Planarity :  0.004   0.049   4367
  Dihedral  :  5.463  81.703   3377
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 12.34 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.03 (0.16), residues: 3035
  helix:  2.28 (0.12), residues: 1780
  sheet: -0.85 (0.33), residues: 260
  loop :  0.34 (0.22), residues: 995

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A2332 
 TYR   0.016   0.001   TYR A1513 
 PHE   0.016   0.001   PHE A2635 
 TRP   0.015   0.001   TRP A2234 
 HIS   0.004   0.001   HIS A3155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (25142)
  covalent geometry    : angle       0.53289 (34089)
  hydrogen bonds       : bond        0.03544 ( 1434)
  hydrogen bonds       : angle       3.84547 ( 4182)

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

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

  6070 Ramachandran restraints generated.
    3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6070 Ramachandran restraints generated.
    3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 244
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1417 MET cc_start: 0.7616 (tmm) cc_final: 0.7208 (tmm)
REVERT: A 1516 PHE cc_start: 0.6171 (m-80) cc_final: 0.5927 (m-10)
REVERT: A 2018 MET cc_start: 0.8219 (mmm) cc_final: 0.7898 (mmm)
REVERT: A 2145 MET cc_start: 0.7993 (tpp) cc_final: 0.7752 (tpp)
REVERT: A 2192 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8162 (p)
REVERT: A 2310 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7965 (mp0)
REVERT: A 2412 MET cc_start: 0.7120 (mmm) cc_final: 0.6745 (tpt)
REVERT: A 2461 MET cc_start: 0.7572 (ttm) cc_final: 0.7154 (ttm)
REVERT: A 2464 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8531 (tm-30)
REVERT: A 2603 MET cc_start: 0.7988 (ttp) cc_final: 0.7709 (tpp)
REVERT: A 2642 ARG cc_start: 0.7093 (ttp-110) cc_final: 0.6770 (ptp-110)
REVERT: A 2752 ASN cc_start: 0.6866 (m-40) cc_final: 0.6413 (m110)
REVERT: A 2839 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7760 (tm-30)
REVERT: A 3552 TYR cc_start: 0.8291 (t80) cc_final: 0.7797 (t80)
REVERT: A 3799 GLN cc_start: 0.7523 (tm-30) cc_final: 0.7221 (tm-30)
REVERT: A 4484 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8092 (mp0)
  outliers start: 41
  outliers final: 29
  residues processed: 271
  average time/residue: 0.1498
  time to fit residues: 66.2782
Evaluate side-chains
  262 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 230
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1674 LEU
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain A residue 1797 LEU
Chi-restraints excluded: chain A residue 2189 MET
Chi-restraints excluded: chain A residue 2192 THR
Chi-restraints excluded: chain A residue 2226 SER
Chi-restraints excluded: chain A residue 2310 GLU
Chi-restraints excluded: chain A residue 2623 SER
Chi-restraints excluded: chain A residue 2630 LEU
Chi-restraints excluded: chain A residue 2871 ILE
Chi-restraints excluded: chain A residue 3005 LEU
Chi-restraints excluded: chain A residue 3047 HIS
Chi-restraints excluded: chain A residue 3155 HIS
Chi-restraints excluded: chain A residue 3168 THR
Chi-restraints excluded: chain A residue 3489 TRP
Chi-restraints excluded: chain A residue 3633 LEU
Chi-restraints excluded: chain A residue 3676 VAL
Chi-restraints excluded: chain A residue 3716 VAL
Chi-restraints excluded: chain A residue 3770 LEU
Chi-restraints excluded: chain A residue 3772 ASN
Chi-restraints excluded: chain A residue 3835 ILE
Chi-restraints excluded: chain A residue 3836 TYR
Chi-restraints excluded: chain A residue 4009 VAL
Chi-restraints excluded: chain A residue 4011 THR
Chi-restraints excluded: chain A residue 4043 MET
Chi-restraints excluded: chain A residue 4055 VAL
Chi-restraints excluded: chain A residue 4113 LEU
Chi-restraints excluded: chain A residue 4340 ILE
Chi-restraints excluded: chain A residue 4445 THR
Chi-restraints excluded: chain A residue 4448 LEU
Chi-restraints excluded: chain A residue 4484 GLU
Chi-restraints excluded: chain A residue 4516 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 136 optimal weight:    6.9990
   chunk 149 optimal weight:    0.6980
   chunk 225 optimal weight:    0.5980
   chunk 296 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 251 optimal weight:    0.7980
   chunk 71 optimal weight:    0.6980
   chunk 214 optimal weight:    0.5980
   chunk 301 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A1482 ASN
** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3057 GLN
** A3175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.135422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.100480 restraints weight = 43908.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.104444 restraints weight = 22507.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.107027 restraints weight = 14720.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 64)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.108766 restraints weight = 11248.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.109821 restraints weight = 9438.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.1775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  25142  Z= 0.120
  Angle     :  0.534  10.651  34089  Z= 0.263
  Chirality :  0.038   0.180   3821
  Planarity :  0.004   0.053   4367
  Dihedral  :  5.330  85.658   3377
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 13.01 %
    Favored  : 85.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.05 (0.16), residues: 3035
  helix:  2.31 (0.12), residues: 1778
  sheet: -0.85 (0.33), residues: 262
  loop :  0.31 (0.22), residues: 995

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A2292 
 TYR   0.015   0.001   TYR A2748 
 PHE   0.041   0.001   PHE A3149 
 TRP   0.015   0.001   TRP A2234 
 HIS   0.004   0.001   HIS A3155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (25142)
  covalent geometry    : angle       0.53412 (34089)
  hydrogen bonds       : bond        0.03508 ( 1434)
  hydrogen bonds       : angle       3.83373 ( 4182)

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

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

  6070 Ramachandran restraints generated.
    3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6070 Ramachandran restraints generated.
    3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 236
  time to evaluate  : 1.017 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1417 MET cc_start: 0.7697 (tmm) cc_final: 0.7319 (tmm)
REVERT: A 1967 MET cc_start: 0.8114 (mmm) cc_final: 0.7864 (tpp)
REVERT: A 2018 MET cc_start: 0.8255 (mmm) cc_final: 0.7961 (mmm)
REVERT: A 2145 MET cc_start: 0.7953 (tpp) cc_final: 0.7685 (tpp)
REVERT: A 2192 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8161 (p)
REVERT: A 2292 ARG cc_start: 0.7115 (mtm-85) cc_final: 0.6498 (mtm110)
REVERT: A 2310 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7996 (mp0)
REVERT: A 2412 MET cc_start: 0.7053 (mmm) cc_final: 0.6685 (tpt)
REVERT: A 2461 MET cc_start: 0.7602 (ttm) cc_final: 0.7102 (mtp)
REVERT: A 2464 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8549 (tm-30)
REVERT: A 2603 MET cc_start: 0.7991 (ttp) cc_final: 0.7723 (tpp)
REVERT: A 2642 ARG cc_start: 0.7099 (ttp-110) cc_final: 0.6776 (ptp-110)
REVERT: A 2752 ASN cc_start: 0.6880 (m-40) cc_final: 0.6408 (m110)
REVERT: A 2839 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7782 (tm-30)
REVERT: A 3552 TYR cc_start: 0.8351 (t80) cc_final: 0.7867 (t80)
REVERT: A 3799 GLN cc_start: 0.7534 (tm-30) cc_final: 0.7229 (tm-30)
REVERT: A 4004 MET cc_start: 0.7544 (tpp) cc_final: 0.7245 (tpp)
REVERT: A 4484 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8119 (mp0)
  outliers start: 41
  outliers final: 31
  residues processed: 265
  average time/residue: 0.1633
  time to fit residues: 70.9567
Evaluate side-chains
  257 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 223
  time to evaluate  : 1.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1674 LEU
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain A residue 1797 LEU
Chi-restraints excluded: chain A residue 2053 MET
Chi-restraints excluded: chain A residue 2189 MET
Chi-restraints excluded: chain A residue 2192 THR
Chi-restraints excluded: chain A residue 2226 SER
Chi-restraints excluded: chain A residue 2310 GLU
Chi-restraints excluded: chain A residue 2352 THR
Chi-restraints excluded: chain A residue 2623 SER
Chi-restraints excluded: chain A residue 2871 ILE
Chi-restraints excluded: chain A residue 2910 VAL
Chi-restraints excluded: chain A residue 2958 VAL
Chi-restraints excluded: chain A residue 3005 LEU
Chi-restraints excluded: chain A residue 3047 HIS
Chi-restraints excluded: chain A residue 3155 HIS
Chi-restraints excluded: chain A residue 3168 THR
Chi-restraints excluded: chain A residue 3489 TRP
Chi-restraints excluded: chain A residue 3633 LEU
Chi-restraints excluded: chain A residue 3676 VAL
Chi-restraints excluded: chain A residue 3716 VAL
Chi-restraints excluded: chain A residue 3770 LEU
Chi-restraints excluded: chain A residue 3772 ASN
Chi-restraints excluded: chain A residue 3835 ILE
Chi-restraints excluded: chain A residue 3836 TYR
Chi-restraints excluded: chain A residue 3929 VAL
Chi-restraints excluded: chain A residue 4009 VAL
Chi-restraints excluded: chain A residue 4011 THR
Chi-restraints excluded: chain A residue 4043 MET
Chi-restraints excluded: chain A residue 4055 VAL
Chi-restraints excluded: chain A residue 4113 LEU
Chi-restraints excluded: chain A residue 4340 ILE
Chi-restraints excluded: chain A residue 4484 GLU
Chi-restraints excluded: chain A residue 4516 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 147 optimal weight:    0.7980
   chunk 170 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 69 optimal weight:    0.8980
   chunk 237 optimal weight:    4.9990
   chunk 98 optimal weight:    5.9990
   chunk 131 optimal weight:   20.0000
   chunk 233 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 261 optimal weight:    0.1980
   chunk 209 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A1482 ASN
** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3057 GLN
** A3534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.133376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.098321 restraints weight = 44033.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.102167 restraints weight = 22694.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.104733 restraints weight = 14958.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.106414 restraints weight = 11458.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.107388 restraints weight = 9651.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  25142  Z= 0.158
  Angle     :  0.574  12.452  34089  Z= 0.281
  Chirality :  0.040   0.178   3821
  Planarity :  0.004   0.053   4367
  Dihedral  :  5.272  88.106   3377
  Min Nonbonded Distance : 1.842

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 13.41 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.98 (0.16), residues: 3035
  helix:  2.25 (0.12), residues: 1775
  sheet: -0.93 (0.32), residues: 262
  loop :  0.32 (0.22), residues: 998

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A2292 
 TYR   0.029   0.001   TYR A1513 
 PHE   0.035   0.002   PHE A3149 
 TRP   0.015   0.001   TRP A2234 
 HIS   0.005   0.001   HIS A2827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (25142)
  covalent geometry    : angle       0.57370 (34089)
  hydrogen bonds       : bond        0.03708 ( 1434)
  hydrogen bonds       : angle       3.89479 ( 4182)

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

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

  6070 Ramachandran restraints generated.
    3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6070 Ramachandran restraints generated.
    3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 234
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2018 MET cc_start: 0.8272 (mmm) cc_final: 0.7985 (mmm)
REVERT: A 2145 MET cc_start: 0.8056 (tpp) cc_final: 0.7807 (tpp)
REVERT: A 2192 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8079 (p)
REVERT: A 2292 ARG cc_start: 0.7000 (mtm-85) cc_final: 0.6394 (mtm110)
REVERT: A 2310 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8024 (mp0)
REVERT: A 2324 LEU cc_start: 0.8134 (tt) cc_final: 0.7221 (tt)
REVERT: A 2412 MET cc_start: 0.7125 (mmm) cc_final: 0.6747 (tpt)
REVERT: A 2461 MET cc_start: 0.7736 (ttm) cc_final: 0.7267 (mtp)
REVERT: A 2464 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8569 (tm-30)
REVERT: A 2603 MET cc_start: 0.8052 (ttp) cc_final: 0.7808 (tpp)
REVERT: A 2752 ASN cc_start: 0.6962 (m-40) cc_final: 0.6484 (m110)
REVERT: A 2839 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7725 (tm-30)
REVERT: A 3552 TYR cc_start: 0.8418 (t80) cc_final: 0.7890 (t80)
REVERT: A 3799 GLN cc_start: 0.7550 (tm-30) cc_final: 0.7238 (tm-30)
REVERT: A 4484 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8064 (mp0)
  outliers start: 44
  outliers final: 36
  residues processed: 264
  average time/residue: 0.1588
  time to fit residues: 67.8894
Evaluate side-chains
  259 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 220
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1482 ASN
Chi-restraints excluded: chain A residue 1674 LEU
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain A residue 1797 LEU
Chi-restraints excluded: chain A residue 1935 THR
Chi-restraints excluded: chain A residue 2053 MET
Chi-restraints excluded: chain A residue 2189 MET
Chi-restraints excluded: chain A residue 2192 THR
Chi-restraints excluded: chain A residue 2226 SER
Chi-restraints excluded: chain A residue 2310 GLU
Chi-restraints excluded: chain A residue 2373 MET
Chi-restraints excluded: chain A residue 2623 SER
Chi-restraints excluded: chain A residue 2733 VAL
Chi-restraints excluded: chain A residue 2871 ILE
Chi-restraints excluded: chain A residue 2910 VAL
Chi-restraints excluded: chain A residue 2958 VAL
Chi-restraints excluded: chain A residue 3005 LEU
Chi-restraints excluded: chain A residue 3047 HIS
Chi-restraints excluded: chain A residue 3155 HIS
Chi-restraints excluded: chain A residue 3168 THR
Chi-restraints excluded: chain A residue 3489 TRP
Chi-restraints excluded: chain A residue 3633 LEU
Chi-restraints excluded: chain A residue 3676 VAL
Chi-restraints excluded: chain A residue 3716 VAL
Chi-restraints excluded: chain A residue 3770 LEU
Chi-restraints excluded: chain A residue 3772 ASN
Chi-restraints excluded: chain A residue 3835 ILE
Chi-restraints excluded: chain A residue 3836 TYR
Chi-restraints excluded: chain A residue 3929 VAL
Chi-restraints excluded: chain A residue 3981 THR
Chi-restraints excluded: chain A residue 4009 VAL
Chi-restraints excluded: chain A residue 4011 THR
Chi-restraints excluded: chain A residue 4043 MET
Chi-restraints excluded: chain A residue 4055 VAL
Chi-restraints excluded: chain A residue 4113 LEU
Chi-restraints excluded: chain A residue 4250 SER
Chi-restraints excluded: chain A residue 4340 ILE
Chi-restraints excluded: chain A residue 4484 GLU
Chi-restraints excluded: chain A residue 4516 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9980
   chunk 181 optimal weight:    0.5980
   chunk 6 optimal weight:    5.9990
   chunk 289 optimal weight:    8.9990
   chunk 85 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 225 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 302 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A1481 GLN
** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3534 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 = 0.3854 r_free = 0.3854 target = 0.134252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.099384 restraints weight = 44055.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.103286 restraints weight = 22534.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.105892 restraints weight = 14771.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 58)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.107580 restraints weight = 11266.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.108658 restraints weight = 9471.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  25142  Z= 0.126
  Angle     :  0.558  11.333  34089  Z= 0.272
  Chirality :  0.039   0.173   3821
  Planarity :  0.004   0.052   4367
  Dihedral  :  5.154  82.339   3377
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 13.53 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.16), residues: 3035
  helix:  2.29 (0.12), residues: 1773
  sheet: -0.96 (0.32), residues: 262
  loop :  0.32 (0.22), residues: 1000

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A2332 
 TYR   0.014   0.001   TYR A2748 
 PHE   0.033   0.001   PHE A3149 
 TRP   0.020   0.001   TRP A1544 
 HIS   0.004   0.001   HIS A2827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (25142)
  covalent geometry    : angle       0.55773 (34089)
  hydrogen bonds       : bond        0.03613 ( 1434)
  hydrogen bonds       : angle       3.85651 ( 4182)

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

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

  6070 Ramachandran restraints generated.
    3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6070 Ramachandran restraints generated.
    3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 231
  time to evaluate  : 1.025 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1417 MET cc_start: 0.7048 (tmm) cc_final: 0.6763 (tmm)
REVERT: A 2018 MET cc_start: 0.8265 (mmm) cc_final: 0.7985 (mmm)
REVERT: A 2145 MET cc_start: 0.7961 (tpp) cc_final: 0.7706 (tpp)
REVERT: A 2192 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8130 (p)
REVERT: A 2292 ARG cc_start: 0.7002 (mtm-85) cc_final: 0.6412 (mtm110)
REVERT: A 2310 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8002 (mp0)
REVERT: A 2412 MET cc_start: 0.7147 (mmm) cc_final: 0.6835 (tpt)
REVERT: A 2461 MET cc_start: 0.7709 (ttm) cc_final: 0.7283 (mtp)
REVERT: A 2464 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8560 (tm-30)
REVERT: A 2603 MET cc_start: 0.8059 (ttp) cc_final: 0.7821 (tpp)
REVERT: A 2752 ASN cc_start: 0.6890 (m-40) cc_final: 0.6406 (m110)
REVERT: A 2839 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7709 (tm-30)
REVERT: A 3043 MET cc_start: 0.6483 (mmp) cc_final: 0.5978 (mmp)
REVERT: A 3552 TYR cc_start: 0.8370 (t80) cc_final: 0.7884 (t80)
REVERT: A 3799 GLN cc_start: 0.7548 (tm-30) cc_final: 0.7238 (tm-30)
REVERT: A 4004 MET cc_start: 0.7655 (tpp) cc_final: 0.7377 (tpp)
REVERT: A 4484 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8091 (mp0)
  outliers start: 43
  outliers final: 35
  residues processed: 260
  average time/residue: 0.1611
  time to fit residues: 68.0181
Evaluate side-chains
  255 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 217
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1674 LEU
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain A residue 1797 LEU
Chi-restraints excluded: chain A residue 1935 THR
Chi-restraints excluded: chain A residue 2189 MET
Chi-restraints excluded: chain A residue 2192 THR
Chi-restraints excluded: chain A residue 2226 SER
Chi-restraints excluded: chain A residue 2310 GLU
Chi-restraints excluded: chain A residue 2352 THR
Chi-restraints excluded: chain A residue 2373 MET
Chi-restraints excluded: chain A residue 2623 SER
Chi-restraints excluded: chain A residue 2733 VAL
Chi-restraints excluded: chain A residue 2799 MET
Chi-restraints excluded: chain A residue 2871 ILE
Chi-restraints excluded: chain A residue 2910 VAL
Chi-restraints excluded: chain A residue 3005 LEU
Chi-restraints excluded: chain A residue 3047 HIS
Chi-restraints excluded: chain A residue 3155 HIS
Chi-restraints excluded: chain A residue 3168 THR
Chi-restraints excluded: chain A residue 3489 TRP
Chi-restraints excluded: chain A residue 3633 LEU
Chi-restraints excluded: chain A residue 3676 VAL
Chi-restraints excluded: chain A residue 3716 VAL
Chi-restraints excluded: chain A residue 3770 LEU
Chi-restraints excluded: chain A residue 3772 ASN
Chi-restraints excluded: chain A residue 3835 ILE
Chi-restraints excluded: chain A residue 3836 TYR
Chi-restraints excluded: chain A residue 3929 VAL
Chi-restraints excluded: chain A residue 3981 THR
Chi-restraints excluded: chain A residue 4009 VAL
Chi-restraints excluded: chain A residue 4011 THR
Chi-restraints excluded: chain A residue 4043 MET
Chi-restraints excluded: chain A residue 4055 VAL
Chi-restraints excluded: chain A residue 4113 LEU
Chi-restraints excluded: chain A residue 4250 SER
Chi-restraints excluded: chain A residue 4340 ILE
Chi-restraints excluded: chain A residue 4484 GLU
Chi-restraints excluded: chain A residue 4516 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 122 optimal weight:    4.9990
   chunk 146 optimal weight:    0.7980
   chunk 242 optimal weight:    0.7980
   chunk 201 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 136 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 80 optimal weight:    0.0970
   chunk 113 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9980
   chunk 154 optimal weight:    1.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A1482 ASN
** A1502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2005 GLN
** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3057 GLN
** A3534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.133721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.098847 restraints weight = 43932.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.102736 restraints weight = 22622.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.105278 restraints weight = 14857.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.106970 restraints weight = 11378.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.108068 restraints weight = 9572.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  25142  Z= 0.140
  Angle     :  0.578  11.808  34089  Z= 0.282
  Chirality :  0.039   0.176   3821
  Planarity :  0.004   0.051   4367
  Dihedral  :  5.056  74.296   3377
  Min Nonbonded Distance : 1.868

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 14.26 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.16), residues: 3035
  helix:  2.25 (0.12), residues: 1772
  sheet: -1.04 (0.32), residues: 272
  loop :  0.32 (0.22), residues: 991

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A2332 
 TYR   0.022   0.001   TYR A2641 
 PHE   0.031   0.001   PHE A3149 
 TRP   0.054   0.001   TRP A1544 
 HIS   0.004   0.001   HIS A2827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (25142)
  covalent geometry    : angle       0.57822 (34089)
  hydrogen bonds       : bond        0.03650 ( 1434)
  hydrogen bonds       : angle       3.89004 ( 4182)

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

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

  6070 Ramachandran restraints generated.
    3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6070 Ramachandran restraints generated.
    3035 Oldfield, 0 Emsley, 3035 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 223
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1417 MET cc_start: 0.7191 (tmm) cc_final: 0.6933 (tmm)
REVERT: A 2018 MET cc_start: 0.8274 (mmm) cc_final: 0.7992 (mmm)
REVERT: A 2145 MET cc_start: 0.8016 (tpp) cc_final: 0.7763 (tpp)
REVERT: A 2192 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8126 (p)
REVERT: A 2292 ARG cc_start: 0.7022 (mtm-85) cc_final: 0.6409 (mtm110)
REVERT: A 2310 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8005 (mp0)
REVERT: A 2332 ARG cc_start: 0.7237 (mmp-170) cc_final: 0.6841 (mmp-170)
REVERT: A 2412 MET cc_start: 0.7141 (mmm) cc_final: 0.6843 (tpt)
REVERT: A 2461 MET cc_start: 0.7760 (ttm) cc_final: 0.7361 (mtp)
REVERT: A 2464 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8573 (tm-30)
REVERT: A 2603 MET cc_start: 0.8134 (ttp) cc_final: 0.7823 (tpp)
REVERT: A 2752 ASN cc_start: 0.6934 (m-40) cc_final: 0.6451 (m110)
REVERT: A 2839 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7719 (tm-30)
REVERT: A 2920 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.6300 (mt)
REVERT: A 3552 TYR cc_start: 0.8367 (t80) cc_final: 0.7859 (t80)
REVERT: A 3799 GLN cc_start: 0.7553 (tm-30) cc_final: 0.7247 (tm-30)
REVERT: A 4004 MET cc_start: 0.7614 (tpp) cc_final: 0.7289 (tpp)
REVERT: A 4021 MET cc_start: 0.8006 (tpp) cc_final: 0.7540 (tpp)
REVERT: A 4484 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8054 (mp0)
  outliers start: 38
  outliers final: 33
  residues processed: 250
  average time/residue: 0.1557
  time to fit residues: 63.4698
Evaluate side-chains
  252 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 215
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1674 LEU
Chi-restraints excluded: chain A residue 1684 VAL
Chi-restraints excluded: chain A residue 1797 LEU
Chi-restraints excluded: chain A residue 2189 MET
Chi-restraints excluded: chain A residue 2192 THR
Chi-restraints excluded: chain A residue 2226 SER
Chi-restraints excluded: chain A residue 2310 GLU
Chi-restraints excluded: chain A residue 2352 THR
Chi-restraints excluded: chain A residue 2373 MET
Chi-restraints excluded: chain A residue 2623 SER
Chi-restraints excluded: chain A residue 2733 VAL
Chi-restraints excluded: chain A residue 2799 MET
Chi-restraints excluded: chain A residue 2871 ILE
Chi-restraints excluded: chain A residue 2920 LEU
Chi-restraints excluded: chain A residue 3005 LEU
Chi-restraints excluded: chain A residue 3047 HIS
Chi-restraints excluded: chain A residue 3155 HIS
Chi-restraints excluded: chain A residue 3168 THR
Chi-restraints excluded: chain A residue 3489 TRP
Chi-restraints excluded: chain A residue 3633 LEU
Chi-restraints excluded: chain A residue 3676 VAL
Chi-restraints excluded: chain A residue 3716 VAL
Chi-restraints excluded: chain A residue 3770 LEU
Chi-restraints excluded: chain A residue 3772 ASN
Chi-restraints excluded: chain A residue 3835 ILE
Chi-restraints excluded: chain A residue 3836 TYR
Chi-restraints excluded: chain A residue 3929 VAL
Chi-restraints excluded: chain A residue 3981 THR
Chi-restraints excluded: chain A residue 4009 VAL
Chi-restraints excluded: chain A residue 4011 THR
Chi-restraints excluded: chain A residue 4043 MET
Chi-restraints excluded: chain A residue 4055 VAL
Chi-restraints excluded: chain A residue 4113 LEU
Chi-restraints excluded: chain A residue 4250 SER
Chi-restraints excluded: chain A residue 4340 ILE
Chi-restraints excluded: chain A residue 4484 GLU
Chi-restraints excluded: chain A residue 4516 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 304
   random chunks:
   chunk 172 optimal weight:    0.9990
   chunk 134 optimal weight:    0.0670
   chunk 298 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   chunk 279 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9990
   chunk 285 optimal weight:    0.5980
   chunk 154 optimal weight:    0.4980
   chunk 290 optimal weight:    0.6980
   chunk 62 optimal weight:    0.0970
   chunk 89 optimal weight:    0.0770
   overall best weight:    0.2674

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

Flipped N/Q/H residues before XYZ refinement:
A1482 ASN
A2134 GLN
** A2416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3057 GLN
** A3534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.136144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.101678 restraints weight = 43792.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.105690 restraints weight = 22265.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.108316 restraints weight = 14481.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.110012 restraints weight = 11007.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.111108 restraints weight = 9232.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  25142  Z= 0.104
  Angle     :  0.554  12.037  34089  Z= 0.269
  Chirality :  0.038   0.174   3821
  Planarity :  0.004   0.050   4367
  Dihedral  :  4.881  64.201   3377
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 14.56 %
    Favored  : 84.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.14 (0.16), residues: 3035
  helix:  2.42 (0.12), residues: 1765
  sheet: -0.92 (0.32), residues: 271
  loop :  0.37 (0.21), residues: 999

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A2642 
 TYR   0.031   0.001   TYR A1513 
 PHE   0.030   0.001   PHE A3149 
 TRP   0.044   0.001   TRP A1544 
 HIS   0.004   0.001   HIS A3155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (25142)
  covalent geometry    : angle       0.55387 (34089)
  hydrogen bonds       : bond        0.03374 ( 1434)
  hydrogen bonds       : angle       3.79799 ( 4182)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4530.04 seconds
wall clock time: 78 minutes 57.24 seconds (4737.24 seconds total)