Starting phenix.real_space_refine
on Wed Mar  4 01:46:08 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mi3_23838/03_2026/7mi3_23838.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mi3_23838/03_2026/7mi3_23838.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mi3_23838/03_2026/7mi3_23838.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mi3_23838/03_2026/7mi3_23838.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mi3_23838/03_2026/7mi3_23838.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mi3_23838/03_2026/7mi3_23838.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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: 8
    Type Number    sf(0)   Gaussians
     Br      2      7.06       5
     P       3      5.49       5
     Mg      1      5.21       5
     S      49      5.16       5
     Cl      2      4.86       5
     C    6197      2.51       5
     N    1624      2.21       5
     O    1804      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9682
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1192, 9590
          Classifications: {'peptide': 1192}
          Link IDs: {'PTRANS': 39, 'TRANS': 1152}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 92
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 92
          Unusual residues: {' MG': 1, 'ATP': 1, 'ZG7': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 2.02, per 1000 atoms: 0.21
  Number of scatterers: 9682
  At special positions: 0
  Unit cell: (89.096, 137.27, 103.082, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     Br      2     34.99
     Cl      2     17.00
     S      49     16.00
     P       3     15.00
     Mg      1     11.99
     O    1804      8.00
     N    1624      7.00
     C    6197      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: 0.82
  Conformation dependent library (CDL) restraints added in 489.4 milliseconds
  

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2272

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 9 sheets defined
      58.1% alpha, 10.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2031 through 2046
    Processing helix  chain 'A' and resid 2050 through 2064
    Processing helix  chain 'A' and resid 2079 through 2096
    Processing helix  chain 'A' and resid 2105 through 2109
    Processing helix  chain 'A' and resid 2110 through 2115
    Processing helix  chain 'A' and resid 2128 through 2140
      removed outlier: 3.560A  pdb=" N   ASP A2140 " --> pdb=" O   ARG A2136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2159 through 2165
      removed outlier: 3.706A  pdb=" N   VAL A2163 " --> pdb=" O   ASP A2159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2166 through 2171
      removed outlier: 3.881A  pdb=" N   LEU A2170 " --> pdb=" O   MET A2166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2203 through 2208
    Processing helix  chain 'A' and resid 2221 through 2241
      removed outlier: 3.803A  pdb=" N   ALA A2236 " --> pdb=" O   LYS A2232 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   ASN A2239 " --> pdb=" O   GLU A2235 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   LYS A2240 " --> pdb=" O   ALA A2236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2242 through 2258
      removed outlier: 4.074A  pdb=" N   LYS A2248 " --> pdb=" O   PHE A2244 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ASP A2255 " --> pdb=" O   ASP A2251 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   SER A2256 " --> pdb=" O   LEU A2252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2259 through 2268
      removed outlier: 3.978A  pdb=" N   THR A2263 " --> pdb=" O   MET A2259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2279 through 2282
    Processing helix  chain 'A' and resid 2283 through 2297
    Processing helix  chain 'A' and resid 2298 through 2303
      removed outlier: 4.231A  pdb=" N   GLN A2303 " --> pdb=" O   ARG A2299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2306 through 2328
    Processing helix  chain 'A' and resid 2332 through 2346
      removed outlier: 3.857A  pdb=" N   GLN A2340 " --> pdb=" O   ARG A2336 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   THR A2341 " --> pdb=" O   ALA A2337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2381 through 2387
    Processing helix  chain 'A' and resid 2394 through 2410
    Processing helix  chain 'A' and resid 2423 through 2435
      removed outlier: 3.842A  pdb=" N   MET A2428 " --> pdb=" O   LYS A2424 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ASN A2434 " --> pdb=" O   ASN A2430 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   SER A2435 " --> pdb=" O   ALA A2431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2450 through 2462
      removed outlier: 4.234A  pdb=" N   ARG A2460 " --> pdb=" O   SER A2456 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   HIS A2461 " --> pdb=" O   ALA A2457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2500 through 2513
    Processing helix  chain 'A' and resid 2547 through 2552
    Processing helix  chain 'A' and resid 2564 through 2579
    Processing helix  chain 'A' and resid 2580 through 2587
      Proline residue:  A2583  - end of helix
      removed outlier: 4.799A  pdb=" N   SER A2587 " --> pdb=" O   GLU A2584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2588 through 2607
    Processing helix  chain 'A' and resid 2619 through 2635
    Processing helix  chain 'A' and resid 2640 through 2657
    Processing helix  chain 'A' and resid 2658 through 2660
      No H-bonds generated for 'chain 'A' and resid 2658 through 2660'
    Processing helix  chain 'A' and resid 2662 through 2681
    Processing helix  chain 'A' and resid 2708 through 2727
    Processing helix  chain 'A' and resid 2735 through 2750
    Processing helix  chain 'A' and resid 2765 through 2778
      removed outlier: 3.526A  pdb=" N   ARG A2771 " --> pdb=" O   THR A2767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2791 through 2809
    Processing helix  chain 'A' and resid 2820 through 2822
      No H-bonds generated for 'chain 'A' and resid 2820 through 2822'
    Processing helix  chain 'A' and resid 2824 through 2837
      removed outlier: 3.957A  pdb=" N   LEU A2828 " --> pdb=" O   GLU A2824 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2840 through 2845
      removed outlier: 4.112A  pdb=" N   GLN A2845 " --> pdb=" O   ASP A2842 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2846 through 2863
    Processing helix  chain 'A' and resid 2869 through 2884
      removed outlier: 3.608A  pdb=" N   LEU A2873 " --> pdb=" O   THR A2869 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2896 through 2905
    Processing helix  chain 'A' and resid 2905 through 2910
    Processing helix  chain 'A' and resid 2921 through 2936
      removed outlier: 3.994A  pdb=" N   VAL A2935 " --> pdb=" O   ASN A2931 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   ILE A2936 " --> pdb=" O   MET A2932 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2941 through 2945
      removed outlier: 3.933A  pdb=" N   VAL A2945 " --> pdb=" O   ASP A2942 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2960 through 2980
    Processing helix  chain 'A' and resid 2989 through 3011
      removed outlier: 3.600A  pdb=" N   VAL A3000 " --> pdb=" O   LEU A2996 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS A3001 " --> pdb=" O   ARG A2997 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3318 through 3334
      removed outlier: 4.525A  pdb=" N   GLY A3322 " --> pdb=" O   GLN A3318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3335 through 3337
      No H-bonds generated for 'chain 'A' and resid 3335 through 3337'
    Processing helix  chain 'A' and resid 3338 through 3356
      removed outlier: 3.746A  pdb=" N   LEU A3352 " --> pdb=" O   ILE A3348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3365 through 3371
    Processing helix  chain 'A' and resid 3372 through 3382
      removed outlier: 4.105A  pdb=" N   LEU A3380 " --> pdb=" O   LYS A3376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3387 through 3400
    Processing helix  chain 'A' and resid 3413 through 3423
      removed outlier: 4.237A  pdb=" N   SER A3419 " --> pdb=" O   ILE A3415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3435 through 3447
    Processing helix  chain 'A' and resid 3459 through 3461
      No H-bonds generated for 'chain 'A' and resid 3459 through 3461'
    Processing helix  chain 'A' and resid 3462 through 3467
      removed outlier: 3.589A  pdb=" N   ILE A3466 " --> pdb=" O   ILE A3462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3506 through 3511
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2098 through 2103
      removed outlier: 6.547A  pdb=" N   ALA A2098 " --> pdb=" O   ARG A2149 " (cutoff:3.500A)
      removed outlier: 7.748A  pdb=" N   TRP A2151 " --> pdb=" O   ALA A2098 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   VAL A2100 " --> pdb=" O   TRP A2151 " (cutoff:3.500A)
      removed outlier: 7.698A  pdb=" N   VAL A2153 " --> pdb=" O   VAL A2100 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   TYR A2102 " --> pdb=" O   VAL A2153 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   ARG A2191 " --> pdb=" O   SER A2148 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   ILE A2150 " --> pdb=" O   ARG A2191 " (cutoff:3.500A)
      removed outlier: 7.497A  pdb=" N   LEU A2193 " --> pdb=" O   ILE A2150 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   VAL A2152 " --> pdb=" O   LEU A2193 " (cutoff:3.500A)
      removed outlier: 7.357A  pdb=" N   GLU A2195 " --> pdb=" O   VAL A2152 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   LEU A2070 " --> pdb=" O   PHE A2194 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   THR A2196 " --> pdb=" O   LEU A2070 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   LEU A2072 " --> pdb=" O   THR A2196 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 2175 through 2177
    Processing sheet with id=AA3, first strand: chain 'A' and resid 2358 through 2361
      removed outlier: 3.589A  pdb=" N   THR A2358 " --> pdb=" O   PHE A2371 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 2438 through 2444
      removed outlier: 6.637A  pdb=" N   ASP A2439 " --> pdb=" O   VAL A2483 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   PHE A2485 " --> pdb=" O   ASP A2439 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   VAL A2441 " --> pdb=" O   PHE A2485 " (cutoff:3.500A)
      removed outlier: 7.258A  pdb=" N   ASP A2487 " --> pdb=" O   VAL A2441 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   ILE A2443 " --> pdb=" O   ASP A2487 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   LEU A2482 " --> pdb=" O   HIS A2530 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   VAL A2532 " --> pdb=" O   LEU A2482 " (cutoff:3.500A)
      removed outlier: 5.944A  pdb=" N   LEU A2484 " --> pdb=" O   VAL A2532 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   ALA A2534 " --> pdb=" O   LEU A2484 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   CYS A2486 " --> pdb=" O   ALA A2534 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   ILE A2414 " --> pdb=" O   GLY A2533 " (cutoff:3.500A)
      removed outlier: 7.998A  pdb=" N   CYS A2535 " --> pdb=" O   ILE A2414 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   LEU A2416 " --> pdb=" O   CYS A2535 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   GLY A2413 " --> pdb=" O   ALA A2555 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   LEU A2557 " --> pdb=" O   GLY A2413 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ILE A2415 " --> pdb=" O   LEU A2557 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 2465 through 2467
      removed outlier: 12.576A  pdb=" N   THR A2472 " --> pdb=" O   GLU A2527 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   GLU A2527 " --> pdb=" O   THR A2472 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   THR A2525 " --> pdb=" O   LEU A2474 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 2696 through 2697
    Processing sheet with id=AA7, first strand: chain 'A' and resid 2780 through 2782
      removed outlier: 6.381A  pdb=" N   LYS A2780 " --> pdb=" O   CYS A2814 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   ILE A2816 " --> pdb=" O   LYS A2780 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   VAL A2782 " --> pdb=" O   ILE A2816 " (cutoff:3.500A)
      removed outlier: 7.828A  pdb=" N   ASP A2818 " --> pdb=" O   VAL A2782 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   HIS A2755 " --> pdb=" O   ILE A2913 " (cutoff:3.500A)
      removed outlier: 7.687A  pdb=" N   ASN A2915 " --> pdb=" O   HIS A2755 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   MET A2757 " --> pdb=" O   ASN A2915 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   MET A2917 " --> pdb=" O   MET A2757 " (cutoff:3.500A)
      removed outlier: 7.746A  pdb=" N   ILE A2759 " --> pdb=" O   MET A2917 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 3426 through 3430
      removed outlier: 6.657A  pdb=" N   VAL A3427 " --> pdb=" O   ILE A3451 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   GLN A3453 " --> pdb=" O   VAL A3427 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   LEU A3429 " --> pdb=" O   GLN A3453 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   VAL A3450 " --> pdb=" O   PHE A3495 " (cutoff:3.500A)
      removed outlier: 7.566A  pdb=" N   HIS A3497 " --> pdb=" O   VAL A3450 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   ILE A3452 " --> pdb=" O   HIS A3497 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 3471 through 3472
      removed outlier: 3.591A  pdb=" N   HIS A3484 " --> pdb=" O   ILE A3481 " (cutoff:3.500A)

    484 hydrogen bonds defined for protein.
    1401 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: 1.86

  Time building geometry restraints manager: 1.14 seconds

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

  Histogram of bond lengths:
        1.13 -     1.29: 1587
        1.29 -     1.46: 3126
        1.46 -     1.62: 5093
        1.62 -     1.78: 18
        1.78 -     1.94: 65
  Bond restraints: 9889
  Sorted by residual:
  bond pdb=" C14 ZG7 A4202 "
       pdb=" N15 ZG7 A4202 "
    ideal  model  delta    sigma   weight residual
    1.328  1.531 -0.203 2.00e-02 2.50e+03 1.03e+02
  bond pdb=" C14 ZG7 A4201 "
       pdb=" N15 ZG7 A4201 "
    ideal  model  delta    sigma   weight residual
    1.328  1.520 -0.192 2.00e-02 2.50e+03 9.21e+01
  bond pdb=" C5  ATP A4203 "
       pdb=" C6  ATP A4203 "
    ideal  model  delta    sigma   weight residual
    1.409  1.479 -0.070 1.00e-02 1.00e+04 4.87e+01
  bond pdb=" C26 ZG7 A4202 "
       pdb=" O27 ZG7 A4202 "
    ideal  model  delta    sigma   weight residual
    1.305  1.166  0.139 2.00e-02 2.50e+03 4.80e+01
  bond pdb=" C16 ZG7 A4202 "
       pdb=" N15 ZG7 A4202 "
    ideal  model  delta    sigma   weight residual
    1.312  1.450 -0.138 2.00e-02 2.50e+03 4.77e+01
  ... (remaining 9884 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.81: 13018
        3.81 -     7.62: 330
        7.62 -    11.43: 46
       11.43 -    15.24: 5
       15.24 -    19.05: 4
  Bond angle restraints: 13403
  Sorted by residual:
  angle pdb=" PA  ATP A4203 "
        pdb=" O3A ATP A4203 "
        pdb=" PB  ATP A4203 "
      ideal   model   delta    sigma   weight residual
     136.83  121.50   15.33 1.00e+00 1.00e+00 2.35e+02
  angle pdb=" PB  ATP A4203 "
        pdb=" O3B ATP A4203 "
        pdb=" PG  ATP A4203 "
      ideal   model   delta    sigma   weight residual
     139.87  128.63   11.24 1.00e+00 1.00e+00 1.26e+02
  angle pdb=" C5  ATP A4203 "
        pdb=" C4  ATP A4203 "
        pdb=" N3  ATP A4203 "
      ideal   model   delta    sigma   weight residual
     126.80  118.41    8.39 1.00e+00 1.00e+00 7.04e+01
  angle pdb=" N   TYR A2115 "
        pdb=" CA  TYR A2115 "
        pdb=" C   TYR A2115 "
      ideal   model   delta    sigma   weight residual
     110.17   99.76   10.41 1.51e+00 4.39e-01 4.75e+01
  angle pdb=" N3  ATP A4203 "
        pdb=" C4  ATP A4203 "
        pdb=" N9  ATP A4203 "
      ideal   model   delta    sigma   weight residual
     127.04  134.67   -7.63 1.15e+00 7.59e-01 4.41e+01
  ... (remaining 13398 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 5544
       17.88 -    35.76: 309
       35.76 -    53.64: 55
       53.64 -    71.53: 26
       71.53 -    89.41: 14
  Dihedral angle restraints: 5948
    sinusoidal: 2446
      harmonic: 3502
  Sorted by residual:
  dihedral pdb=" CA  ASP A2105 "
           pdb=" C   ASP A2105 "
           pdb=" N   THR A2106 "
           pdb=" CA  THR A2106 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.51  -26.49     0      5.00e+00 4.00e-02 2.81e+01
  dihedral pdb=" CA  GLN A2639 "
           pdb=" C   GLN A2639 "
           pdb=" N   THR A2640 "
           pdb=" CA  THR A2640 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.29   25.71     0      5.00e+00 4.00e-02 2.64e+01
  dihedral pdb=" CA  GLU A2810 "
           pdb=" C   GLU A2810 "
           pdb=" N   SER A2811 "
           pdb=" CA  SER A2811 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.77  -23.23     0      5.00e+00 4.00e-02 2.16e+01
  ... (remaining 5945 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 1157
       0.085 -    0.169: 315
       0.169 -    0.254: 37
       0.254 -    0.338: 7
       0.338 -    0.423: 4
  Chirality restraints: 1520
  Sorted by residual:
  chirality pdb=" CB  ILE A2226 "
            pdb=" CA  ILE A2226 "
            pdb=" CG1 ILE A2226 "
            pdb=" CG2 ILE A2226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.22    0.42 2.00e-01 2.50e+01 4.47e+00
  chirality pdb=" CB  ILE A2141 "
            pdb=" CA  ILE A2141 "
            pdb=" CG1 ILE A2141 "
            pdb=" CG2 ILE A2141 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    3.00   -0.35 2.00e-01 2.50e+01 3.09e+00
  chirality pdb=" CA  LEU A2366 "
            pdb=" N   LEU A2366 "
            pdb=" C   LEU A2366 "
            pdb=" CB  LEU A2366 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.09e+00
  ... (remaining 1517 not shown)

  Planarity restraints: 1686
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C08 ZG7 A4202 "   -0.014 2.00e-02 2.50e+03   2.73e-02 2.61e+01
        pdb=" C11 ZG7 A4202 "    0.067 2.00e-02 2.50e+03
        pdb=" C14 ZG7 A4202 "   -0.009 2.00e-02 2.50e+03
        pdb=" C16 ZG7 A4202 "   -0.015 2.00e-02 2.50e+03
        pdb=" C17 ZG7 A4202 "   -0.012 2.00e-02 2.50e+03
        pdb=" C26 ZG7 A4202 "    0.002 2.00e-02 2.50e+03
        pdb=" C28 ZG7 A4202 "   -0.018 2.00e-02 2.50e+03
        pdb=" C29 ZG7 A4202 "    0.003 2.00e-02 2.50e+03
        pdb=" N12 ZG7 A4202 "   -0.005 2.00e-02 2.50e+03
        pdb=" N13 ZG7 A4202 "   -0.029 2.00e-02 2.50e+03
        pdb=" N15 ZG7 A4202 "   -0.009 2.00e-02 2.50e+03
        pdb=" N30 ZG7 A4202 "    0.010 2.00e-02 2.50e+03
        pdb=" O18 ZG7 A4202 "    0.056 2.00e-02 2.50e+03
        pdb=" O27 ZG7 A4202 "   -0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A2728 "   -0.018 2.00e-02 2.50e+03   3.57e-02 1.28e+01
        pdb=" C   LEU A2728 "    0.062 2.00e-02 2.50e+03
        pdb=" O   LEU A2728 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   GLU A2729 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C02 ZG7 A4202 "   -0.003 2.00e-02 2.50e+03   2.42e-02 1.17e+01
        pdb=" C03 ZG7 A4202 "   -0.003 2.00e-02 2.50e+03
        pdb=" C04 ZG7 A4202 "   -0.006 2.00e-02 2.50e+03
        pdb=" C05 ZG7 A4202 "    0.059 2.00e-02 2.50e+03
        pdb=" C06 ZG7 A4202 "   -0.002 2.00e-02 2.50e+03
        pdb=" C07 ZG7 A4202 "   -0.005 2.00e-02 2.50e+03
        pdb=" C08 ZG7 A4202 "   -0.034 2.00e-02 2.50e+03
        pdb="CL01 ZG7 A4202 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1683 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 68
        2.56 -     3.15: 8195
        3.15 -     3.73: 14809
        3.73 -     4.32: 20558
        4.32 -     4.90: 33965
  Nonbonded interactions: 77595
  Sorted by model distance:
  nonbonded pdb=" O3G ATP A4203 "
            pdb="MG    MG A4204 "
     model   vdw
     1.978 2.170
  nonbonded pdb=" OG1 THR A2081 "
            pdb="MG    MG A4204 "
     model   vdw
     2.003 2.170
  nonbonded pdb=" O1B ATP A4203 "
            pdb="MG    MG A4204 "
     model   vdw
     2.038 2.170
  nonbonded pdb=" OD1 ASN A2832 "
            pdb=" OG  SER A2905 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" NH1 ARG A2763 "
            pdb=" O   SER A3511 "
     model   vdw
     2.298 3.120
  ... (remaining 77590 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.640
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
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      :  0.012   0.203   9889  Z= 0.533
  Angle     :  1.474  19.050  13403  Z= 0.824
  Chirality :  0.078   0.423   1520
  Planarity :  0.008   0.054   1686
  Dihedral  : 13.199  89.407   3676
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  6.82 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  :  4.52 %
    Favored  : 93.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.80 (0.22), residues: 1188
  helix: -0.54 (0.19), residues: 584
  sheet: -1.71 (0.43), residues: 125
  loop : -1.75 (0.26), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.036   0.004   ARG A2830 
 TYR   0.057   0.006   TYR A3330 
 PHE   0.050   0.004   PHE A2266 
 TRP   0.048   0.004   TRP A3379 
 HIS   0.025   0.003   HIS A3517 

Details of bonding type rmsd
  covalent geometry    : bond        0.01164 ( 9889)
  covalent geometry    : angle       1.47403 (13403)
  hydrogen bonds       : bond        0.11158 (  484)
  hydrogen bonds       : angle       6.37173 ( 1401)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 222
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2105 ASP cc_start: 0.8023 (m-30) cc_final: 0.7510 (m-30)
REVERT: A 2180 ASN cc_start: 0.8596 (t0) cc_final: 0.8357 (t0)
REVERT: A 2202 THR cc_start: 0.8417 (m) cc_final: 0.8216 (t)
REVERT: A 2218 ASP cc_start: 0.7822 (m-30) cc_final: 0.7612 (m-30)
REVERT: A 2411 LYS cc_start: 0.9360 (mtmm) cc_final: 0.9124 (mmmt)
REVERT: A 2707 VAL cc_start: 0.9216 (t) cc_final: 0.8640 (m)
REVERT: A 2792 LEU cc_start: 0.8765 (tp) cc_final: 0.8417 (tp)
REVERT: A 2849 TYR cc_start: 0.9283 (t80) cc_final: 0.9035 (t80)
REVERT: A 2960 THR cc_start: 0.7673 (OUTLIER) cc_final: 0.6231 (p)
REVERT: A 3344 ASP cc_start: 0.8986 (m-30) cc_final: 0.8673 (m-30)
REVERT: A 3358 VAL cc_start: 0.9000 (t) cc_final: 0.8722 (p)
REVERT: A 3369 TYR cc_start: 0.8303 (t80) cc_final: 0.7941 (t80)
REVERT: A 3394 MET cc_start: 0.9073 (tpt) cc_final: 0.8458 (tmm)
REVERT: A 3438 LYS cc_start: 0.8734 (ttpp) cc_final: 0.8342 (tptp)
REVERT: A 3486 VAL cc_start: 0.8615 (t) cc_final: 0.8397 (m)
  outliers start: 21
  outliers final: 7
  residues processed: 239
  average time/residue: 0.1247
  time to fit residues: 39.4816
Evaluate side-chains
  118 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2131 THR
Chi-restraints excluded: chain A residue 2295 ILE
Chi-restraints excluded: chain A residue 2476 LYS
Chi-restraints excluded: chain A residue 2702 LEU
Chi-restraints excluded: chain A residue 2842 ASP
Chi-restraints excluded: chain A residue 2958 ILE
Chi-restraints excluded: chain A residue 2960 THR
Chi-restraints excluded: chain A residue 3385 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    7.9990
   chunk 117 optimal weight:    5.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A2300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2363 ASN
A2481 ASN
A2500 GLN
A2508 GLN
A2569 GLN
A2714 ASN
A2854 ASN
** A3399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.074341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.058130 restraints weight = 30812.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.060569 restraints weight = 15053.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.062233 restraints weight = 9466.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.063360 restraints weight = 6945.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.064037 restraints weight = 5623.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3103
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3103 r_free = 0.3103    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3103 r_free = 0.3103    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3103
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9889  Z= 0.158
  Angle     :  0.682   9.343  13403  Z= 0.354
  Chirality :  0.045   0.213   1520
  Planarity :  0.004   0.037   1686
  Dihedral  :  8.462  89.622   1351
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.53 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  :  9.32 %
    Favored  : 87.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.24), residues: 1188
  helix:  1.31 (0.21), residues: 588
  sheet: -0.89 (0.47), residues: 122
  loop : -1.16 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A2646 
 TYR   0.017   0.001   TYR A2571 
 PHE   0.019   0.001   PHE A2244 
 TRP   0.025   0.002   TRP A2084 
 HIS   0.009   0.001   HIS A3413 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 9889)
  covalent geometry    : angle       0.68236 (13403)
  hydrogen bonds       : bond        0.04330 (  484)
  hydrogen bonds       : angle       4.92554 ( 1401)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 143
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2105 ASP cc_start: 0.7998 (m-30) cc_final: 0.7704 (m-30)
REVERT: A 2411 LYS cc_start: 0.9341 (mtmm) cc_final: 0.9082 (mmmt)
REVERT: A 2428 MET cc_start: 0.9018 (ttp) cc_final: 0.8566 (tmm)
REVERT: A 2623 THR cc_start: 0.9582 (OUTLIER) cc_final: 0.9119 (p)
REVERT: A 2801 LYS cc_start: 0.9258 (tptt) cc_final: 0.9032 (tptp)
REVERT: A 2805 ASP cc_start: 0.8729 (m-30) cc_final: 0.8405 (m-30)
REVERT: A 2849 TYR cc_start: 0.9280 (t80) cc_final: 0.9028 (t80)
REVERT: A 2872 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8455 (pt0)
REVERT: A 2904 SER cc_start: 0.9421 (m) cc_final: 0.9074 (p)
REVERT: A 3315 LYS cc_start: 0.9095 (tptt) cc_final: 0.8823 (tptt)
REVERT: A 3358 VAL cc_start: 0.9060 (t) cc_final: 0.8831 (t)
REVERT: A 3480 GLU cc_start: 0.7432 (mp0) cc_final: 0.7199 (pm20)
  outliers start: 32
  outliers final: 20
  residues processed: 168
  average time/residue: 0.1103
  time to fit residues: 25.7410
Evaluate side-chains
  123 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2127 ASP
Chi-restraints excluded: chain A residue 2131 THR
Chi-restraints excluded: chain A residue 2237 LEU
Chi-restraints excluded: chain A residue 2267 THR
Chi-restraints excluded: chain A residue 2476 LYS
Chi-restraints excluded: chain A residue 2509 LEU
Chi-restraints excluded: chain A residue 2623 THR
Chi-restraints excluded: chain A residue 2728 LEU
Chi-restraints excluded: chain A residue 2769 LEU
Chi-restraints excluded: chain A residue 2825 THR
Chi-restraints excluded: chain A residue 2866 LEU
Chi-restraints excluded: chain A residue 2872 GLU
Chi-restraints excluded: chain A residue 2919 ASP
Chi-restraints excluded: chain A residue 2942 ASP
Chi-restraints excluded: chain A residue 3002 LEU
Chi-restraints excluded: chain A residue 3320 LEU
Chi-restraints excluded: chain A residue 3330 TYR
Chi-restraints excluded: chain A residue 3338 ASN
Chi-restraints excluded: chain A residue 3425 LYS
Chi-restraints excluded: chain A residue 3459 ASP
Chi-restraints excluded: chain A residue 3469 GLU
Chi-restraints excluded: chain A residue 3472 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 110 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 117 optimal weight:    4.9990
   chunk 3 optimal weight:    0.5980
   chunk 64 optimal weight:   10.0000
   chunk 98 optimal weight:    9.9990
   chunk 114 optimal weight:    7.9990
   chunk 77 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 73 optimal weight:    0.8980
   overall best weight:    3.0986

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

Flipped N/Q/H residues before XYZ refinement:
A2274 HIS
** A2500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2598 HIS
** A3497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3521 ASN ** 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 = 0.3294 r_free = 0.3294 target = 0.072546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.056402 restraints weight = 30910.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.058769 restraints weight = 15131.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.060383 restraints weight = 9536.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.061518 restraints weight = 7014.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.062262 restraints weight = 5669.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.3118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9889  Z= 0.191
  Angle     :  0.635   8.706  13403  Z= 0.329
  Chirality :  0.044   0.156   1520
  Planarity :  0.004   0.047   1686
  Dihedral  :  8.165  89.784   1340
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.03 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 12.36 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.25), residues: 1188
  helix:  1.57 (0.22), residues: 593
  sheet: -0.75 (0.41), residues: 155
  loop : -0.83 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A3365 
 TYR   0.017   0.002   TYR A2571 
 PHE   0.014   0.001   PHE A2972 
 TRP   0.023   0.002   TRP A2125 
 HIS   0.008   0.001   HIS A3517 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 9889)
  covalent geometry    : angle       0.63467 (13403)
  hydrogen bonds       : bond        0.04101 (  484)
  hydrogen bonds       : angle       4.67710 ( 1401)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 112
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2105 ASP cc_start: 0.8069 (m-30) cc_final: 0.7765 (m-30)
REVERT: A 2411 LYS cc_start: 0.9359 (mtmm) cc_final: 0.9135 (mmmt)
REVERT: A 2428 MET cc_start: 0.9039 (ttp) cc_final: 0.8797 (tmm)
REVERT: A 2623 THR cc_start: 0.9587 (OUTLIER) cc_final: 0.9112 (p)
REVERT: A 2849 TYR cc_start: 0.9319 (t80) cc_final: 0.9049 (t80)
REVERT: A 2872 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8558 (pt0)
REVERT: A 2904 SER cc_start: 0.9459 (m) cc_final: 0.9141 (p)
REVERT: A 3315 LYS cc_start: 0.9121 (tptt) cc_final: 0.8796 (tptt)
REVERT: A 3330 TYR cc_start: 0.9161 (OUTLIER) cc_final: 0.8258 (t80)
REVERT: A 3402 ASP cc_start: 0.7478 (t0) cc_final: 0.7273 (t0)
  outliers start: 34
  outliers final: 21
  residues processed: 139
  average time/residue: 0.1076
  time to fit residues: 20.9343
Evaluate side-chains
  126 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2127 ASP
Chi-restraints excluded: chain A residue 2131 THR
Chi-restraints excluded: chain A residue 2267 THR
Chi-restraints excluded: chain A residue 2476 LYS
Chi-restraints excluded: chain A residue 2509 LEU
Chi-restraints excluded: chain A residue 2623 THR
Chi-restraints excluded: chain A residue 2658 ASP
Chi-restraints excluded: chain A residue 2728 LEU
Chi-restraints excluded: chain A residue 2769 LEU
Chi-restraints excluded: chain A residue 2825 THR
Chi-restraints excluded: chain A residue 2866 LEU
Chi-restraints excluded: chain A residue 2872 GLU
Chi-restraints excluded: chain A residue 2942 ASP
Chi-restraints excluded: chain A residue 2945 VAL
Chi-restraints excluded: chain A residue 2984 VAL
Chi-restraints excluded: chain A residue 3002 LEU
Chi-restraints excluded: chain A residue 3320 LEU
Chi-restraints excluded: chain A residue 3330 TYR
Chi-restraints excluded: chain A residue 3353 LEU
Chi-restraints excluded: chain A residue 3394 MET
Chi-restraints excluded: chain A residue 3425 LYS
Chi-restraints excluded: chain A residue 3459 ASP
Chi-restraints excluded: chain A residue 3469 GLU
Chi-restraints excluded: chain A residue 3472 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 57 optimal weight:    0.0370
   chunk 1 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 17 optimal weight:   40.0000
   chunk 8 optimal weight:    4.9990
   chunk 72 optimal weight:    8.9990
   chunk 110 optimal weight:    3.9990
   chunk 26 optimal weight:    8.9990
   chunk 10 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    1.8064

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

Flipped N/Q/H residues before XYZ refinement:
A2500 GLN
A3497 HIS
** A3521 ASN ** 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 = 0.3309 r_free = 0.3309 target = 0.073140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.057165 restraints weight = 30874.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.059520 restraints weight = 15000.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.061170 restraints weight = 9415.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.062302 restraints weight = 6859.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.063036 restraints weight = 5545.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.3413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9889  Z= 0.132
  Angle     :  0.584   8.103  13403  Z= 0.300
  Chirality :  0.042   0.180   1520
  Planarity :  0.004   0.048   1686
  Dihedral  :  7.914  84.931   1340
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.11 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 13.10 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.25), residues: 1188
  helix:  1.67 (0.22), residues: 597
  sheet: -0.62 (0.42), residues: 146
  loop : -0.76 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2646 
 TYR   0.015   0.001   TYR A2571 
 PHE   0.019   0.001   PHE A2992 
 TRP   0.022   0.001   TRP A2084 
 HIS   0.007   0.001   HIS A3517 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9889)
  covalent geometry    : angle       0.58446 (13403)
  hydrogen bonds       : bond        0.03617 (  484)
  hydrogen bonds       : angle       4.51832 ( 1401)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 116
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2105 ASP cc_start: 0.8092 (m-30) cc_final: 0.7773 (m-30)
REVERT: A 2209 ARG cc_start: 0.7643 (mtm-85) cc_final: 0.7322 (mtm-85)
REVERT: A 2411 LYS cc_start: 0.9357 (mtmm) cc_final: 0.9144 (mmmt)
REVERT: A 2428 MET cc_start: 0.9021 (ttp) cc_final: 0.8819 (tmm)
REVERT: A 2623 THR cc_start: 0.9587 (OUTLIER) cc_final: 0.9134 (p)
REVERT: A 2819 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8200 (tm-30)
REVERT: A 2849 TYR cc_start: 0.9314 (t80) cc_final: 0.9054 (t80)
REVERT: A 2872 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8548 (pt0)
REVERT: A 2904 SER cc_start: 0.9460 (m) cc_final: 0.9167 (p)
REVERT: A 3315 LYS cc_start: 0.9125 (tptt) cc_final: 0.8759 (tptt)
REVERT: A 3330 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.8348 (t80)
REVERT: A 3340 ARG cc_start: 0.8194 (tpp-160) cc_final: 0.7879 (tpp80)
REVERT: A 3381 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8422 (mm-30)
REVERT: A 3469 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7454 (mp0)
  outliers start: 33
  outliers final: 19
  residues processed: 140
  average time/residue: 0.1084
  time to fit residues: 21.1957
Evaluate side-chains
  129 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2127 ASP
Chi-restraints excluded: chain A residue 2131 THR
Chi-restraints excluded: chain A residue 2237 LEU
Chi-restraints excluded: chain A residue 2476 LYS
Chi-restraints excluded: chain A residue 2623 THR
Chi-restraints excluded: chain A residue 2658 ASP
Chi-restraints excluded: chain A residue 2679 LYS
Chi-restraints excluded: chain A residue 2728 LEU
Chi-restraints excluded: chain A residue 2823 LEU
Chi-restraints excluded: chain A residue 2825 THR
Chi-restraints excluded: chain A residue 2866 LEU
Chi-restraints excluded: chain A residue 2872 GLU
Chi-restraints excluded: chain A residue 2942 ASP
Chi-restraints excluded: chain A residue 2945 VAL
Chi-restraints excluded: chain A residue 2984 VAL
Chi-restraints excluded: chain A residue 3002 LEU
Chi-restraints excluded: chain A residue 3320 LEU
Chi-restraints excluded: chain A residue 3330 TYR
Chi-restraints excluded: chain A residue 3338 ASN
Chi-restraints excluded: chain A residue 3353 LEU
Chi-restraints excluded: chain A residue 3425 LYS
Chi-restraints excluded: chain A residue 3459 ASP
Chi-restraints excluded: chain A residue 3469 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 46 optimal weight:    7.9990
   chunk 84 optimal weight:    9.9990
   chunk 69 optimal weight:   10.0000
   chunk 52 optimal weight:    5.9990
   chunk 74 optimal weight:    0.4980
   chunk 8 optimal weight:    5.9990
   chunk 101 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 78 optimal weight:    5.9990
   chunk 94 optimal weight:    6.9990
   overall best weight:    2.4986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.072347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.056351 restraints weight = 30846.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.058695 restraints weight = 14990.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.060332 restraints weight = 9426.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.061414 restraints weight = 6874.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.062159 restraints weight = 5599.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8605
moved from start:          0.3625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   9889  Z= 0.158
  Angle     :  0.599   8.554  13403  Z= 0.306
  Chirality :  0.043   0.178   1520
  Planarity :  0.004   0.053   1686
  Dihedral  :  7.867  84.666   1340
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.11 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 13.38 %
    Favored  : 83.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.25), residues: 1188
  helix:  1.76 (0.21), residues: 604
  sheet: -0.34 (0.41), residues: 156
  loop : -0.75 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2646 
 TYR   0.015   0.001   TYR A2571 
 PHE   0.039   0.001   PHE A2371 
 TRP   0.021   0.001   TRP A2084 
 HIS   0.008   0.001   HIS A3517 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 9889)
  covalent geometry    : angle       0.59852 (13403)
  hydrogen bonds       : bond        0.03652 (  484)
  hydrogen bonds       : angle       4.43981 ( 1401)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 110
  time to evaluate  : 0.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2105 ASP cc_start: 0.8137 (m-30) cc_final: 0.7812 (m-30)
REVERT: A 2411 LYS cc_start: 0.9380 (mtmm) cc_final: 0.9177 (mmmt)
REVERT: A 2623 THR cc_start: 0.9590 (OUTLIER) cc_final: 0.9141 (p)
REVERT: A 2819 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8215 (tm-30)
REVERT: A 2849 TYR cc_start: 0.9330 (t80) cc_final: 0.9067 (t80)
REVERT: A 2872 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8563 (pt0)
REVERT: A 3315 LYS cc_start: 0.9153 (tptt) cc_final: 0.8818 (tptt)
REVERT: A 3330 TYR cc_start: 0.9094 (OUTLIER) cc_final: 0.8451 (t80)
REVERT: A 3344 ASP cc_start: 0.8932 (m-30) cc_final: 0.8715 (t0)
REVERT: A 3469 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7565 (mp0)
  outliers start: 34
  outliers final: 21
  residues processed: 134
  average time/residue: 0.1111
  time to fit residues: 20.7480
Evaluate side-chains
  123 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 98
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2106 THR
Chi-restraints excluded: chain A residue 2131 THR
Chi-restraints excluded: chain A residue 2142 THR
Chi-restraints excluded: chain A residue 2237 LEU
Chi-restraints excluded: chain A residue 2476 LYS
Chi-restraints excluded: chain A residue 2509 LEU
Chi-restraints excluded: chain A residue 2623 THR
Chi-restraints excluded: chain A residue 2658 ASP
Chi-restraints excluded: chain A residue 2694 LEU
Chi-restraints excluded: chain A residue 2728 LEU
Chi-restraints excluded: chain A residue 2769 LEU
Chi-restraints excluded: chain A residue 2823 LEU
Chi-restraints excluded: chain A residue 2825 THR
Chi-restraints excluded: chain A residue 2866 LEU
Chi-restraints excluded: chain A residue 2872 GLU
Chi-restraints excluded: chain A residue 2935 VAL
Chi-restraints excluded: chain A residue 2942 ASP
Chi-restraints excluded: chain A residue 2945 VAL
Chi-restraints excluded: chain A residue 2984 VAL
Chi-restraints excluded: chain A residue 3002 LEU
Chi-restraints excluded: chain A residue 3330 TYR
Chi-restraints excluded: chain A residue 3338 ASN
Chi-restraints excluded: chain A residue 3425 LYS
Chi-restraints excluded: chain A residue 3469 GLU
Chi-restraints excluded: chain A residue 3486 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 92 optimal weight:    0.1980
   chunk 60 optimal weight:    5.9990
   chunk 98 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 90 optimal weight:    3.9990
   chunk 99 optimal weight:    6.9990
   chunk 102 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 110 optimal weight:    4.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** A3521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.072509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.056397 restraints weight = 31446.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.058683 restraints weight = 15450.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.060286 restraints weight = 9798.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.061385 restraints weight = 7175.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.062121 restraints weight = 5827.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.3860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9889  Z= 0.116
  Angle     :  0.574   8.985  13403  Z= 0.291
  Chirality :  0.042   0.168   1520
  Planarity :  0.004   0.051   1686
  Dihedral  :  7.704  82.256   1340
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 14.02 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.25), residues: 1188
  helix:  1.82 (0.21), residues: 611
  sheet: -0.22 (0.41), residues: 156
  loop : -0.65 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2646 
 TYR   0.014   0.001   TYR A2571 
 PHE   0.017   0.001   PHE A2244 
 TRP   0.021   0.001   TRP A2084 
 HIS   0.005   0.001   HIS A3517 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9889)
  covalent geometry    : angle       0.57421 (13403)
  hydrogen bonds       : bond        0.03347 (  484)
  hydrogen bonds       : angle       4.31645 ( 1401)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 112
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2105 ASP cc_start: 0.8110 (m-30) cc_final: 0.7770 (m-30)
REVERT: A 2623 THR cc_start: 0.9582 (OUTLIER) cc_final: 0.9150 (p)
REVERT: A 2819 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8187 (tm-30)
REVERT: A 2849 TYR cc_start: 0.9320 (t80) cc_final: 0.9074 (t80)
REVERT: A 2872 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8592 (pt0)
REVERT: A 2904 SER cc_start: 0.9454 (m) cc_final: 0.9171 (p)
REVERT: A 3315 LYS cc_start: 0.9148 (tptt) cc_final: 0.8743 (tptt)
REVERT: A 3330 TYR cc_start: 0.9024 (OUTLIER) cc_final: 0.8518 (t80)
REVERT: A 3344 ASP cc_start: 0.8907 (m-30) cc_final: 0.8701 (t0)
REVERT: A 3377 MET cc_start: 0.8577 (ppp) cc_final: 0.8366 (ppp)
REVERT: A 3379 TRP cc_start: 0.9040 (m-10) cc_final: 0.8705 (m-90)
REVERT: A 3469 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7589 (mp0)
REVERT: A 3480 GLU cc_start: 0.8367 (pt0) cc_final: 0.7901 (pm20)
  outliers start: 32
  outliers final: 19
  residues processed: 137
  average time/residue: 0.0997
  time to fit residues: 19.5034
Evaluate side-chains
  123 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2127 ASP
Chi-restraints excluded: chain A residue 2131 THR
Chi-restraints excluded: chain A residue 2142 THR
Chi-restraints excluded: chain A residue 2476 LYS
Chi-restraints excluded: chain A residue 2509 LEU
Chi-restraints excluded: chain A residue 2623 THR
Chi-restraints excluded: chain A residue 2658 ASP
Chi-restraints excluded: chain A residue 2679 LYS
Chi-restraints excluded: chain A residue 2694 LEU
Chi-restraints excluded: chain A residue 2728 LEU
Chi-restraints excluded: chain A residue 2769 LEU
Chi-restraints excluded: chain A residue 2823 LEU
Chi-restraints excluded: chain A residue 2866 LEU
Chi-restraints excluded: chain A residue 2923 LYS
Chi-restraints excluded: chain A residue 2935 VAL
Chi-restraints excluded: chain A residue 2942 ASP
Chi-restraints excluded: chain A residue 2984 VAL
Chi-restraints excluded: chain A residue 3002 LEU
Chi-restraints excluded: chain A residue 3330 TYR
Chi-restraints excluded: chain A residue 3338 ASN
Chi-restraints excluded: chain A residue 3425 LYS
Chi-restraints excluded: chain A residue 3469 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 40 optimal weight:    7.9990
   chunk 45 optimal weight:    0.8980
   chunk 80 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0470
   chunk 87 optimal weight:    8.9990
   chunk 79 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 99 optimal weight:    9.9990
   chunk 65 optimal weight:    4.9990
   overall best weight:    0.9882

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

Flipped N/Q/H residues before XYZ refinement:
A2735 HIS
** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3521 ASN ** 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 = 0.3293 r_free = 0.3293 target = 0.073176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.057139 restraints weight = 31101.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.059401 restraints weight = 15436.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.060976 restraints weight = 9833.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.061959 restraints weight = 7257.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.062786 restraints weight = 5958.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.4102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9889  Z= 0.105
  Angle     :  0.567   8.534  13403  Z= 0.283
  Chirality :  0.041   0.164   1520
  Planarity :  0.004   0.058   1686
  Dihedral  :  7.639  83.994   1340
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.85 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.25), residues: 1188
  helix:  1.91 (0.21), residues: 609
  sheet: -0.36 (0.42), residues: 149
  loop : -0.59 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A3445 
 TYR   0.013   0.001   TYR A2571 
 PHE   0.016   0.001   PHE A2720 
 TRP   0.020   0.001   TRP A2084 
 HIS   0.005   0.001   HIS A3517 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 9889)
  covalent geometry    : angle       0.56673 (13403)
  hydrogen bonds       : bond        0.03180 (  484)
  hydrogen bonds       : angle       4.23795 ( 1401)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 115
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2105 ASP cc_start: 0.8109 (m-30) cc_final: 0.7761 (m-30)
REVERT: A 2222 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7725 (mt)
REVERT: A 2623 THR cc_start: 0.9583 (OUTLIER) cc_final: 0.9175 (p)
REVERT: A 2819 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8151 (tm-30)
REVERT: A 2849 TYR cc_start: 0.9307 (t80) cc_final: 0.9054 (t80)
REVERT: A 2872 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8600 (pt0)
REVERT: A 2904 SER cc_start: 0.9458 (m) cc_final: 0.9182 (p)
REVERT: A 3315 LYS cc_start: 0.9151 (tptt) cc_final: 0.8737 (tptt)
REVERT: A 3330 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.8515 (t80)
REVERT: A 3344 ASP cc_start: 0.8943 (m-30) cc_final: 0.8715 (t0)
REVERT: A 3379 TRP cc_start: 0.9029 (m-10) cc_final: 0.8733 (m-90)
REVERT: A 3469 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7611 (mp0)
REVERT: A 3480 GLU cc_start: 0.8363 (pt0) cc_final: 0.7894 (pm20)
  outliers start: 26
  outliers final: 21
  residues processed: 135
  average time/residue: 0.0965
  time to fit residues: 18.7855
Evaluate side-chains
  126 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2106 THR
Chi-restraints excluded: chain A residue 2127 ASP
Chi-restraints excluded: chain A residue 2142 THR
Chi-restraints excluded: chain A residue 2222 ILE
Chi-restraints excluded: chain A residue 2237 LEU
Chi-restraints excluded: chain A residue 2426 MET
Chi-restraints excluded: chain A residue 2476 LYS
Chi-restraints excluded: chain A residue 2509 LEU
Chi-restraints excluded: chain A residue 2623 THR
Chi-restraints excluded: chain A residue 2658 ASP
Chi-restraints excluded: chain A residue 2679 LYS
Chi-restraints excluded: chain A residue 2694 LEU
Chi-restraints excluded: chain A residue 2728 LEU
Chi-restraints excluded: chain A residue 2769 LEU
Chi-restraints excluded: chain A residue 2823 LEU
Chi-restraints excluded: chain A residue 2866 LEU
Chi-restraints excluded: chain A residue 2923 LYS
Chi-restraints excluded: chain A residue 2935 VAL
Chi-restraints excluded: chain A residue 2942 ASP
Chi-restraints excluded: chain A residue 2945 VAL
Chi-restraints excluded: chain A residue 2984 VAL
Chi-restraints excluded: chain A residue 3002 LEU
Chi-restraints excluded: chain A residue 3330 TYR
Chi-restraints excluded: chain A residue 3425 LYS
Chi-restraints excluded: chain A residue 3469 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 64 optimal weight:   10.0000
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    8.9990
   chunk 57 optimal weight:    0.8980
   chunk 105 optimal weight:    7.9990
   chunk 90 optimal weight:    4.9990
   chunk 85 optimal weight:    3.9990
   chunk 32 optimal weight:   10.0000
   chunk 15 optimal weight:   10.0000
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.071945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.056057 restraints weight = 31033.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.058288 restraints weight = 15292.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.059843 restraints weight = 9728.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.060893 restraints weight = 7171.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.061604 restraints weight = 5843.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8605
moved from start:          0.4162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9889  Z= 0.143
  Angle     :  0.593  10.282  13403  Z= 0.296
  Chirality :  0.042   0.166   1520
  Planarity :  0.004   0.063   1686
  Dihedral  :  7.658  84.533   1339
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 15.04 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.25), residues: 1188
  helix:  2.09 (0.22), residues: 600
  sheet: -0.04 (0.41), residues: 156
  loop : -0.64 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A3445 
 TYR   0.015   0.001   TYR A2571 
 PHE   0.045   0.001   PHE A3366 
 TRP   0.020   0.001   TRP A2084 
 HIS   0.006   0.001   HIS A3517 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 9889)
  covalent geometry    : angle       0.59272 (13403)
  hydrogen bonds       : bond        0.03385 (  484)
  hydrogen bonds       : angle       4.27018 ( 1401)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 104
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: A 2105 ASP cc_start: 0.8154 (m-30) cc_final: 0.7823 (m-30)
REVERT: A 2222 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7828 (mt)
REVERT: A 2243 MET cc_start: 0.8848 (ppp) cc_final: 0.8647 (ppp)
REVERT: A 2623 THR cc_start: 0.9586 (OUTLIER) cc_final: 0.9159 (p)
REVERT: A 2819 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8180 (tm-30)
REVERT: A 2849 TYR cc_start: 0.9332 (t80) cc_final: 0.9095 (t80)
REVERT: A 2872 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8604 (pt0)
REVERT: A 3315 LYS cc_start: 0.9140 (tptt) cc_final: 0.8736 (tptt)
REVERT: A 3379 TRP cc_start: 0.9055 (m-10) cc_final: 0.8682 (m-90)
REVERT: A 3469 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7684 (mp0)
REVERT: A 3480 GLU cc_start: 0.8365 (pt0) cc_final: 0.7854 (pm20)
  outliers start: 36
  outliers final: 24
  residues processed: 131
  average time/residue: 0.1007
  time to fit residues: 18.7973
Evaluate side-chains
  127 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 100
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2106 THR
Chi-restraints excluded: chain A residue 2142 THR
Chi-restraints excluded: chain A residue 2222 ILE
Chi-restraints excluded: chain A residue 2237 LEU
Chi-restraints excluded: chain A residue 2249 LEU
Chi-restraints excluded: chain A residue 2426 MET
Chi-restraints excluded: chain A residue 2476 LYS
Chi-restraints excluded: chain A residue 2509 LEU
Chi-restraints excluded: chain A residue 2623 THR
Chi-restraints excluded: chain A residue 2658 ASP
Chi-restraints excluded: chain A residue 2661 VAL
Chi-restraints excluded: chain A residue 2694 LEU
Chi-restraints excluded: chain A residue 2728 LEU
Chi-restraints excluded: chain A residue 2769 LEU
Chi-restraints excluded: chain A residue 2823 LEU
Chi-restraints excluded: chain A residue 2842 ASP
Chi-restraints excluded: chain A residue 2866 LEU
Chi-restraints excluded: chain A residue 2892 CYS
Chi-restraints excluded: chain A residue 2935 VAL
Chi-restraints excluded: chain A residue 2942 ASP
Chi-restraints excluded: chain A residue 2945 VAL
Chi-restraints excluded: chain A residue 2984 VAL
Chi-restraints excluded: chain A residue 3002 LEU
Chi-restraints excluded: chain A residue 3338 ASN
Chi-restraints excluded: chain A residue 3425 LYS
Chi-restraints excluded: chain A residue 3469 GLU
Chi-restraints excluded: chain A residue 3479 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 80 optimal weight:    4.9990
   chunk 30 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 55 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0470
   chunk 7 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.8086

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

Flipped N/Q/H residues before XYZ refinement:
** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.072494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.056399 restraints weight = 31071.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.058669 restraints weight = 15362.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.060246 restraints weight = 9746.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.061332 restraints weight = 7198.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.061995 restraints weight = 5849.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
moved from start:          0.4299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9889  Z= 0.128
  Angle     :  0.580   8.808  13403  Z= 0.292
  Chirality :  0.042   0.170   1520
  Planarity :  0.004   0.063   1686
  Dihedral  :  7.651  86.775   1339
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 15.31 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.25), residues: 1188
  helix:  2.22 (0.22), residues: 594
  sheet:  0.01 (0.41), residues: 156
  loop : -0.55 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A3365 
 TYR   0.014   0.001   TYR A2571 
 PHE   0.040   0.001   PHE A3366 
 TRP   0.021   0.001   TRP A2084 
 HIS   0.006   0.001   HIS A3517 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9889)
  covalent geometry    : angle       0.57970 (13403)
  hydrogen bonds       : bond        0.03328 (  484)
  hydrogen bonds       : angle       4.25232 ( 1401)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 102
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2222 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7822 (mt)
REVERT: A 2623 THR cc_start: 0.9579 (OUTLIER) cc_final: 0.9177 (p)
REVERT: A 2819 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8179 (tm-30)
REVERT: A 2849 TYR cc_start: 0.9336 (t80) cc_final: 0.9095 (t80)
REVERT: A 2872 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8599 (pt0)
REVERT: A 3315 LYS cc_start: 0.9127 (tptt) cc_final: 0.8685 (tptt)
REVERT: A 3330 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.8111 (t80)
REVERT: A 3379 TRP cc_start: 0.9054 (m-10) cc_final: 0.8693 (m-90)
REVERT: A 3469 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7684 (mp0)
  outliers start: 31
  outliers final: 23
  residues processed: 127
  average time/residue: 0.1049
  time to fit residues: 18.7676
Evaluate side-chains
  126 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2106 THR
Chi-restraints excluded: chain A residue 2127 ASP
Chi-restraints excluded: chain A residue 2131 THR
Chi-restraints excluded: chain A residue 2142 THR
Chi-restraints excluded: chain A residue 2222 ILE
Chi-restraints excluded: chain A residue 2249 LEU
Chi-restraints excluded: chain A residue 2426 MET
Chi-restraints excluded: chain A residue 2476 LYS
Chi-restraints excluded: chain A residue 2509 LEU
Chi-restraints excluded: chain A residue 2623 THR
Chi-restraints excluded: chain A residue 2658 ASP
Chi-restraints excluded: chain A residue 2661 VAL
Chi-restraints excluded: chain A residue 2694 LEU
Chi-restraints excluded: chain A residue 2716 ILE
Chi-restraints excluded: chain A residue 2728 LEU
Chi-restraints excluded: chain A residue 2823 LEU
Chi-restraints excluded: chain A residue 2842 ASP
Chi-restraints excluded: chain A residue 2866 LEU
Chi-restraints excluded: chain A residue 2935 VAL
Chi-restraints excluded: chain A residue 2942 ASP
Chi-restraints excluded: chain A residue 2945 VAL
Chi-restraints excluded: chain A residue 2984 VAL
Chi-restraints excluded: chain A residue 3002 LEU
Chi-restraints excluded: chain A residue 3330 TYR
Chi-restraints excluded: chain A residue 3425 LYS
Chi-restraints excluded: chain A residue 3469 GLU
Chi-restraints excluded: chain A residue 3479 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 69 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 104 optimal weight:    4.9990
   chunk 106 optimal weight:    5.9990
   chunk 85 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 42 optimal weight:    7.9990
   chunk 111 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
A2383 HIS
** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3521 ASN ** 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 = 0.3255 r_free = 0.3255 target = 0.071334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.055334 restraints weight = 30793.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.057537 restraints weight = 15374.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.059097 restraints weight = 9832.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.060137 restraints weight = 7253.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.060764 restraints weight = 5952.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.4356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9889  Z= 0.165
  Angle     :  0.629  10.928  13403  Z= 0.317
  Chirality :  0.043   0.202   1520
  Planarity :  0.004   0.069   1686
  Dihedral  :  7.754  88.653   1339
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 15.13 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.25), residues: 1188
  helix:  2.20 (0.22), residues: 595
  sheet:  0.09 (0.41), residues: 158
  loop : -0.53 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A3365 
 TYR   0.015   0.001   TYR A2571 
 PHE   0.023   0.002   PHE A3366 
 TRP   0.019   0.001   TRP A2084 
 HIS   0.007   0.001   HIS A3517 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 9889)
  covalent geometry    : angle       0.62886 (13403)
  hydrogen bonds       : bond        0.03604 (  484)
  hydrogen bonds       : angle       4.36082 ( 1401)

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 101
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2105 ASP cc_start: 0.8100 (m-30) cc_final: 0.7844 (m-30)
REVERT: A 2222 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7866 (mt)
REVERT: A 2623 THR cc_start: 0.9590 (OUTLIER) cc_final: 0.9170 (p)
REVERT: A 2819 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8217 (tm-30)
REVERT: A 2849 TYR cc_start: 0.9359 (t80) cc_final: 0.9118 (t80)
REVERT: A 2872 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8597 (pt0)
REVERT: A 3315 LYS cc_start: 0.9127 (tptt) cc_final: 0.8720 (tptt)
REVERT: A 3330 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.7994 (t80)
REVERT: A 3379 TRP cc_start: 0.9044 (m-10) cc_final: 0.8611 (m-90)
  outliers start: 31
  outliers final: 23
  residues processed: 128
  average time/residue: 0.1045
  time to fit residues: 18.7730
Evaluate side-chains
  120 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2106 THR
Chi-restraints excluded: chain A residue 2127 ASP
Chi-restraints excluded: chain A residue 2142 THR
Chi-restraints excluded: chain A residue 2222 ILE
Chi-restraints excluded: chain A residue 2249 LEU
Chi-restraints excluded: chain A residue 2476 LYS
Chi-restraints excluded: chain A residue 2509 LEU
Chi-restraints excluded: chain A residue 2623 THR
Chi-restraints excluded: chain A residue 2658 ASP
Chi-restraints excluded: chain A residue 2661 VAL
Chi-restraints excluded: chain A residue 2694 LEU
Chi-restraints excluded: chain A residue 2716 ILE
Chi-restraints excluded: chain A residue 2728 LEU
Chi-restraints excluded: chain A residue 2823 LEU
Chi-restraints excluded: chain A residue 2842 ASP
Chi-restraints excluded: chain A residue 2866 LEU
Chi-restraints excluded: chain A residue 2892 CYS
Chi-restraints excluded: chain A residue 2935 VAL
Chi-restraints excluded: chain A residue 2942 ASP
Chi-restraints excluded: chain A residue 2945 VAL
Chi-restraints excluded: chain A residue 2984 VAL
Chi-restraints excluded: chain A residue 3002 LEU
Chi-restraints excluded: chain A residue 3330 TYR
Chi-restraints excluded: chain A residue 3425 LYS
Chi-restraints excluded: chain A residue 3469 GLU
Chi-restraints excluded: chain A residue 3479 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 85 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0000
   chunk 32 optimal weight:    0.7980
   chunk 42 optimal weight:    8.9990
   chunk 111 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 69 optimal weight:    6.9990
   chunk 11 optimal weight:    9.9990
   chunk 60 optimal weight:    0.9980
   chunk 58 optimal weight:    7.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A3453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3521 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.071909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.055954 restraints weight = 30648.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.058177 restraints weight = 15243.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.059727 restraints weight = 9695.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.060784 restraints weight = 7159.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.061399 restraints weight = 5851.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.4457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9889  Z= 0.137
  Angle     :  0.633  14.343  13403  Z= 0.316
  Chirality :  0.043   0.217   1520
  Planarity :  0.004   0.068   1686
  Dihedral  :  7.699  86.197   1339
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 15.96 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.42 (0.25), residues: 1188
  helix:  2.22 (0.22), residues: 595
  sheet:  0.16 (0.41), residues: 157
  loop : -0.54 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A3445 
 TYR   0.015   0.001   TYR A2571 
 PHE   0.051   0.001   PHE A3366 
 TRP   0.021   0.001   TRP A2084 
 HIS   0.007   0.001   HIS A3517 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9889)
  covalent geometry    : angle       0.63330 (13403)
  hydrogen bonds       : bond        0.03407 (  484)
  hydrogen bonds       : angle       4.36282 ( 1401)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2087.21 seconds
wall clock time: 36 minutes 43.48 seconds (2203.48 seconds total)