Starting phenix.real_space_refine
on Wed Feb  4 09:35:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9n5k_48924/02_2026/9n5k_48924_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9n5k_48924/02_2026/9n5k_48924.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9n5k_48924/02_2026/9n5k_48924_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9n5k_48924/02_2026/9n5k_48924_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9n5k_48924/02_2026/9n5k_48924.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9n5k_48924/02_2026/9n5k_48924.map"
  }
  resolution = 4.7
  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=   0.005
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: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    5916      2.51       5
     N    1693      2.21       5
     O    1858      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9494
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6260
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1075, 6260
          Classifications: {'peptide': 1075}
          Incomplete info: {'truncation_to_alanine': 748}
          Link IDs: {'CIS': 3, 'PCIS': 7, 'PTRANS': 34, 'TRANS': 1030}
          Unresolved chain link angles: 29
          Unresolved non-hydrogen bonds: 2633
          Unresolved non-hydrogen angles: 3348
          Unresolved non-hydrogen dihedrals: 2183
          Unresolved non-hydrogen chiralities: 229
          Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 23, 'ASN:plan1': 83, 'PHE:plan': 42, 'ASP:plan': 57, 'GLU:plan': 49, 'TYR:plan': 33, 'ARG:plan': 9, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 1368
    Chain: "D"
      Number of atoms: 3234
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 401, 3234
          Classifications: {'peptide': 401}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 16, 'TRANS': 380}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 14
  Time building chain proxies: 1.79, per 1000 atoms: 0.19
  Number of scatterers: 9494
  At special positions: 0
  Unit cell: (92.07, 139.5, 114.39, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      27     16.00
     O    1858      8.00
     N    1693      7.00
     C    5916      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=11, symmetry=0
    Simple disulfide: pdb=" SG  CYS A2835 " - pdb=" SG  CYS A2846 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A2986 " - pdb=" SG  CYS A3010 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3024 " - pdb=" SG  CYS A3090 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3035 " - pdb=" SG  CYS A3088 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  49 " - pdb=" SG  CYS D  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 102 " - pdb=" SG  CYS D 156 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 227 " - pdb=" SG  CYS D 275 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 234 " - pdb=" SG  CYS D 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 298 " - pdb=" SG  CYS D 327 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 344 " - pdb=" SG  CYS D 412 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 352 " - pdb=" SG  CYS D 410 " distance=2.03

  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: 0.68
  Conformation dependent library (CDL) restraints added in 520.9 milliseconds
  

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2856

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 28 sheets defined
      11.4% alpha, 26.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2061 through 2065
      removed outlier: 3.901A  pdb=" N   THR A2065 " --> pdb=" O   PRO A2062 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2102 through 2106
    Processing helix  chain 'A' and resid 2135 through 2139
    Processing helix  chain 'A' and resid 2152 through 2155
    Processing helix  chain 'A' and resid 2300 through 2304
      removed outlier: 4.124A  pdb=" N   ILE A2304 " --> pdb=" O   LEU A2301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2312 through 2317
    Processing helix  chain 'A' and resid 2330 through 2334
    Processing helix  chain 'A' and resid 2381 through 2383
      No H-bonds generated for 'chain 'A' and resid 2381 through 2383'
    Processing helix  chain 'A' and resid 2404 through 2409
    Processing helix  chain 'A' and resid 2409 through 2427
      removed outlier: 3.685A  pdb=" N   GLN A2413 " --> pdb=" O   LYS A2409 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLU A2416 " --> pdb=" O   GLN A2412 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   GLU A2417 " --> pdb=" O   GLN A2413 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   GLN A2418 " --> pdb=" O   GLN A2414 " (cutoff:3.500A)
      removed outlier: 5.288A  pdb=" N   GLN A2419 " --> pdb=" O   GLU A2415 " (cutoff:3.500A)
      removed outlier: 4.605A  pdb=" N   GLU A2420 " --> pdb=" O   GLU A2416 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   GLN A2421 " --> pdb=" O   GLU A2417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2442 through 2446
      removed outlier: 3.845A  pdb=" N   ASP A2446 " --> pdb=" O   ILE A2443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2457 through 2461
    Processing helix  chain 'A' and resid 2535 through 2542
    Processing helix  chain 'A' and resid 2543 through 2545
      No H-bonds generated for 'chain 'A' and resid 2543 through 2545'
    Processing helix  chain 'A' and resid 2586 through 2591
    Processing helix  chain 'A' and resid 2647 through 2649
      No H-bonds generated for 'chain 'A' and resid 2647 through 2649'
    Processing helix  chain 'A' and resid 2671 through 2684
    Processing helix  chain 'A' and resid 2815 through 2826
      removed outlier: 3.682A  pdb=" N   MET A2819 " --> pdb=" O   GLU A2815 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2910 through 2915
      removed outlier: 3.959A  pdb=" N   ILE A2914 " --> pdb=" O   ASN A2910 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3051 through 3055
    Processing helix  chain 'D' and resid 33 through 40
      removed outlier: 3.607A  pdb=" N   ASN D  38 " --> pdb=" O   SER D  35 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   GLU D  40 " --> pdb=" O   LEU D  37 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 122
    Processing helix  chain 'D' and resid 204 through 210
      removed outlier: 5.484A  pdb=" N   VAL D 209 " --> pdb=" O   SER D 206 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   SER D 210 " --> pdb=" O   ASN D 207 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 240 through 244
      removed outlier: 4.349A  pdb=" N   LEU D 243 " --> pdb=" O   GLU D 240 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 276 through 280
    Processing helix  chain 'D' and resid 365 through 367
      No H-bonds generated for 'chain 'D' and resid 365 through 367'
    Processing helix  chain 'D' and resid 371 through 376
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2054 through 2057
      removed outlier: 6.876A  pdb=" N   HIS A2054 " --> pdb=" O   ILE A2085 " (cutoff:3.500A)
      removed outlier: 8.319A  pdb=" N   GLN A2087 " --> pdb=" O   HIS A2054 " (cutoff:3.500A)
      removed outlier: 7.258A  pdb=" N   CYS A2056 " --> pdb=" O   GLN A2087 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LEU A2088 " --> pdb=" O   GLU A2158 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   GLU A2158 " --> pdb=" O   LEU A2088 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   GLY A2159 " --> pdb=" O   ILE A2147 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   ILE A2147 " --> pdb=" O   GLY A2159 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   SER A2161 " --> pdb=" O   ASN A2145 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ASN A2145 " --> pdb=" O   SER A2161 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 2073 through 2076
    Processing sheet with id=AA3, first strand: chain 'A' and resid 2073 through 2076
      removed outlier: 6.793A  pdb=" N   ILE A2177 " --> pdb=" O   ARG A2189 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 2124 through 2126
    Processing sheet with id=AA5, first strand: chain 'A' and resid 2205 through 2209
      removed outlier: 3.779A  pdb=" N   CYS A2208 " --> pdb=" O   GLY A2240 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   LYS A2242 " --> pdb=" O   CYS A2208 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 2226 through 2227
      removed outlier: 6.873A  pdb=" N   LYS A2227 " --> pdb=" O   THR A2366 " (cutoff:3.500A)
      removed outlier: 8.161A  pdb=" N   GLN A2368 " --> pdb=" O   LYS A2227 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLY A2365 " --> pdb=" O   CYS A2356 " (cutoff:3.500A)
      removed outlier: 5.724A  pdb=" N   ILE A2350 " --> pdb=" O   SER A2371 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 2230 through 2233
      removed outlier: 4.062A  pdb=" N   GLU A2370 " --> pdb=" O   VAL A2231 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ILE A2233 " --> pdb=" O   GLU A2370 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLY A2365 " --> pdb=" O   CYS A2356 " (cutoff:3.500A)
      removed outlier: 5.724A  pdb=" N   ILE A2350 " --> pdb=" O   SER A2371 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   TYR A2262 " --> pdb=" O   ASN A2351 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 2385 through 2390
      removed outlier: 5.742A  pdb=" N   ILE A2386 " --> pdb=" O   LYS A2473 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   ILE A2475 " --> pdb=" O   ILE A2386 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   ASN A2388 " --> pdb=" O   ILE A2475 " (cutoff:3.500A)
      removed outlier: 7.957A  pdb=" N   LYS A2477 " --> pdb=" O   ASN A2388 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   LEU A2390 " --> pdb=" O   LYS A2477 " (cutoff:3.500A)
      removed outlier: 5.851A  pdb=" N   GLN A2472 " --> pdb=" O   LEU A2653 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   LEU A2655 " --> pdb=" O   GLN A2472 " (cutoff:3.500A)
      removed outlier: 5.760A  pdb=" N   SER A2474 " --> pdb=" O   LEU A2655 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   HIS A2657 " --> pdb=" O   SER A2474 " (cutoff:3.500A)
      removed outlier: 5.939A  pdb=" N   CYS A2476 " --> pdb=" O   HIS A2657 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LYS A2640 " --> pdb=" O   SER A2652 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   PHE A2634 " --> pdb=" O   ILE A2658 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   TYR A2569 " --> pdb=" O   PHE A2637 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 2393 through 2395
      removed outlier: 5.732A  pdb=" N   HIS A2450 " --> pdb=" O   THR A2487 " (cutoff:3.500A)
      removed outlier: 7.176A  pdb=" N   LYS A2489 " --> pdb=" O   HIS A2450 " (cutoff:3.500A)
      removed outlier: 5.765A  pdb=" N   CYS A2452 " --> pdb=" O   LYS A2489 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   LEU A2595 " --> pdb=" O   LEU A2623 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 2705 through 2709
      removed outlier: 6.047A  pdb=" N   CYS A2706 " --> pdb=" O   HIS A2811 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   LYS A2813 " --> pdb=" O   CYS A2706 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   ILE A2708 " --> pdb=" O   LYS A2813 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   CYS A2802 " --> pdb=" O   ILE A2810 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   LEU A2800 " --> pdb=" O   MET A2812 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 2830 through 2833
      removed outlier: 4.385A  pdb=" N   SER A2866 " --> pdb=" O   ASP A2833 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   VAL A2863 " --> pdb=" O   LYS A2971 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   PHE A2973 " --> pdb=" O   VAL A2863 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   TYR A2865 " --> pdb=" O   PHE A2973 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   HIS A2975 " --> pdb=" O   TYR A2865 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   ILE A2867 " --> pdb=" O   HIS A2975 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ASN A2893 " --> pdb=" O   GLU A2950 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 2836 through 2838
    Processing sheet with id=AB4, first strand: chain 'A' and resid 2876 through 2880
      removed outlier: 3.811A  pdb=" N   THR A2921 " --> pdb=" O   ILE A2934 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 2902 through 2904
      removed outlier: 3.665A  pdb=" N   ASN A2904 " --> pdb=" O   LYS A2907 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 2957 through 2960
    Processing sheet with id=AB7, first strand: chain 'A' and resid 2996 through 2999
      removed outlier: 5.059A  pdb=" N   PHE A2996 " --> pdb=" O   ILE A2983 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   GLY A2985 " --> pdb=" O   PHE A2996 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   TYR A2998 " --> pdb=" O   GLY A2985 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   GLY A3021 " --> pdb=" O   HIS A2984 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ALA A3023 " --> pdb=" O   CYS A2986 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLU A3059 " --> pdb=" O   ILE A3076 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 3009 through 3014
    Processing sheet with id=AB9, first strand: chain 'A' and resid 3038 through 3039
    Processing sheet with id=AC1, first strand: chain 'D' and resid 31 through 32
    Processing sheet with id=AC2, first strand: chain 'D' and resid 48 through 50
      removed outlier: 3.516A  pdb=" N   ILE D 144 " --> pdb=" O   ASP D  80 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 69 through 70
      removed outlier: 3.765A  pdb=" N   ILE D  69 " --> pdb=" O   SER D 172 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ARG D 178 " --> pdb=" O   ILE D  73 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   SER D  75 " --> pdb=" O   ARG D 178 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'D' and resid 69 through 70
      removed outlier: 3.765A  pdb=" N   ILE D  69 " --> pdb=" O   SER D 172 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'D' and resid 105 through 109
      removed outlier: 6.430A  pdb=" N   VAL D 114 " --> pdb=" O   THR D 108 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'D' and resid 186 through 191
      removed outlier: 6.150A  pdb=" N   LEU D 187 " --> pdb=" O   VAL D 224 " (cutoff:3.500A)
      removed outlier: 7.780A  pdb=" N   ALA D 226 " --> pdb=" O   LEU D 187 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   THR D 189 " --> pdb=" O   ALA D 226 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ILE D 250 " --> pdb=" O   ILE D 257 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'D' and resid 212 through 217
    Processing sheet with id=AC8, first strand: chain 'D' and resid 310 through 313
      removed outlier: 7.938A  pdb=" N   ILE D 295 " --> pdb=" O   THR D 311 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   SER D 313 " --> pdb=" O   ILE D 295 " (cutoff:3.500A)
      removed outlier: 10.685A  pdb=" N   GLY D 297 " --> pdb=" O   SER D 313 " (cutoff:3.500A)
      removed outlier: 4.929A  pdb=" N   GLY D 341 " --> pdb=" O   HIS D 296 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'D' and resid 325 through 331
      removed outlier: 3.579A  pdb=" N   ILE D 325 " --> pdb=" O   SER D 418 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ILE D 411 " --> pdb=" O   ILE D 349 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ASP D 347 " --> pdb=" O   LYS D 413 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'D' and resid 356 through 357

    283 hydrogen bonds defined for protein.
    696 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: 2.00

  Time building geometry restraints manager: 0.93 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3308
        1.34 -     1.46: 1367
        1.46 -     1.58: 4923
        1.58 -     1.70: 0
        1.70 -     1.81: 30
  Bond restraints: 9628
  Sorted by residual:
  bond pdb=" N   ILE A2770 "
       pdb=" CA  ILE A2770 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 9.30e-03 1.16e+04 1.69e+01
  bond pdb=" N   ILE A2451 "
       pdb=" CA  ILE A2451 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.036 1.19e-02 7.06e+03 9.36e+00
  bond pdb=" N   ILE A2784 "
       pdb=" CA  ILE A2784 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.24e-02 6.50e+03 8.86e+00
  bond pdb=" N   VAL A2619 "
       pdb=" CA  VAL A2619 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.14e-02 7.69e+03 8.77e+00
  bond pdb=" N   ILE A2488 "
       pdb=" CA  ILE A2488 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.035 1.20e-02 6.94e+03 8.67e+00
  ... (remaining 9623 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.90: 12340
        0.90 -     1.80: 693
        1.80 -     2.70: 109
        2.70 -     3.60: 49
        3.60 -     4.50: 12
  Bond angle restraints: 13203
  Sorted by residual:
  angle pdb=" N   ILE A2770 "
        pdb=" CA  ILE A2770 "
        pdb=" C   ILE A2770 "
      ideal   model   delta    sigma   weight residual
     113.20  109.70    3.50 9.60e-01 1.09e+00 1.33e+01
  angle pdb=" CA  ILE A2784 "
        pdb=" C   ILE A2784 "
        pdb=" O   ILE A2784 "
      ideal   model   delta    sigma   weight residual
     121.64  118.18    3.46 9.80e-01 1.04e+00 1.25e+01
  angle pdb=" CA  VAL A2619 "
        pdb=" C   VAL A2619 "
        pdb=" O   VAL A2619 "
      ideal   model   delta    sigma   weight residual
     121.28  117.77    3.51 1.06e+00 8.90e-01 1.10e+01
  angle pdb=" CA  THR A2781 "
        pdb=" C   THR A2781 "
        pdb=" O   THR A2781 "
      ideal   model   delta    sigma   weight residual
     121.87  118.12    3.75 1.16e+00 7.43e-01 1.05e+01
  angle pdb=" CA  THR A2651 "
        pdb=" C   THR A2651 "
        pdb=" O   THR A2651 "
      ideal   model   delta    sigma   weight residual
     121.23  118.03    3.20 1.07e+00 8.73e-01 8.96e+00
  ... (remaining 13198 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.66: 5392
       14.66 -    29.32: 299
       29.32 -    43.98: 86
       43.98 -    58.63: 13
       58.63 -    73.29: 2
  Dihedral angle restraints: 5792
    sinusoidal: 1422
      harmonic: 4370
  Sorted by residual:
  dihedral pdb=" CB  CYS D 298 "
           pdb=" SG  CYS D 298 "
           pdb=" SG  CYS D 327 "
           pdb=" CB  CYS D 327 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -133.41   47.41     1      1.00e+01 1.00e-02 3.10e+01
  dihedral pdb=" CB  CYS D 352 "
           pdb=" SG  CYS D 352 "
           pdb=" SG  CYS D 410 "
           pdb=" CB  CYS D 410 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -125.51   39.51     1      1.00e+01 1.00e-02 2.19e+01
  dihedral pdb=" CA  LYS A2288 "
           pdb=" C   LYS A2288 "
           pdb=" N   ASP A2289 "
           pdb=" CA  ASP A2289 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.56  -16.44     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 5789 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1201
       0.042 -    0.084: 229
       0.084 -    0.126: 171
       0.126 -    0.168: 19
       0.168 -    0.209: 4
  Chirality restraints: 1624
  Sorted by residual:
  chirality pdb=" CA  VAL A2485 "
            pdb=" N   VAL A2485 "
            pdb=" C   VAL A2485 "
            pdb=" CB  VAL A2485 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" CA  ILE A2768 "
            pdb=" N   ILE A2768 "
            pdb=" C   ILE A2768 "
            pdb=" CB  ILE A2768 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  ILE A2488 "
            pdb=" N   ILE A2488 "
            pdb=" C   ILE A2488 "
            pdb=" CB  ILE A2488 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.18 2.00e-01 2.50e+01 8.41e-01
  ... (remaining 1621 not shown)

  Planarity restraints: 1775
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A2288 "   -0.007 2.00e-02 2.50e+03   1.45e-02 2.11e+00
        pdb=" C   LYS A2288 "    0.025 2.00e-02 2.50e+03
        pdb=" O   LYS A2288 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ASP A2289 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A3104 "    0.024 5.00e-02 4.00e+02   3.59e-02 2.06e+00
        pdb=" N   PRO A3105 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A3105 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A3105 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A2283 "   -0.007 2.00e-02 2.50e+03   1.36e-02 1.84e+00
        pdb=" C   TYR A2283 "    0.023 2.00e-02 2.50e+03
        pdb=" O   TYR A2283 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ASN A2284 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1772 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2729
        2.80 -     3.33: 8372
        3.33 -     3.85: 14472
        3.85 -     4.38: 15757
        4.38 -     4.90: 27371
  Nonbonded interactions: 68701
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU D 205 "
            pdb=" OH  TYR D 282 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" NZ  LYS A3000 "
            pdb=" OD2 ASP A3008 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" ND2 ASN D 247 "
            pdb=" O   LYS D 259 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" OD2 ASP A3006 "
            pdb=" OH  TYR A3097 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   ASN A3034 "
            pdb=" OG  SER A3037 "
     model   vdw
     2.306 3.040
  ... (remaining 68696 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.370
  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:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     9.460
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4141
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9639  Z= 0.184
  Angle     :  0.505   4.496  13225  Z= 0.312
  Chirality :  0.049   0.209   1624
  Planarity :  0.002   0.036   1775
  Dihedral  : 10.584  73.292   2903
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.25 %
    Cis-general     : 0.35 %
    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: -1.50 (0.23), residues: 1472
  helix: -0.78 (0.60), residues: 84
  sheet: -0.38 (0.27), residues: 437
  loop : -1.36 (0.21), residues: 951

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2871 
 TYR   0.008   0.001   TYR A3107 
 PHE   0.020   0.001   PHE D 147 
 TRP   0.002   0.000   TRP A2872 
 HIS   0.001   0.000   HIS D 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9628)
  covalent geometry    : angle       0.50409 (13203)
  SS BOND              : bond        0.00164 (   11)
  SS BOND              : angle       0.71610 (   22)
  hydrogen bonds       : bond        0.26587 (  273)
  hydrogen bonds       : angle      11.04110 (  696)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  174 MET cc_start: 0.0273 (tmm) cc_final: 0.0066 (tmm)
REVERT: D  373 ASP cc_start: 0.7946 (m-30) cc_final: 0.7643 (t0)
REVERT: D  421 MET cc_start: -0.1167 (tmm) cc_final: -0.2433 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.0984
  time to fit residues: 10.3867
Evaluate side-chains
  51 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:   20.0000
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    0.0170
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    9.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:   10.0000
   overall best weight:    3.2026

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

Flipped N/Q/H residues before XYZ refinement:
A2860 HIS
A2942 HIS
A2977 ASN
A3017 ASN
A3027 HIS
A3078 ASN
** D  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 136 ASN
D 252 HIS
D 330 HIS
D 377 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.114948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.073707 restraints weight = 70530.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.073369 restraints weight = 73527.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.073369 restraints weight = 75699.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.073369 restraints weight = 75699.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.073369 restraints weight = 75699.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6035
moved from start:          0.3686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.153   9639  Z= 0.340
  Angle     :  0.889  13.692  13225  Z= 0.496
  Chirality :  0.053   0.204   1624
  Planarity :  0.006   0.056   1775
  Dihedral  :  6.030  24.717   1527
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 23.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.38 %
    Favored  : 90.62 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  6.18 %
    Favored  : 92.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.25 %
    Cis-general     : 0.35 %
    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: -2.27 (0.21), residues: 1472
  helix: -1.51 (0.54), residues: 92
  sheet: -0.73 (0.26), residues: 406
  loop : -1.97 (0.19), residues: 974

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A2871 
 TYR   0.034   0.004   TYR D 336 
 PHE   0.049   0.004   PHE A3019 
 TRP   0.009   0.004   TRP A2872 
 HIS   0.015   0.003   HIS D 252 

Details of bonding type rmsd
  covalent geometry    : bond        0.00688 ( 9628)
  covalent geometry    : angle       0.88743 (13203)
  SS BOND              : bond        0.00451 (   11)
  SS BOND              : angle       1.46219 (   22)
  hydrogen bonds       : bond        0.06262 (  273)
  hydrogen bonds       : angle       8.37067 (  696)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2895 PHE cc_start: 0.8702 (m-10) cc_final: 0.8185 (t80)
REVERT: A 3086 PHE cc_start: 0.9412 (p90) cc_final: 0.9174 (p90)
REVERT: D  376 ILE cc_start: 0.8076 (pt) cc_final: 0.7521 (pt)
REVERT: D  421 MET cc_start: 0.7076 (tmm) cc_final: 0.5020 (tpt)
  outliers start: 7
  outliers final: 3
  residues processed: 68
  average time/residue: 0.0927
  time to fit residues: 9.0467
Evaluate side-chains
  43 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 25 optimal weight:   40.0000
   chunk 87 optimal weight:    1.9990
   chunk 66 optimal weight:   20.0000
   chunk 5 optimal weight:    9.9990
   chunk 69 optimal weight:    6.9990
   chunk 15 optimal weight:   20.0000
   chunk 8 optimal weight:    7.9990
   chunk 103 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9980
   chunk 1 optimal weight:   20.0000
   chunk 120 optimal weight:    7.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A2975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  53 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.104938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.064054 restraints weight = 69238.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.064053 restraints weight = 72953.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.064053 restraints weight = 72956.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.064053 restraints weight = 72956.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.064053 restraints weight = 72956.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6215
moved from start:          0.6247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.206   9639  Z= 0.391
  Angle     :  0.960  14.495  13225  Z= 0.547
  Chirality :  0.056   0.298   1624
  Planarity :  0.006   0.060   1775
  Dihedral  :  7.196  34.351   1527
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 34.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.01 %
    Favored  : 88.99 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  6.49 %
    Favored  : 92.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.25 %
    Cis-general     : 0.35 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -3.11 (0.21), residues: 1472
  helix: -2.03 (0.44), residues: 116
  sheet: -1.38 (0.27), residues: 380
  loop : -2.51 (0.19), residues: 976

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.002   ARG A3100 
 TYR   0.064   0.004   TYR A2998 
 PHE   0.042   0.004   PHE D 147 
 TRP   0.009   0.003   TRP A2872 
 HIS   0.017   0.003   HIS A2984 

Details of bonding type rmsd
  covalent geometry    : bond        0.00771 ( 9628)
  covalent geometry    : angle       0.95834 (13203)
  SS BOND              : bond        0.02116 (   11)
  SS BOND              : angle       1.80849 (   22)
  hydrogen bonds       : bond        0.06613 (  273)
  hydrogen bonds       : angle       9.27733 (  696)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2895 PHE cc_start: 0.8856 (m-10) cc_final: 0.8450 (t80)
REVERT: A 3035 CYS cc_start: 0.5344 (OUTLIER) cc_final: 0.4711 (t)
REVERT: A 3086 PHE cc_start: 0.9353 (p90) cc_final: 0.8902 (p90)
REVERT: D  421 MET cc_start: 0.7015 (tmm) cc_final: 0.6431 (tmm)
  outliers start: 7
  outliers final: 3
  residues processed: 52
  average time/residue: 0.0964
  time to fit residues: 7.1929
Evaluate side-chains
  39 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 78 optimal weight:   30.0000
   chunk 105 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9980
   chunk 24 optimal weight:    7.9990
   chunk 5 optimal weight:    9.9990
   chunk 31 optimal weight:   30.0000
   chunk 13 optimal weight:    7.9990
   chunk 66 optimal weight:    6.9990
   chunk 133 optimal weight:    0.0170
   chunk 94 optimal weight:    0.7980
   chunk 64 optimal weight:    7.9990
   overall best weight:    2.9622

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

Flipped N/Q/H residues before XYZ refinement:
A2860 HIS
A2975 HIS
** A2994 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A3046 ASN
** A3106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.104313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.064303 restraints weight = 74452.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.064303 restraints weight = 78485.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.064303 restraints weight = 78485.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.064303 restraints weight = 78485.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.064303 restraints weight = 78485.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6260
moved from start:          0.6986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.145   9639  Z= 0.289
  Angle     :  0.790  11.322  13225  Z= 0.448
  Chirality :  0.052   0.206   1624
  Planarity :  0.006   0.077   1775
  Dihedral  :  6.935  33.247   1527
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 29.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.35 %
    Favored  : 88.65 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  4.64 %
    Favored  : 95.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.25 %
    Cis-general     : 0.35 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -3.25 (0.21), residues: 1472
  helix: -1.86 (0.45), residues: 116
  sheet: -1.53 (0.26), residues: 391
  loop : -2.62 (0.19), residues: 965

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A3100 
 TYR   0.041   0.003   TYR A2998 
 PHE   0.036   0.003   PHE D 155 
 TRP   0.013   0.004   TRP A2872 
 HIS   0.012   0.003   HIS A2994 

Details of bonding type rmsd
  covalent geometry    : bond        0.00596 ( 9628)
  covalent geometry    : angle       0.78712 (13203)
  SS BOND              : bond        0.00834 (   11)
  SS BOND              : angle       1.81843 (   22)
  hydrogen bonds       : bond        0.04962 (  273)
  hydrogen bonds       : angle       9.00369 (  696)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2895 PHE cc_start: 0.8958 (m-10) cc_final: 0.8557 (t80)
REVERT: A 3086 PHE cc_start: 0.9332 (p90) cc_final: 0.8869 (p90)
REVERT: D  376 ILE cc_start: 0.8024 (pt) cc_final: 0.7060 (pt)
REVERT: D  421 MET cc_start: 0.6561 (tmm) cc_final: 0.6192 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0879
  time to fit residues: 5.5562
Evaluate side-chains
  34 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 114 optimal weight:    0.8980
   chunk 107 optimal weight:    0.9980
   chunk 71 optimal weight:   10.0000
   chunk 12 optimal weight:   20.0000
   chunk 145 optimal weight:    8.9990
   chunk 33 optimal weight:   10.0000
   chunk 13 optimal weight:    3.9990
   chunk 41 optimal weight:   20.0000
   chunk 129 optimal weight:    1.9990
   chunk 23 optimal weight:   30.0000
   overall best weight:    3.3786

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

Flipped N/Q/H residues before XYZ refinement:
D  58 ASN
D 136 ASN
** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 375 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.099243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.059045 restraints weight = 77039.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.058213 restraints weight = 84441.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.058213 restraints weight = 88554.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.058213 restraints weight = 88554.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.058213 restraints weight = 88554.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6366
moved from start:          0.8342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.160   9639  Z= 0.337
  Angle     :  0.886  13.375  13225  Z= 0.501
  Chirality :  0.055   0.285   1624
  Planarity :  0.006   0.054   1775
  Dihedral  :  7.605  37.233   1527
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 39.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.27 %
    Favored  : 85.73 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  5.10 %
    Favored  : 94.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.25 %
    Cis-general     : 0.35 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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: -3.73 (0.20), residues: 1472
  helix: -2.01 (0.42), residues: 126
  sheet: -1.93 (0.26), residues: 375
  loop : -2.94 (0.18), residues: 971

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.036   0.003   ARG A3115 
 TYR   0.043   0.004   TYR A3107 
 PHE   0.068   0.004   PHE D 155 
 TRP   0.013   0.003   TRP A2872 
 HIS   0.017   0.004   HIS D 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00697 ( 9628)
  covalent geometry    : angle       0.88326 (13203)
  SS BOND              : bond        0.01826 (   11)
  SS BOND              : angle       1.96306 (   22)
  hydrogen bonds       : bond        0.05405 (  273)
  hydrogen bonds       : angle       9.34518 (  696)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  421 MET cc_start: 0.7341 (tmm) cc_final: 0.6147 (tpt)
  outliers start: 4
  outliers final: 2
  residues processed: 48
  average time/residue: 0.0841
  time to fit residues: 6.0604
Evaluate side-chains
  37 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 35
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 146 optimal weight:    5.9990
   chunk 22 optimal weight:    8.9990
   chunk 27 optimal weight:    9.9990
   chunk 49 optimal weight:   40.0000
   chunk 74 optimal weight:    4.9990
   chunk 35 optimal weight:    9.9990
   chunk 46 optimal weight:    0.0970
   chunk 0 optimal weight:   20.0000
   chunk 17 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    2.7584

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

Flipped N/Q/H residues before XYZ refinement:
** D 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 355 GLN
D 375 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.100632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.062513 restraints weight = 72201.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.062476 restraints weight = 76476.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.062476 restraints weight = 76848.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.062476 restraints weight = 76848.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.062476 restraints weight = 76848.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6618
moved from start:          0.8916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.126   9639  Z= 0.266
  Angle     :  0.788  11.329  13225  Z= 0.441
  Chirality :  0.052   0.274   1624
  Planarity :  0.005   0.072   1775
  Dihedral  :  7.320  33.863   1527
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 33.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.70 %
    Favored  : 87.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.25 %
    Cis-general     : 0.35 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -3.69 (0.20), residues: 1472
  helix: -1.85 (0.44), residues: 121
  sheet: -1.85 (0.27), residues: 361
  loop : -2.95 (0.18), residues: 990

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A3100 
 TYR   0.032   0.003   TYR A2998 
 PHE   0.051   0.003   PHE D 155 
 TRP   0.009   0.003   TRP A2872 
 HIS   0.016   0.002   HIS D 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00553 ( 9628)
  covalent geometry    : angle       0.78579 (13203)
  SS BOND              : bond        0.00609 (   11)
  SS BOND              : angle       1.64143 (   22)
  hydrogen bonds       : bond        0.04673 (  273)
  hydrogen bonds       : angle       8.93081 (  696)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  421 MET cc_start: 0.5152 (tmm) cc_final: 0.4908 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.0874
  time to fit residues: 5.5197
Evaluate side-chains
  34 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 61 optimal weight:    6.9990
   chunk 60 optimal weight:    9.9990
   chunk 115 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 88 optimal weight:    5.9990
   chunk 104 optimal weight:    3.9990
   chunk 130 optimal weight:    0.3980
   chunk 76 optimal weight:    0.4980
   chunk 131 optimal weight:    3.9990
   chunk 27 optimal weight:   30.0000
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
A2960 GLN
** A3078 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.100897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.063148 restraints weight = 71826.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.062578 restraints weight = 77044.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.062578 restraints weight = 79188.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.062578 restraints weight = 79188.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.062578 restraints weight = 79188.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6602
moved from start:          0.9245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.116   9639  Z= 0.226
  Angle     :  0.736  11.513  13225  Z= 0.412
  Chirality :  0.052   0.248   1624
  Planarity :  0.005   0.055   1775
  Dihedral  :  6.998  32.183   1527
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 30.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.52 %
    Favored  : 86.48 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  2.47 %
    Favored  : 97.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.25 %
    Cis-general     : 0.35 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -3.69 (0.20), residues: 1472
  helix: -1.70 (0.44), residues: 121
  sheet: -2.00 (0.27), residues: 375
  loop : -2.91 (0.18), residues: 976

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A3100 
 TYR   0.031   0.003   TYR A3107 
 PHE   0.041   0.003   PHE D 155 
 TRP   0.007   0.003   TRP A2872 
 HIS   0.019   0.003   HIS A2994 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 9628)
  covalent geometry    : angle       0.73437 (13203)
  SS BOND              : bond        0.00335 (   11)
  SS BOND              : angle       1.27808 (   22)
  hydrogen bonds       : bond        0.04285 (  273)
  hydrogen bonds       : angle       8.60401 (  696)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2960 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8709 (pm20)
REVERT: A 3086 PHE cc_start: 0.9526 (p90) cc_final: 0.9048 (p90)
REVERT: D  129 GLU cc_start: 0.8977 (mp0) cc_final: 0.8702 (mp0)
  outliers start: 1
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0719
  time to fit residues: 5.2783
Evaluate side-chains
  32 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 31
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 87 optimal weight:   10.0000
   chunk 127 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 141 optimal weight:    0.9980
   chunk 131 optimal weight:    8.9990
   chunk 25 optimal weight:   30.0000
   chunk 97 optimal weight:    0.5980
   chunk 98 optimal weight:    0.9980
   chunk 75 optimal weight:    9.9990
   chunk 30 optimal weight:   20.0000
   chunk 76 optimal weight:    9.9990
   overall best weight:    2.5184

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

Flipped N/Q/H residues before XYZ refinement:
** D 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 355 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.098456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.058363 restraints weight = 73898.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.057248 restraints weight = 83615.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.057188 restraints weight = 91146.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.056308 restraints weight = 91986.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.056307 restraints weight = 98175.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6565
moved from start:          0.9986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.205   9639  Z= 0.259
  Angle     :  0.769  10.378  13225  Z= 0.433
  Chirality :  0.052   0.243   1624
  Planarity :  0.005   0.061   1775
  Dihedral  :  7.181  34.207   1527
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 35.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.86 %
    Favored  : 86.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.25 %
    Cis-general     : 0.35 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -3.76 (0.20), residues: 1472
  helix: -1.76 (0.43), residues: 127
  sheet: -2.01 (0.27), residues: 371
  loop : -2.98 (0.18), residues: 974

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  83 
 TYR   0.036   0.003   TYR A3107 
 PHE   0.048   0.003   PHE D 155 
 TRP   0.011   0.004   TRP A2872 
 HIS   0.020   0.003   HIS A2994 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 ( 9628)
  covalent geometry    : angle       0.76808 (13203)
  SS BOND              : bond        0.00456 (   11)
  SS BOND              : angle       1.37567 (   22)
  hydrogen bonds       : bond        0.04539 (  273)
  hydrogen bonds       : angle       8.73877 (  696)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  129 GLU cc_start: 0.9066 (mp0) cc_final: 0.8769 (mp0)
REVERT: D  421 MET cc_start: 0.7324 (tmm) cc_final: 0.6766 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0762
  time to fit residues: 5.5946
Evaluate side-chains
  38 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 114 optimal weight:    0.7980
   chunk 137 optimal weight:    0.5980
   chunk 142 optimal weight:    0.3980
   chunk 65 optimal weight:    7.9990
   chunk 98 optimal weight:    5.9990
   chunk 17 optimal weight:   20.0000
   chunk 120 optimal weight:    0.0370
   chunk 135 optimal weight:    0.6980
   chunk 74 optimal weight:   20.0000
   chunk 62 optimal weight:   20.0000
   chunk 146 optimal weight:    7.9990
   overall best weight:    0.5058

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

Flipped N/Q/H residues before XYZ refinement:
** D 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 247 ASN
D 254 ASN
** D 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.106316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.082110 restraints weight = 96326.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.081668 restraints weight = 102943.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.081668 restraints weight = 107547.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.081668 restraints weight = 107547.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.081668 restraints weight = 107547.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6614
moved from start:          0.9652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9639  Z= 0.132
  Angle     :  0.621   8.454  13225  Z= 0.347
  Chirality :  0.050   0.233   1624
  Planarity :  0.004   0.050   1775
  Dihedral  :  6.119  28.427   1527
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 19.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.19 %
    Favored  : 89.81 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.31 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.25 %
    Cis-general     : 0.35 %
    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: -3.33 (0.21), residues: 1472
  helix: -1.48 (0.47), residues: 123
  sheet: -1.82 (0.26), residues: 387
  loop : -2.63 (0.19), residues: 962

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 140 
 TYR   0.031   0.002   TYR A2998 
 PHE   0.022   0.002   PHE A2891 
 TRP   0.004   0.001   TRP A2872 
 HIS   0.014   0.002   HIS D 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9628)
  covalent geometry    : angle       0.61927 (13203)
  SS BOND              : bond        0.00317 (   11)
  SS BOND              : angle       1.39038 (   22)
  hydrogen bonds       : bond        0.03346 (  273)
  hydrogen bonds       : angle       7.79776 (  696)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 45
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2995 LEU cc_start: 0.9343 (mp) cc_final: 0.9119 (tp)
REVERT: A 3086 PHE cc_start: 0.9602 (p90) cc_final: 0.9019 (p90)
  outliers start: 1
  outliers final: 1
  residues processed: 46
  average time/residue: 0.0763
  time to fit residues: 5.2410
Evaluate side-chains
  36 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 35
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 79 optimal weight:    0.8980
   chunk 130 optimal weight:    0.8980
   chunk 98 optimal weight:    5.9990
   chunk 21 optimal weight:    9.9990
   chunk 27 optimal weight:    0.5980
   chunk 91 optimal weight:    0.0970
   chunk 122 optimal weight:    3.9990
   chunk 126 optimal weight:    0.9990
   chunk 109 optimal weight:    8.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** D 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.106398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.082149 restraints weight = 95449.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.081637 restraints weight = 101402.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.081637 restraints weight = 105670.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.081637 restraints weight = 105670.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.081637 restraints weight = 105670.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6609
moved from start:          0.9662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   9639  Z= 0.127
  Angle     :  0.599   8.942  13225  Z= 0.335
  Chirality :  0.049   0.193   1624
  Planarity :  0.004   0.050   1775
  Dihedral  :  5.763  26.440   1527
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 19.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.71 %
    Favored  : 90.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.25 %
    Cis-general     : 0.35 %
    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: -3.12 (0.21), residues: 1472
  helix: -1.32 (0.49), residues: 117
  sheet: -1.66 (0.27), residues: 374
  loop : -2.48 (0.19), residues: 981

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A2927 
 TYR   0.017   0.002   TYR A2998 
 PHE   0.021   0.002   PHE A2891 
 TRP   0.005   0.002   TRP A2872 
 HIS   0.011   0.002   HIS A2994 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9628)
  covalent geometry    : angle       0.59774 (13203)
  SS BOND              : bond        0.00311 (   11)
  SS BOND              : angle       1.18433 (   22)
  hydrogen bonds       : bond        0.03196 (  273)
  hydrogen bonds       : angle       7.35149 (  696)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2995 LEU cc_start: 0.9331 (mp) cc_final: 0.9106 (tp)
REVERT: A 3086 PHE cc_start: 0.9633 (p90) cc_final: 0.9063 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0654
  time to fit residues: 4.1784
Evaluate side-chains
  33 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 69 optimal weight:    8.9990
   chunk 14 optimal weight:    7.9990
   chunk 115 optimal weight:    1.9990
   chunk 137 optimal weight:    1.9990
   chunk 120 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   chunk 32 optimal weight:   50.0000
   chunk 58 optimal weight:    8.9990
   chunk 35 optimal weight:    6.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** D 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 355 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.100451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.063680 restraints weight = 69136.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.063171 restraints weight = 73149.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.063171 restraints weight = 75815.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.063171 restraints weight = 75815.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.063171 restraints weight = 75815.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6567
moved from start:          1.0146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.130   9639  Z= 0.192
  Angle     :  0.659   8.488  13225  Z= 0.371
  Chirality :  0.050   0.218   1624
  Planarity :  0.005   0.050   1775
  Dihedral  :  6.145  32.671   1527
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 27.17
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 13.04 %
    Favored  : 86.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.25 %
    Cis-general     : 0.35 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -3.20 (0.21), residues: 1472
  helix: -1.24 (0.49), residues: 117
  sheet: -1.70 (0.27), residues: 369
  loop : -2.57 (0.19), residues: 986

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A2927 
 TYR   0.030   0.003   TYR A3107 
 PHE   0.037   0.003   PHE D 155 
 TRP   0.007   0.003   TRP A2872 
 HIS   0.010   0.002   HIS A2994 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 9628)
  covalent geometry    : angle       0.65759 (13203)
  SS BOND              : bond        0.00299 (   11)
  SS BOND              : angle       1.30636 (   22)
  hydrogen bonds       : bond        0.03803 (  273)
  hydrogen bonds       : angle       7.65637 (  696)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2064.85 seconds
wall clock time: 36 minutes 14.98 seconds (2174.98 seconds total)