Starting phenix.real_space_refine
on Mon Apr  6 00:33:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ybn_72753/04_2026/9ybn_72753.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ybn_72753/04_2026/9ybn_72753.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ybn_72753/04_2026/9ybn_72753.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ybn_72753/04_2026/9ybn_72753.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ybn_72753/04_2026/9ybn_72753.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ybn_72753/04_2026/9ybn_72753.map"
  }
  resolution = 2.53
  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=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P      19      5.49       5
     S      96      5.16       5
     C    8758      2.51       5
     N    2405      2.21       5
     O    2679      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13959
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 13557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1696, 13557
          Classifications: {'peptide': 1696}
          Link IDs: {'PTRANS': 51, 'TRANS': 1644}
          Chain breaks: 11
    Chain: "B"
      Number of atoms: 255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 255
          Classifications: {'RNA': 12}
          Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 4}
          Link IDs: {'rna2p': 2, 'rna3p': 9}
    Chain: "C"
      Number of atoms: 145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 145
          Classifications: {'RNA': 7}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 5, 'rna3p_pur': 1}
          Link IDs: {'rna2p': 5, 'rna3p': 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2818  SG  CYS A1294      80.737  52.234  85.883  1.00 88.09           S
  ATOM    825  SG  CYS A1028      90.088  74.374  37.366  1.00101.67           S
  ATOM    844  SG  CYS A1031      92.718  71.699  36.600  1.00118.03           S
  ATOM   1087  SG  CYS A1062      93.810  74.362  38.858  1.00110.68           S
  ATOM   1107  SG  CYS A1065      91.560  72.440  40.350  1.00102.54           S

  Time building chain proxies: 3.24, per 1000 atoms: 0.23
  Number of scatterers: 13959
  At special positions: 0
  Unit cell: (110.667, 123.061, 129.259, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      96     16.00
     P      19     15.00
     O    2679      8.00
     N    2405      7.00
     C    8758      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.27
  Conformation dependent library (CDL) restraints added in 659.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A6001 "
        pdb="ZN    ZN A6001 " - pdb=" SG  CYS A1294 "
        pdb="ZN    ZN A6001 " - pdb=" ND1 HIS A1365 "
        pdb="ZN    ZN A6001 " - pdb=" NE2 HIS A1090 "
      pdb="  ZN A6002 "
        pdb="ZN    ZN A6002 " - pdb=" SG  CYS A1065 "
        pdb="ZN    ZN A6002 " - pdb=" SG  CYS A1062 "
        pdb="ZN    ZN A6002 " - pdb=" SG  CYS A1031 "
        pdb="ZN    ZN A6002 " - pdb=" SG  CYS A1028 "
      Number of angles added : 6


  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3244

  Finding SS restraints...
    Secondary structure from input PDB file:
      83 helices and 11 sheets defined
      63.7% alpha, 5.8% beta
      1 base pairs and 5 stacking pairs defined.
    Time for finding SS restraints: 1.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 930 through 946
      removed outlier: 3.561A  pdb=" N   VAL A 934 " --> pdb=" O   SER A 930 " (cutoff:3.500A)
      removed outlier: 5.105A  pdb=" N   GLU A 943 " --> pdb=" O   GLU A 939 " (cutoff:3.500A)
      removed outlier: 5.227A  pdb=" N   HIS A 944 " --> pdb=" O   LYS A 940 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 955 through 967
    Processing helix  chain 'A' and resid 973 through 987
    Processing helix  chain 'A' and resid 987 through 997
    Processing helix  chain 'A' and resid 1008 through 1027
      removed outlier: 3.803A  pdb=" N   LYS A1024 " --> pdb=" O   SER A1020 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   SER A1025 " --> pdb=" O   GLU A1021 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1028 through 1042
      removed outlier: 3.611A  pdb=" N   THR A1042 " --> pdb=" O   ALA A1038 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1044 through 1057
      removed outlier: 4.045A  pdb=" N   GLN A1057 " --> pdb=" O   ALA A1053 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1076 through 1081
    Processing helix  chain 'A' and resid 1084 through 1088
      removed outlier: 3.635A  pdb=" N   VAL A1087 " --> pdb=" O   LYS A1084 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1100 through 1102
      No H-bonds generated for 'chain 'A' and resid 1100 through 1102'
    Processing helix  chain 'A' and resid 1103 through 1111
      removed outlier: 4.193A  pdb=" N   ASP A1107 " --> pdb=" O   LEU A1103 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ARG A1108 " --> pdb=" O   THR A1104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1118 through 1140
    Processing helix  chain 'A' and resid 1173 through 1187
    Processing helix  chain 'A' and resid 1196 through 1209
    Processing helix  chain 'A' and resid 1221 through 1232
      removed outlier: 3.762A  pdb=" N   LEU A1225 " --> pdb=" O   PRO A1221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1237 through 1254
      removed outlier: 3.567A  pdb=" N   VAL A1241 " --> pdb=" O   LYS A1237 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLU A1254 " --> pdb=" O   LYS A1250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1266 through 1281
      removed outlier: 3.586A  pdb=" N   LEU A1270 " --> pdb=" O   SER A1266 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   CYS A1273 " --> pdb=" O   GLU A1269 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   PHE A1279 " --> pdb=" O   ASP A1275 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   LYS A1280 " --> pdb=" O   VAL A1276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1297 through 1309
    Processing helix  chain 'A' and resid 1315 through 1328
    Processing helix  chain 'A' and resid 1330 through 1350
    Processing helix  chain 'A' and resid 1401 through 1426
      removed outlier: 4.043A  pdb=" N   LEU A1407 " --> pdb=" O   ARG A1403 " (cutoff:3.500A)
      removed outlier: 5.424A  pdb=" N   LEU A1412 " --> pdb=" O   GLY A1408 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   TYR A1413 " --> pdb=" O   SER A1409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1428 through 1434
      removed outlier: 3.679A  pdb=" N   VAL A1431 " --> pdb=" O   CYS A1428 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ASN A1433 " --> pdb=" O   GLU A1430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1436 through 1463
      removed outlier: 3.662A  pdb=" N   GLU A1463 " --> pdb=" O   THR A1459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1465 through 1481
      removed outlier: 3.799A  pdb=" N   SER A1469 " --> pdb=" O   ARG A1465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1487 through 1505
    Processing helix  chain 'A' and resid 1507 through 1513
    Processing helix  chain 'A' and resid 1515 through 1524
    Processing helix  chain 'A' and resid 1524 through 1531
    Processing helix  chain 'A' and resid 1532 through 1534
      No H-bonds generated for 'chain 'A' and resid 1532 through 1534'
    Processing helix  chain 'A' and resid 1538 through 1543
    Processing helix  chain 'A' and resid 1544 through 1547
      removed outlier: 3.578A  pdb=" N   SER A1547 " --> pdb=" O   LYS A1544 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1544 through 1547'
    Processing helix  chain 'A' and resid 1552 through 1571
    Processing helix  chain 'A' and resid 1572 through 1581
      removed outlier: 4.139A  pdb=" N   LYS A1581 " --> pdb=" O   VAL A1577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1603 through 1612
    Processing helix  chain 'A' and resid 1613 through 1616
      removed outlier: 3.521A  pdb=" N   ILE A1616 " --> pdb=" O   ASN A1613 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1613 through 1616'
    Processing helix  chain 'A' and resid 1623 through 1651
      removed outlier: 3.779A  pdb=" N   GLY A1627 " --> pdb=" O   ASN A1623 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1658 through 1666
    Processing helix  chain 'A' and resid 1758 through 1773
      removed outlier: 3.570A  pdb=" N   ILE A1762 " --> pdb=" O   ASN A1758 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1780 through 1791
    Processing helix  chain 'A' and resid 1792 through 1795
    Processing helix  chain 'A' and resid 1796 through 1805
    Processing helix  chain 'A' and resid 1806 through 1810
    Processing helix  chain 'A' and resid 1831 through 1853
    Processing helix  chain 'A' and resid 1869 through 1879
      removed outlier: 3.994A  pdb=" N   VAL A1879 " --> pdb=" O   LEU A1875 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1883 through 1895
    Processing helix  chain 'A' and resid 2250 through 2260
    Processing helix  chain 'A' and resid 2286 through 2305
    Processing helix  chain 'A' and resid 2316 through 2336
    Processing helix  chain 'A' and resid 2367 through 2379
    Processing helix  chain 'A' and resid 2382 through 2397
    Processing helix  chain 'A' and resid 2404 through 2419
      removed outlier: 3.531A  pdb=" N   LEU A2415 " --> pdb=" O   ILE A2411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2420 through 2422
      No H-bonds generated for 'chain 'A' and resid 2420 through 2422'
    Processing helix  chain 'A' and resid 2429 through 2440
    Processing helix  chain 'A' and resid 2441 through 2445
      removed outlier: 3.549A  pdb=" N   ASP A2445 " --> pdb=" O   ASP A2442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2447 through 2457
    Processing helix  chain 'A' and resid 2458 through 2461
    Processing helix  chain 'A' and resid 2476 through 2503
      removed outlier: 4.298A  pdb=" N   VAL A2489 " --> pdb=" O   SER A2485 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   LEU A2490 " --> pdb=" O   LEU A2486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2530 through 2559
      removed outlier: 5.454A  pdb=" N   TRP A2542 " --> pdb=" O   ASP A2538 " (cutoff:3.500A)
      removed outlier: 5.465A  pdb=" N   LYS A2543 " --> pdb=" O   GLU A2539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2590 through 2595
      removed outlier: 4.103A  pdb=" N   PHE A2595 " --> pdb=" O   ILE A2591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2595 through 2600
      removed outlier: 3.937A  pdb=" N   ILE A2599 " --> pdb=" O   PHE A2595 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ASN A2600 " --> pdb=" O   THR A2596 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2595 through 2600'
    Processing helix  chain 'A' and resid 2605 through 2622
    Processing helix  chain 'A' and resid 2626 through 2645
      removed outlier: 3.717A  pdb=" N   PHE A2641 " --> pdb=" O   ARG A2637 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   HIS A2644 " --> pdb=" O   ILE A2640 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   VAL A2645 " --> pdb=" O   PHE A2641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2645 through 2657
      removed outlier: 6.468A  pdb=" N   ILE A2654 " --> pdb=" O   ARG A2650 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   LEU A2655 " --> pdb=" O   ARG A2651 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2658 through 2659
      No H-bonds generated for 'chain 'A' and resid 2658 through 2659'
    Processing helix  chain 'A' and resid 2660 through 2664
      removed outlier: 3.595A  pdb=" N   GLY A2664 " --> pdb=" O   SER A2661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2670 through 2676
      removed outlier: 4.713A  pdb=" N   SER A2676 " --> pdb=" O   SER A2672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2678 through 2697
    Processing helix  chain 'A' and resid 2753 through 2764
    Processing helix  chain 'A' and resid 2770 through 2783
    Processing helix  chain 'A' and resid 2806 through 2815
    Processing helix  chain 'A' and resid 2816 through 2836
      removed outlier: 4.001A  pdb=" N   SER A2826 " --> pdb=" O   ASN A2822 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   VAL A2827 " --> pdb=" O   ARG A2823 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2899 through 2912
    Processing helix  chain 'A' and resid 2944 through 2955
    Processing helix  chain 'A' and resid 2993 through 3004
      removed outlier: 3.626A  pdb=" N   CYS A3004 " --> pdb=" O   THR A3000 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3043 through 3060
    Processing helix  chain 'A' and resid 3062 through 3073
    Processing helix  chain 'A' and resid 3095 through 3100
    Processing helix  chain 'A' and resid 3104 through 3114
    Processing helix  chain 'A' and resid 3114 through 3121
      removed outlier: 4.477A  pdb=" N   ILE A3118 " --> pdb=" O   ASP A3114 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   SER A3119 " --> pdb=" O   GLU A3115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3130 through 3139
    Processing helix  chain 'A' and resid 3142 through 3162
      removed outlier: 3.526A  pdb=" N   PHE A3146 " --> pdb=" O   PHE A3142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3167 through 3183
    Processing helix  chain 'A' and resid 3208 through 3217
      removed outlier: 3.901A  pdb=" N   ILE A3217 " --> pdb=" O   VAL A3213 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 971 through 972
      removed outlier: 6.941A  pdb=" N   VAL A 971 " --> pdb=" O   TYR A1755 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1003 through 1004
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1151 through 1153
      removed outlier: 4.019A  pdb=" N   CYS A1143 " --> pdb=" O   VAL A1220 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1357 through 1362
      removed outlier: 3.987A  pdb=" N   LEU A1383 " --> pdb=" O   LYS A1373 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   LEU A1386 " --> pdb=" O   GLY A1396 " (cutoff:3.500A)
      removed outlier: 5.830A  pdb=" N   GLY A1396 " --> pdb=" O   LEU A1386 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 2267 through 2268
      removed outlier: 7.479A  pdb=" N   ALA A2268 " --> pdb=" O   GLU A2402 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 2507 through 2514
    Processing sheet with id=AA7, first strand: chain 'A' and resid 2575 through 2576
    Processing sheet with id=AA8, first strand: chain 'A' and resid 2958 through 2960
      removed outlier: 4.241A  pdb=" N   ILE A2990 " --> pdb=" O   ASP A2960 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 3005 through 3009
      removed outlier: 6.491A  pdb=" N   SER A3005 " --> pdb=" O   LEU A3039 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   VAL A3041 " --> pdb=" O   SER A3005 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   SER A3007 " --> pdb=" O   VAL A3041 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 3078 through 3081
      removed outlier: 3.828A  pdb=" N   SER A3078 " --> pdb=" O   ARG A3224 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 3086 through 3090
      removed outlier: 4.014A  pdb=" N   PHE A3195 " --> pdb=" O   THR A3090 " (cutoff:3.500A)

    772 hydrogen bonds defined for protein.
    2256 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      3 hydrogen bonds
      6 hydrogen bond angles
      0 basepair planarities
      1 basepair parallelities
      5 stacking parallelities
  Total time for adding SS restraints: 2.80

  Time building geometry restraints manager: 1.68 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: 4202
        1.34 -     1.46: 2741
        1.46 -     1.58: 7108
        1.58 -     1.70: 36
        1.70 -     1.82: 140
  Bond restraints: 14227
  Sorted by residual:
  bond pdb=" C   VAL A1288 "
       pdb=" N   PRO A1289 "
    ideal  model  delta    sigma   weight residual
    1.336  1.387 -0.051 1.20e-02 6.94e+03 1.83e+01
  bond pdb=" C   LEU A2946 "
       pdb=" N   PRO A2947 "
    ideal  model  delta    sigma   weight residual
    1.335  1.360 -0.024 1.36e-02 5.41e+03 3.19e+00
  bond pdb=" CA  VAL A1570 "
       pdb=" C   VAL A1570 "
    ideal  model  delta    sigma   weight residual
    1.520  1.546 -0.026 1.54e-02 4.22e+03 2.79e+00
  bond pdb=" CA  PHE A2633 "
       pdb=" CB  PHE A2633 "
    ideal  model  delta    sigma   weight residual
    1.528  1.554 -0.026 1.66e-02 3.63e+03 2.47e+00
  bond pdb=" CA  GLN A2560 "
       pdb=" C   GLN A2560 "
    ideal  model  delta    sigma   weight residual
    1.523  1.544 -0.021 1.45e-02 4.76e+03 2.14e+00
  ... (remaining 14222 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 18836
        2.07 -     4.15: 366
        4.15 -     6.22: 47
        6.22 -     8.29: 11
        8.29 -    10.37: 6
  Bond angle restraints: 19266
  Sorted by residual:
  angle pdb=" C   ARG A1827 "
        pdb=" N   THR A1828 "
        pdb=" CA  THR A1828 "
      ideal   model   delta    sigma   weight residual
     121.54  129.93   -8.39 1.91e+00 2.74e-01 1.93e+01
  angle pdb=" CA  VAL A1570 "
        pdb=" CB  VAL A1570 "
        pdb=" CG1 VAL A1570 "
      ideal   model   delta    sigma   weight residual
     110.40  116.80   -6.40 1.70e+00 3.46e-01 1.42e+01
  angle pdb=" CB  ARG A1246 "
        pdb=" CG  ARG A1246 "
        pdb=" CD  ARG A1246 "
      ideal   model   delta    sigma   weight residual
     111.30  119.80   -8.50 2.30e+00 1.89e-01 1.37e+01
  angle pdb=" C   SER A1652 "
        pdb=" N   ASP A1653 "
        pdb=" CA  ASP A1653 "
      ideal   model   delta    sigma   weight residual
     121.54  128.40   -6.86 1.91e+00 2.74e-01 1.29e+01
  angle pdb=" CA  GLN A2560 "
        pdb=" CB  GLN A2560 "
        pdb=" CG  GLN A2560 "
      ideal   model   delta    sigma   weight residual
     114.10  121.27   -7.17 2.00e+00 2.50e-01 1.28e+01
  ... (remaining 19261 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.28: 8625
       35.28 -    70.56: 103
       70.56 -   105.84: 9
      105.84 -   141.12: 0
      141.12 -   176.40: 2
  Dihedral angle restraints: 8739
    sinusoidal: 3762
      harmonic: 4977
  Sorted by residual:
  dihedral pdb=" O4'   U C  18 "
           pdb=" C1'   U C  18 "
           pdb=" N1    U C  18 "
           pdb=" C2    U C  18 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   48.40 -176.40     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U C  20 "
           pdb=" C1'   U C  20 "
           pdb=" N1    U C  20 "
           pdb=" C2    U C  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   59.67  172.33     1      1.70e+01 3.46e-03 6.61e+01
  dihedral pdb=" CA  PHE A1505 "
           pdb=" C   PHE A1505 "
           pdb=" N   LEU A1506 "
           pdb=" CA  LEU A1506 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.81  -25.19     0      5.00e+00 4.00e-02 2.54e+01
  ... (remaining 8736 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1746
       0.053 -    0.107: 391
       0.107 -    0.160: 85
       0.160 -    0.213: 8
       0.213 -    0.266: 3
  Chirality restraints: 2233
  Sorted by residual:
  chirality pdb=" CB  ILE A1553 "
            pdb=" CA  ILE A1553 "
            pdb=" CG1 ILE A1553 "
            pdb=" CG2 ILE A1553 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" CG  LEU A1323 "
            pdb=" CB  LEU A1323 "
            pdb=" CD1 LEU A1323 "
            pdb=" CD2 LEU A1323 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.33   -0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" C3'   A B   7 "
            pdb=" C4'   A B   7 "
            pdb=" O3'   A B   7 "
            pdb=" C2'   A B   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.72    0.25 2.00e-01 2.50e+01 1.52e+00
  ... (remaining 2230 not shown)

  Planarity restraints: 2376
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A2605 "    0.042 5.00e-02 4.00e+02   6.33e-02 6.42e+00
        pdb=" N   PRO A2606 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A2606 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A2606 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 927 "   -0.038 5.00e-02 4.00e+02   5.71e-02 5.22e+00
        pdb=" N   PRO A 928 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A 928 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 928 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A2633 "   -0.016 2.00e-02 2.50e+03   1.63e-02 4.66e+00
        pdb=" CG  PHE A2633 "    0.038 2.00e-02 2.50e+03
        pdb=" CD1 PHE A2633 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE A2633 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE A2633 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A2633 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE A2633 "    0.000 2.00e-02 2.50e+03
  ... (remaining 2373 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 31
        2.54 -     3.13: 9921
        3.13 -     3.72: 21085
        3.72 -     4.31: 31290
        4.31 -     4.90: 51226
  Nonbonded interactions: 113553
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A2788 "
            pdb="ZN    ZN A6001 "
     model   vdw
     1.953 2.230
  nonbonded pdb=" O   LEU A3178 "
            pdb=" OG  SER A3182 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" OG  SER A2515 "
            pdb=" OD1 ASP A2517 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" O2'   U C  20 "
            pdb=" O4'   G C  21 "
     model   vdw
     2.348 3.040
  nonbonded pdb=" O   CYS A1350 "
            pdb=" NH1 ARG A1402 "
     model   vdw
     2.381 3.120
  ... (remaining 113548 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.700
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     17.670
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:9.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
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      :  0.004   0.052  14234  Z= 0.195
  Angle     :  0.750  18.266  19272  Z= 0.412
  Chirality :  0.048   0.266   2233
  Planarity :  0.006   0.075   2376
  Dihedral  : 12.602 176.402   5495
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 2.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.17), residues: 1672
  helix: -0.53 (0.13), residues: 985
  sheet:  0.15 (0.50), residues: 95
  loop : -0.52 (0.23), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A1246 
 TYR   0.018   0.002   TYR A1308 
 PHE   0.038   0.002   PHE A2633 
 TRP   0.016   0.001   TRP A2542 
 HIS   0.006   0.001   HIS A1579 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (14227)
  covalent geometry    : angle       0.73113 (19266)
  hydrogen bonds       : bond        0.12819 (  775)
  hydrogen bonds       : angle       5.32329 ( 2262)
  metal coordination   : bond        0.00784 (    7)
  metal coordination   : angle       9.61678 (    6)

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

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

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 0.586 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  932 LYS cc_start: 0.8369 (tttt) cc_final: 0.7861 (mppt)
REVERT: A 1006 GLN cc_start: 0.8791 (mt0) cc_final: 0.8365 (tt0)
REVERT: A 1036 LYS cc_start: 0.8587 (tttt) cc_final: 0.8365 (tttm)
REVERT: A 1040 ASP cc_start: 0.8345 (m-30) cc_final: 0.8095 (m-30)
REVERT: A 1123 ARG cc_start: 0.8794 (ttt180) cc_final: 0.8577 (ttm170)
REVERT: A 1130 TYR cc_start: 0.7748 (m-80) cc_final: 0.7488 (m-80)
REVERT: A 1150 GLN cc_start: 0.8514 (tt0) cc_final: 0.7818 (mm110)
REVERT: A 1215 LYS cc_start: 0.9062 (mttt) cc_final: 0.8625 (mmtm)
REVERT: A 1344 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7610 (pt0)
REVERT: A 1490 ASP cc_start: 0.7904 (m-30) cc_final: 0.7471 (t0)
REVERT: A 1811 VAL cc_start: 0.8404 (t) cc_final: 0.8162 (p)
REVERT: A 2263 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8116 (pp20)
REVERT: A 2416 ARG cc_start: 0.8226 (ttp80) cc_final: 0.7982 (tmm160)
REVERT: A 2473 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8371 (mm110)
REVERT: A 2539 GLU cc_start: 0.8492 (tt0) cc_final: 0.8214 (pt0)
REVERT: A 2581 MET cc_start: 0.8704 (tmm) cc_final: 0.8217 (tmm)
REVERT: A 2785 ASN cc_start: 0.7741 (m-40) cc_final: 0.7460 (p0)
REVERT: A 2858 LYS cc_start: 0.9071 (pttt) cc_final: 0.8852 (pttp)
REVERT: A 2901 GLN cc_start: 0.8618 (mt0) cc_final: 0.8107 (mp10)
REVERT: A 2905 LYS cc_start: 0.8775 (mttt) cc_final: 0.8515 (mttp)
REVERT: A 3011 HIS cc_start: 0.7860 (m-70) cc_final: 0.7256 (p90)
REVERT: A 3127 ASP cc_start: 0.8608 (m-30) cc_final: 0.8346 (t0)
REVERT: A 3136 PHE cc_start: 0.8863 (t80) cc_final: 0.8432 (t80)
REVERT: A 3139 MET cc_start: 0.8588 (ptm) cc_final: 0.8192 (ptt)
REVERT: A 3140 GLN cc_start: 0.8707 (mt0) cc_final: 0.8273 (mt0)
REVERT: A 3169 GLN cc_start: 0.8762 (mt0) cc_final: 0.8519 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 247
  average time/residue: 0.8185
  time to fit residues: 216.4866
Evaluate side-chains
  152 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 98 optimal weight:    0.4980
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    0.4980
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    0.2980
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 149 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 987 ASN
** A1354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1517 GLN
A2396 ASN
A2695 GLN
A3059 GLN
A3186 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.110119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.079000 restraints weight = 21794.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3087 rms_B_bonded: 2.38
r_work: 0.2953 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2830 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.1674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14234  Z= 0.116
  Angle     :  0.519  13.426  19272  Z= 0.268
  Chirality :  0.038   0.191   2233
  Planarity :  0.004   0.042   2376
  Dihedral  : 10.985 177.357   2099
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  7.13 %
    Favored  : 91.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.20), residues: 1672
  helix:  1.35 (0.16), residues: 999
  sheet:  0.33 (0.52), residues: 89
  loop : -0.27 (0.24), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1805 
 TYR   0.013   0.001   TYR A2262 
 PHE   0.031   0.001   PHE A2633 
 TRP   0.014   0.001   TRP A2542 
 HIS   0.004   0.001   HIS A1776 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (14227)
  covalent geometry    : angle       0.49969 (19266)
  hydrogen bonds       : bond        0.04530 (  775)
  hydrogen bonds       : angle       3.85120 ( 2262)
  metal coordination   : bond        0.00615 (    7)
  metal coordination   : angle       7.97469 (    6)

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

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

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 167
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  932 LYS cc_start: 0.8343 (tttt) cc_final: 0.7925 (mppt)
REVERT: A 1006 GLN cc_start: 0.8734 (mt0) cc_final: 0.8388 (tt0)
REVERT: A 1036 LYS cc_start: 0.8627 (tttt) cc_final: 0.8395 (tttm)
REVERT: A 1040 ASP cc_start: 0.8471 (m-30) cc_final: 0.8204 (m-30)
REVERT: A 1084 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7746 (mtpp)
REVERT: A 1130 TYR cc_start: 0.7631 (m-80) cc_final: 0.7429 (m-10)
REVERT: A 1136 MET cc_start: 0.7823 (mtp) cc_final: 0.7544 (mtp)
REVERT: A 1138 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7943 (mpp)
REVERT: A 1141 ILE cc_start: 0.7597 (mt) cc_final: 0.7272 (mm)
REVERT: A 1150 GLN cc_start: 0.8537 (tt0) cc_final: 0.7839 (mm110)
REVERT: A 1215 LYS cc_start: 0.9071 (mttt) cc_final: 0.8635 (mmtm)
REVERT: A 1344 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7673 (pt0)
REVERT: A 1811 VAL cc_start: 0.8335 (t) cc_final: 0.8102 (p)
REVERT: A 1830 MET cc_start: 0.7163 (ptt) cc_final: 0.6818 (ptt)
REVERT: A 1837 LYS cc_start: 0.8983 (tttt) cc_final: 0.8534 (mmtm)
REVERT: A 1886 GLN cc_start: 0.7073 (mt0) cc_final: 0.6774 (mt0)
REVERT: A 2263 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8127 (pp20)
REVERT: A 2319 GLU cc_start: 0.7771 (mp0) cc_final: 0.7425 (tt0)
REVERT: A 2416 ARG cc_start: 0.8304 (ttp80) cc_final: 0.8088 (tmm160)
REVERT: A 2463 MET cc_start: 0.8174 (mtp) cc_final: 0.7653 (mtm)
REVERT: A 2473 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8285 (mm110)
REVERT: A 2610 MET cc_start: 0.8164 (ttt) cc_final: 0.7904 (ttt)
REVERT: A 2785 ASN cc_start: 0.7602 (m-40) cc_final: 0.7350 (p0)
REVERT: A 2901 GLN cc_start: 0.8651 (mt0) cc_final: 0.8236 (mp10)
REVERT: A 3011 HIS cc_start: 0.8040 (m-70) cc_final: 0.7455 (p90)
REVERT: A 3098 GLN cc_start: 0.8023 (tp40) cc_final: 0.7694 (tp40)
REVERT: A 3114 ASP cc_start: 0.6466 (t0) cc_final: 0.6084 (t70)
REVERT: A 3127 ASP cc_start: 0.8537 (m-30) cc_final: 0.8281 (t0)
  outliers start: 16
  outliers final: 8
  residues processed: 176
  average time/residue: 0.7204
  time to fit residues: 137.5122
Evaluate side-chains
  155 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 145
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  935 LEU
Chi-restraints excluded: chain A residue 1084 LYS
Chi-restraints excluded: chain A residue 1138 MET
Chi-restraints excluded: chain A residue 2254 LEU
Chi-restraints excluded: chain A residue 2360 THR
Chi-restraints excluded: chain A residue 2398 CYS
Chi-restraints excluded: chain A residue 2621 MET
Chi-restraints excluded: chain A residue 2951 ILE
Chi-restraints excluded: chain A residue 2964 LEU
Chi-restraints excluded: chain A residue 3099 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 133 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A1354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1517 GLN
A1886 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.107510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.076024 restraints weight = 21927.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.3035 rms_B_bonded: 2.35
r_work: 0.2898 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2775 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14234  Z= 0.141
  Angle     :  0.518  10.053  19272  Z= 0.268
  Chirality :  0.039   0.198   2233
  Planarity :  0.004   0.039   2376
  Dihedral  : 10.869 178.516   2099
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  8.61 %
    Favored  : 89.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.62 (0.20), residues: 1672
  helix:  1.91 (0.16), residues: 1000
  sheet:  0.36 (0.52), residues: 89
  loop : -0.22 (0.25), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1805 
 TYR   0.018   0.001   TYR A2262 
 PHE   0.029   0.001   PHE A2633 
 TRP   0.014   0.001   TRP A2542 
 HIS   0.005   0.001   HIS A1776 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (14227)
  covalent geometry    : angle       0.50608 (19266)
  hydrogen bonds       : bond        0.04962 (  775)
  hydrogen bonds       : angle       3.79757 ( 2262)
  metal coordination   : bond        0.00655 (    7)
  metal coordination   : angle       6.36083 (    6)

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

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

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 151
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  932 LYS cc_start: 0.8302 (tttt) cc_final: 0.7882 (mppt)
REVERT: A 1006 GLN cc_start: 0.8857 (mt0) cc_final: 0.8447 (tt0)
REVERT: A 1036 LYS cc_start: 0.8638 (tttt) cc_final: 0.8404 (tttm)
REVERT: A 1040 ASP cc_start: 0.8318 (m-30) cc_final: 0.8030 (m-30)
REVERT: A 1058 LEU cc_start: 0.8826 (mp) cc_final: 0.8625 (mp)
REVERT: A 1084 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7805 (mtpp)
REVERT: A 1123 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8295 (ttm170)
REVERT: A 1130 TYR cc_start: 0.7699 (m-80) cc_final: 0.7469 (m-10)
REVERT: A 1136 MET cc_start: 0.7895 (mtp) cc_final: 0.7610 (mtp)
REVERT: A 1141 ILE cc_start: 0.7604 (mt) cc_final: 0.7290 (mm)
REVERT: A 1150 GLN cc_start: 0.8531 (tt0) cc_final: 0.7838 (mm110)
REVERT: A 1215 LYS cc_start: 0.9140 (mttt) cc_final: 0.8689 (mmtm)
REVERT: A 1344 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7613 (pt0)
REVERT: A 1517 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.8035 (mm110)
REVERT: A 1811 VAL cc_start: 0.8369 (t) cc_final: 0.8149 (p)
REVERT: A 1830 MET cc_start: 0.7105 (ptt) cc_final: 0.6775 (ptt)
REVERT: A 2263 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8089 (pp20)
REVERT: A 2319 GLU cc_start: 0.7810 (mp0) cc_final: 0.7438 (tt0)
REVERT: A 2463 MET cc_start: 0.8310 (mtp) cc_final: 0.7764 (mtm)
REVERT: A 2473 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8292 (mm110)
REVERT: A 2610 MET cc_start: 0.8123 (ttt) cc_final: 0.7877 (ttt)
REVERT: A 2646 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7929 (tt0)
REVERT: A 2785 ASN cc_start: 0.7597 (m-40) cc_final: 0.7373 (p0)
REVERT: A 2901 GLN cc_start: 0.8613 (mt0) cc_final: 0.8178 (mp10)
REVERT: A 3011 HIS cc_start: 0.8065 (m-70) cc_final: 0.7486 (p90)
REVERT: A 3094 SER cc_start: 0.7866 (OUTLIER) cc_final: 0.7610 (m)
REVERT: A 3098 GLN cc_start: 0.8073 (tp40) cc_final: 0.7745 (tp40)
REVERT: A 3127 ASP cc_start: 0.8478 (m-30) cc_final: 0.8271 (t0)
  outliers start: 29
  outliers final: 14
  residues processed: 171
  average time/residue: 0.7132
  time to fit residues: 132.5466
Evaluate side-chains
  161 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 142
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  935 LEU
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1084 LYS
Chi-restraints excluded: chain A residue 1123 ARG
Chi-restraints excluded: chain A residue 1517 GLN
Chi-restraints excluded: chain A residue 1522 LEU
Chi-restraints excluded: chain A residue 2398 CYS
Chi-restraints excluded: chain A residue 2425 VAL
Chi-restraints excluded: chain A residue 2621 MET
Chi-restraints excluded: chain A residue 2624 SER
Chi-restraints excluded: chain A residue 2646 GLU
Chi-restraints excluded: chain A residue 2784 CYS
Chi-restraints excluded: chain A residue 2951 ILE
Chi-restraints excluded: chain A residue 2964 LEU
Chi-restraints excluded: chain A residue 3062 ASP
Chi-restraints excluded: chain A residue 3094 SER
Chi-restraints excluded: chain A residue 3099 VAL
Chi-restraints excluded: chain A residue 3132 LEU
Chi-restraints excluded: chain A residue 3168 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 146 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0370
   chunk 28 optimal weight:    1.9990
   chunk 159 optimal weight:    0.0030
   chunk 30 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 157 optimal weight:    2.9990
   chunk 132 optimal weight:    2.9990
   chunk 158 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.8070

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

Flipped N/Q/H residues before XYZ refinement:
A1247 ASN
A1517 GLN
A2611 GLN
A3140 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.108409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.076921 restraints weight = 22043.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 2.36
r_work: 0.2906 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2782 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14234  Z= 0.127
  Angle     :  0.494   9.825  19272  Z= 0.256
  Chirality :  0.038   0.187   2233
  Planarity :  0.003   0.036   2376
  Dihedral  : 10.781 178.327   2099
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  9.51 %
    Favored  : 88.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.21), residues: 1672
  helix:  2.15 (0.16), residues: 1000
  sheet:  0.38 (0.52), residues: 89
  loop : -0.20 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1246 
 TYR   0.020   0.001   TYR A2262 
 PHE   0.029   0.001   PHE A2633 
 TRP   0.013   0.001   TRP A2542 
 HIS   0.004   0.001   HIS A1776 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (14227)
  covalent geometry    : angle       0.48376 (19266)
  hydrogen bonds       : bond        0.04552 (  775)
  hydrogen bonds       : angle       3.70242 ( 2262)
  metal coordination   : bond        0.00529 (    7)
  metal coordination   : angle       5.56976 (    6)

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

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

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 151
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
REVERT: A  932 LYS cc_start: 0.8296 (tttt) cc_final: 0.7878 (mppt)
REVERT: A 1006 GLN cc_start: 0.8856 (mt0) cc_final: 0.8467 (tt0)
REVERT: A 1036 LYS cc_start: 0.8638 (tttt) cc_final: 0.8430 (tttm)
REVERT: A 1040 ASP cc_start: 0.8337 (m-30) cc_final: 0.8054 (m-30)
REVERT: A 1058 LEU cc_start: 0.8783 (mp) cc_final: 0.8567 (mp)
REVERT: A 1084 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7819 (mtpp)
REVERT: A 1122 ARG cc_start: 0.7563 (mtt90) cc_final: 0.7345 (mtt90)
REVERT: A 1130 TYR cc_start: 0.7726 (m-80) cc_final: 0.7503 (m-80)
REVERT: A 1136 MET cc_start: 0.7865 (mtp) cc_final: 0.7603 (mtp)
REVERT: A 1138 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7726 (mpp)
REVERT: A 1141 ILE cc_start: 0.7563 (mt) cc_final: 0.7240 (mm)
REVERT: A 1150 GLN cc_start: 0.8523 (tt0) cc_final: 0.7843 (mm110)
REVERT: A 1215 LYS cc_start: 0.9168 (mttt) cc_final: 0.8706 (mmtm)
REVERT: A 1246 ARG cc_start: 0.8519 (tmm-80) cc_final: 0.8239 (ttm-80)
REVERT: A 1344 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7617 (pt0)
REVERT: A 1830 MET cc_start: 0.7069 (ptt) cc_final: 0.6694 (ptt)
REVERT: A 1837 LYS cc_start: 0.8670 (tptp) cc_final: 0.8368 (mmpt)
REVERT: A 2263 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8076 (pp20)
REVERT: A 2319 GLU cc_start: 0.7804 (mp0) cc_final: 0.7429 (tt0)
REVERT: A 2463 MET cc_start: 0.8281 (mtp) cc_final: 0.7697 (mtm)
REVERT: A 2610 MET cc_start: 0.8140 (ttt) cc_final: 0.7900 (ttt)
REVERT: A 2785 ASN cc_start: 0.7618 (m-40) cc_final: 0.7369 (p0)
REVERT: A 2901 GLN cc_start: 0.8653 (mt0) cc_final: 0.8182 (mp10)
REVERT: A 3011 HIS cc_start: 0.8120 (m-70) cc_final: 0.7474 (p90)
REVERT: A 3098 GLN cc_start: 0.8052 (tp40) cc_final: 0.7731 (tp40)
REVERT: A 3186 GLN cc_start: 0.8485 (mt0) cc_final: 0.8254 (mt0)
  outliers start: 29
  outliers final: 13
  residues processed: 170
  average time/residue: 0.7058
  time to fit residues: 130.3913
Evaluate side-chains
  159 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 144
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  935 LEU
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1084 LYS
Chi-restraints excluded: chain A residue 1138 MET
Chi-restraints excluded: chain A residue 1522 LEU
Chi-restraints excluded: chain A residue 2398 CYS
Chi-restraints excluded: chain A residue 2621 MET
Chi-restraints excluded: chain A residue 2624 SER
Chi-restraints excluded: chain A residue 2784 CYS
Chi-restraints excluded: chain A residue 2951 ILE
Chi-restraints excluded: chain A residue 2964 LEU
Chi-restraints excluded: chain A residue 3099 VAL
Chi-restraints excluded: chain A residue 3132 LEU
Chi-restraints excluded: chain A residue 3179 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 120 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 158 optimal weight:    6.9990
   chunk 72 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 141 optimal weight:    1.9990
   chunk 118 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A1247 ASN
A1354 ASN
A1516 GLN
A1517 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.106969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.075357 restraints weight = 22066.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3014 rms_B_bonded: 2.36
r_work: 0.2877 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2753 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  14234  Z= 0.156
  Angle     :  0.526   9.594  19272  Z= 0.273
  Chirality :  0.040   0.208   2233
  Planarity :  0.003   0.036   2376
  Dihedral  : 10.767 178.749   2099
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 10.53 %
    Favored  : 87.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.21), residues: 1672
  helix:  2.19 (0.16), residues: 999
  sheet:  0.23 (0.50), residues: 89
  loop : -0.29 (0.26), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1638 
 TYR   0.024   0.001   TYR A2262 
 PHE   0.029   0.001   PHE A2633 
 TRP   0.013   0.001   TRP A2542 
 HIS   0.005   0.001   HIS A1776 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (14227)
  covalent geometry    : angle       0.51658 (19266)
  hydrogen bonds       : bond        0.05036 (  775)
  hydrogen bonds       : angle       3.79092 ( 2262)
  metal coordination   : bond        0.00634 (    7)
  metal coordination   : angle       5.55003 (    6)

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

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

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
REVERT: A  932 LYS cc_start: 0.8306 (tttt) cc_final: 0.7879 (mppt)
REVERT: A 1006 GLN cc_start: 0.8853 (mt0) cc_final: 0.8426 (tt0)
REVERT: A 1036 LYS cc_start: 0.8646 (tttt) cc_final: 0.8441 (tttm)
REVERT: A 1040 ASP cc_start: 0.8311 (m-30) cc_final: 0.8066 (m-30)
REVERT: A 1084 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.7901 (mtpp)
REVERT: A 1130 TYR cc_start: 0.7735 (m-80) cc_final: 0.7499 (m-10)
REVERT: A 1136 MET cc_start: 0.7873 (mtp) cc_final: 0.7641 (mtp)
REVERT: A 1138 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7819 (mpp)
REVERT: A 1141 ILE cc_start: 0.7579 (mt) cc_final: 0.7254 (mm)
REVERT: A 1150 GLN cc_start: 0.8558 (tt0) cc_final: 0.7779 (mm110)
REVERT: A 1215 LYS cc_start: 0.9203 (mttt) cc_final: 0.8636 (mmpt)
REVERT: A 1246 ARG cc_start: 0.8543 (ttm-80) cc_final: 0.8207 (ttm-80)
REVERT: A 1250 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8183 (tppt)
REVERT: A 1344 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7644 (pt0)
REVERT: A 1517 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.8046 (mm110)
REVERT: A 1830 MET cc_start: 0.7064 (ptt) cc_final: 0.6684 (ptt)
REVERT: A 1837 LYS cc_start: 0.8745 (tptp) cc_final: 0.8366 (mmtm)
REVERT: A 1849 LYS cc_start: 0.8727 (mtpp) cc_final: 0.8248 (mttt)
REVERT: A 2263 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8070 (pp20)
REVERT: A 2319 GLU cc_start: 0.7851 (mp0) cc_final: 0.7477 (tt0)
REVERT: A 2463 MET cc_start: 0.8336 (mtp) cc_final: 0.7752 (mtm)
REVERT: A 2610 MET cc_start: 0.8168 (ttt) cc_final: 0.7837 (ttt)
REVERT: A 2646 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7952 (tt0)
REVERT: A 2785 ASN cc_start: 0.7629 (m-40) cc_final: 0.7409 (p0)
REVERT: A 2901 GLN cc_start: 0.8655 (mt0) cc_final: 0.8160 (mp10)
REVERT: A 3011 HIS cc_start: 0.8056 (m-70) cc_final: 0.7442 (p90)
REVERT: A 3127 ASP cc_start: 0.8197 (t0) cc_final: 0.7924 (t0)
REVERT: A 3186 GLN cc_start: 0.8507 (mt0) cc_final: 0.8254 (mt0)
  outliers start: 29
  outliers final: 14
  residues processed: 165
  average time/residue: 0.6879
  time to fit residues: 123.3450
Evaluate side-chains
  159 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  935 LEU
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1084 LYS
Chi-restraints excluded: chain A residue 1138 MET
Chi-restraints excluded: chain A residue 1517 GLN
Chi-restraints excluded: chain A residue 1522 LEU
Chi-restraints excluded: chain A residue 2398 CYS
Chi-restraints excluded: chain A residue 2611 GLN
Chi-restraints excluded: chain A residue 2621 MET
Chi-restraints excluded: chain A residue 2624 SER
Chi-restraints excluded: chain A residue 2646 GLU
Chi-restraints excluded: chain A residue 2784 CYS
Chi-restraints excluded: chain A residue 2951 ILE
Chi-restraints excluded: chain A residue 2964 LEU
Chi-restraints excluded: chain A residue 3062 ASP
Chi-restraints excluded: chain A residue 3091 LYS
Chi-restraints excluded: chain A residue 3099 VAL
Chi-restraints excluded: chain A residue 3179 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0020
   chunk 53 optimal weight:    0.7980
   chunk 164 optimal weight:    0.7980
   chunk 92 optimal weight:    3.9990
   chunk 158 optimal weight:    1.9990
   chunk 161 optimal weight:    0.8980
   chunk 137 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.6588

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

Flipped N/Q/H residues before XYZ refinement:
A1247 ASN
** A1354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1517 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.108690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.077263 restraints weight = 21908.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 2.35
r_work: 0.2912 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2789 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.2287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14234  Z= 0.117
  Angle     :  0.489  10.208  19272  Z= 0.254
  Chirality :  0.038   0.180   2233
  Planarity :  0.003   0.036   2376
  Dihedral  : 10.703 178.307   2099
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 11.18 %
    Favored  : 87.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.02 (0.21), residues: 1672
  helix:  2.37 (0.16), residues: 994
  sheet:  0.31 (0.50), residues: 89
  loop : -0.29 (0.26), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1638 
 TYR   0.021   0.001   TYR A2262 
 PHE   0.028   0.001   PHE A2633 
 TRP   0.013   0.001   TRP A2542 
 HIS   0.004   0.001   HIS A1776 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (14227)
  covalent geometry    : angle       0.48127 (19266)
  hydrogen bonds       : bond        0.04265 (  775)
  hydrogen bonds       : angle       3.66251 ( 2262)
  metal coordination   : bond        0.00435 (    7)
  metal coordination   : angle       4.93995 (    6)

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

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

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 152
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
REVERT: A  932 LYS cc_start: 0.8172 (tttt) cc_final: 0.7769 (mppt)
REVERT: A 1006 GLN cc_start: 0.8850 (mt0) cc_final: 0.8464 (tt0)
REVERT: A 1040 ASP cc_start: 0.8316 (m-30) cc_final: 0.8058 (m-30)
REVERT: A 1084 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.7871 (mtpp)
REVERT: A 1122 ARG cc_start: 0.7577 (mtt90) cc_final: 0.7356 (mtt90)
REVERT: A 1130 TYR cc_start: 0.7737 (m-10) cc_final: 0.7513 (m-80)
REVERT: A 1136 MET cc_start: 0.7879 (mtp) cc_final: 0.7640 (mtp)
REVERT: A 1138 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7734 (mpp)
REVERT: A 1141 ILE cc_start: 0.7552 (mt) cc_final: 0.7219 (mm)
REVERT: A 1150 GLN cc_start: 0.8523 (tt0) cc_final: 0.7755 (mm110)
REVERT: A 1215 LYS cc_start: 0.9165 (mttt) cc_final: 0.8588 (mmpt)
REVERT: A 1246 ARG cc_start: 0.8508 (ttm-80) cc_final: 0.8125 (ttm-80)
REVERT: A 1344 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7628 (pt0)
REVERT: A 1830 MET cc_start: 0.7048 (ptt) cc_final: 0.6621 (ptt)
REVERT: A 1837 LYS cc_start: 0.8754 (tptp) cc_final: 0.8374 (mmtm)
REVERT: A 1849 LYS cc_start: 0.8694 (mtpp) cc_final: 0.8202 (mttt)
REVERT: A 1886 GLN cc_start: 0.6853 (OUTLIER) cc_final: 0.6526 (mt0)
REVERT: A 2263 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8018 (pp20)
REVERT: A 2319 GLU cc_start: 0.7777 (mp0) cc_final: 0.7403 (tt0)
REVERT: A 2463 MET cc_start: 0.8318 (mtp) cc_final: 0.7728 (mtm)
REVERT: A 2646 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7902 (tt0)
REVERT: A 2785 ASN cc_start: 0.7562 (m-40) cc_final: 0.7345 (p0)
REVERT: A 2901 GLN cc_start: 0.8630 (mt0) cc_final: 0.8142 (mp10)
REVERT: A 3011 HIS cc_start: 0.8107 (m-70) cc_final: 0.7460 (p90)
REVERT: A 3098 GLN cc_start: 0.7910 (tp40) cc_final: 0.7675 (mm110)
REVERT: A 3127 ASP cc_start: 0.8360 (t0) cc_final: 0.8016 (t0)
  outliers start: 27
  outliers final: 13
  residues processed: 169
  average time/residue: 0.6993
  time to fit residues: 128.3191
Evaluate side-chains
  158 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  935 LEU
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1084 LYS
Chi-restraints excluded: chain A residue 1138 MET
Chi-restraints excluded: chain A residue 1522 LEU
Chi-restraints excluded: chain A residue 1886 GLN
Chi-restraints excluded: chain A residue 2398 CYS
Chi-restraints excluded: chain A residue 2621 MET
Chi-restraints excluded: chain A residue 2624 SER
Chi-restraints excluded: chain A residue 2646 GLU
Chi-restraints excluded: chain A residue 2784 CYS
Chi-restraints excluded: chain A residue 2830 ILE
Chi-restraints excluded: chain A residue 2951 ILE
Chi-restraints excluded: chain A residue 2964 LEU
Chi-restraints excluded: chain A residue 3099 VAL
Chi-restraints excluded: chain A residue 3179 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 151 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 103 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 150 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 132 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 84 optimal weight:    2.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A1247 ASN
A1354 ASN
A1491 HIS
A1517 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.105586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.073802 restraints weight = 22072.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 2.38
r_work: 0.2848 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2725 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  14234  Z= 0.199
  Angle     :  0.568  10.739  19272  Z= 0.295
  Chirality :  0.041   0.222   2233
  Planarity :  0.004   0.035   2376
  Dihedral  : 10.798 179.174   2099
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 11.56 %
    Favored  : 86.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.73 (0.21), residues: 1672
  helix:  2.11 (0.16), residues: 999
  sheet:  0.17 (0.49), residues: 89
  loop : -0.38 (0.26), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1638 
 TYR   0.032   0.002   TYR A2262 
 PHE   0.032   0.001   PHE A2633 
 TRP   0.012   0.002   TRP A2542 
 HIS   0.005   0.001   HIS A1776 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 (14227)
  covalent geometry    : angle       0.55983 (19266)
  hydrogen bonds       : bond        0.05583 (  775)
  hydrogen bonds       : angle       3.92030 ( 2262)
  metal coordination   : bond        0.00761 (    7)
  metal coordination   : angle       5.45875 (    6)

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

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

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
REVERT: A  932 LYS cc_start: 0.8214 (tttt) cc_final: 0.7783 (mppt)
REVERT: A 1084 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.7945 (mtpp)
REVERT: A 1130 TYR cc_start: 0.7734 (m-10) cc_final: 0.7502 (m-10)
REVERT: A 1136 MET cc_start: 0.7925 (mtp) cc_final: 0.7695 (mtp)
REVERT: A 1138 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7752 (mpp)
REVERT: A 1141 ILE cc_start: 0.7585 (mt) cc_final: 0.7216 (mm)
REVERT: A 1150 GLN cc_start: 0.8575 (tt0) cc_final: 0.7746 (mm110)
REVERT: A 1215 LYS cc_start: 0.9221 (mttt) cc_final: 0.8666 (mmpt)
REVERT: A 1344 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7630 (pt0)
REVERT: A 1517 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7980 (mm110)
REVERT: A 1830 MET cc_start: 0.7168 (ptt) cc_final: 0.6831 (ptt)
REVERT: A 1837 LYS cc_start: 0.8750 (tptp) cc_final: 0.8349 (mmtm)
REVERT: A 2263 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8090 (pp20)
REVERT: A 2319 GLU cc_start: 0.7873 (mp0) cc_final: 0.7489 (tt0)
REVERT: A 2463 MET cc_start: 0.8353 (mtp) cc_final: 0.7743 (mtm)
REVERT: A 2646 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7974 (tt0)
REVERT: A 2785 ASN cc_start: 0.7658 (m-40) cc_final: 0.7446 (p0)
REVERT: A 2901 GLN cc_start: 0.8641 (mt0) cc_final: 0.8144 (mp10)
REVERT: A 3011 HIS cc_start: 0.8059 (m-70) cc_final: 0.7411 (p90)
REVERT: A 3097 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7902 (pp20)
REVERT: A 3127 ASP cc_start: 0.8580 (t0) cc_final: 0.8222 (t0)
REVERT: A 3133 LYS cc_start: 0.8492 (mppt) cc_final: 0.8230 (pptt)
  outliers start: 29
  outliers final: 17
  residues processed: 165
  average time/residue: 0.7092
  time to fit residues: 127.2475
Evaluate side-chains
  162 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  935 LEU
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1084 LYS
Chi-restraints excluded: chain A residue 1138 MET
Chi-restraints excluded: chain A residue 1376 SER
Chi-restraints excluded: chain A residue 1517 GLN
Chi-restraints excluded: chain A residue 1522 LEU
Chi-restraints excluded: chain A residue 1585 LEU
Chi-restraints excluded: chain A residue 2345 ASN
Chi-restraints excluded: chain A residue 2398 CYS
Chi-restraints excluded: chain A residue 2621 MET
Chi-restraints excluded: chain A residue 2624 SER
Chi-restraints excluded: chain A residue 2646 GLU
Chi-restraints excluded: chain A residue 2784 CYS
Chi-restraints excluded: chain A residue 2830 ILE
Chi-restraints excluded: chain A residue 2951 ILE
Chi-restraints excluded: chain A residue 2964 LEU
Chi-restraints excluded: chain A residue 3091 LYS
Chi-restraints excluded: chain A residue 3099 VAL
Chi-restraints excluded: chain A residue 3132 LEU
Chi-restraints excluded: chain A residue 3179 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 169 optimal weight:    5.9990
   chunk 164 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 158 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A1247 ASN
A1354 ASN
A1517 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.106784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.074988 restraints weight = 21920.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 2.39
r_work: 0.2880 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2757 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  14234  Z= 0.141
  Angle     :  0.526  11.090  19272  Z= 0.274
  Chirality :  0.039   0.195   2233
  Planarity :  0.004   0.036   2376
  Dihedral  : 10.745 178.668   2099
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 12.27 %
    Favored  : 86.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.90 (0.21), residues: 1672
  helix:  2.29 (0.16), residues: 993
  sheet:  0.21 (0.50), residues: 89
  loop : -0.36 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A1246 
 TYR   0.026   0.001   TYR A2262 
 PHE   0.029   0.001   PHE A2633 
 TRP   0.013   0.001   TRP A2542 
 HIS   0.004   0.001   HIS A1776 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (14227)
  covalent geometry    : angle       0.51864 (19266)
  hydrogen bonds       : bond        0.04688 (  775)
  hydrogen bonds       : angle       3.77373 ( 2262)
  metal coordination   : bond        0.00521 (    7)
  metal coordination   : angle       5.01552 (    6)

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

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

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
REVERT: A  932 LYS cc_start: 0.8198 (tttt) cc_final: 0.7779 (mppt)
REVERT: A 1006 GLN cc_start: 0.8829 (mt0) cc_final: 0.8485 (tt0)
REVERT: A 1122 ARG cc_start: 0.7578 (mtt90) cc_final: 0.7341 (mtt90)
REVERT: A 1130 TYR cc_start: 0.7719 (m-10) cc_final: 0.7480 (m-10)
REVERT: A 1138 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7703 (mpp)
REVERT: A 1141 ILE cc_start: 0.7583 (mt) cc_final: 0.7196 (mm)
REVERT: A 1150 GLN cc_start: 0.8572 (tt0) cc_final: 0.7736 (mm110)
REVERT: A 1215 LYS cc_start: 0.9177 (mttt) cc_final: 0.8608 (mmpt)
REVERT: A 1246 ARG cc_start: 0.8465 (tmm-80) cc_final: 0.8124 (ttm-80)
REVERT: A 1344 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7625 (pt0)
REVERT: A 1830 MET cc_start: 0.7111 (ptt) cc_final: 0.6717 (ptt)
REVERT: A 1837 LYS cc_start: 0.8751 (tptp) cc_final: 0.8349 (mmtm)
REVERT: A 1849 LYS cc_start: 0.8682 (mtpp) cc_final: 0.8245 (mttt)
REVERT: A 2263 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8048 (pp20)
REVERT: A 2319 GLU cc_start: 0.7788 (mp0) cc_final: 0.7411 (tt0)
REVERT: A 2463 MET cc_start: 0.8353 (mtp) cc_final: 0.7766 (mtm)
REVERT: A 2646 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7905 (tt0)
REVERT: A 2785 ASN cc_start: 0.7610 (m-40) cc_final: 0.7398 (p0)
REVERT: A 2901 GLN cc_start: 0.8614 (mt0) cc_final: 0.8105 (mp10)
REVERT: A 3011 HIS cc_start: 0.8063 (m-70) cc_final: 0.7458 (p90)
REVERT: A 3097 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7885 (pp20)
REVERT: A 3127 ASP cc_start: 0.8573 (t0) cc_final: 0.8195 (t0)
  outliers start: 23
  outliers final: 16
  residues processed: 162
  average time/residue: 0.6891
  time to fit residues: 121.3913
Evaluate side-chains
  162 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 144
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  935 LEU
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1138 MET
Chi-restraints excluded: chain A residue 1376 SER
Chi-restraints excluded: chain A residue 1458 ILE
Chi-restraints excluded: chain A residue 1522 LEU
Chi-restraints excluded: chain A residue 2345 ASN
Chi-restraints excluded: chain A residue 2398 CYS
Chi-restraints excluded: chain A residue 2621 MET
Chi-restraints excluded: chain A residue 2624 SER
Chi-restraints excluded: chain A residue 2646 GLU
Chi-restraints excluded: chain A residue 2784 CYS
Chi-restraints excluded: chain A residue 2830 ILE
Chi-restraints excluded: chain A residue 2951 ILE
Chi-restraints excluded: chain A residue 2964 LEU
Chi-restraints excluded: chain A residue 3091 LYS
Chi-restraints excluded: chain A residue 3099 VAL
Chi-restraints excluded: chain A residue 3179 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 142 optimal weight:    2.9990
   chunk 154 optimal weight:    0.8980
   chunk 120 optimal weight:    3.9990
   chunk 152 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0980
   chunk 160 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 117 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A1247 ASN
A1354 ASN
A1517 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.106591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.075122 restraints weight = 22037.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3021 rms_B_bonded: 2.36
r_work: 0.2885 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2762 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.2458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  14234  Z= 0.141
  Angle     :  0.532  11.530  19272  Z= 0.276
  Chirality :  0.039   0.192   2233
  Planarity :  0.004   0.036   2376
  Dihedral  : 10.720 178.776   2099
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 12.72 %
    Favored  : 85.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.93 (0.21), residues: 1672
  helix:  2.33 (0.16), residues: 993
  sheet:  0.25 (0.50), residues: 89
  loop : -0.39 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A1246 
 TYR   0.027   0.001   TYR A2262 
 PHE   0.028   0.001   PHE A2633 
 TRP   0.013   0.001   TRP A2542 
 HIS   0.004   0.001   HIS A1776 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (14227)
  covalent geometry    : angle       0.52482 (19266)
  hydrogen bonds       : bond        0.04685 (  775)
  hydrogen bonds       : angle       3.76122 ( 2262)
  metal coordination   : bond        0.00520 (    7)
  metal coordination   : angle       4.95804 (    6)

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

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

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 143
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
REVERT: A  932 LYS cc_start: 0.8191 (tttt) cc_final: 0.7787 (mppt)
REVERT: A 1006 GLN cc_start: 0.8803 (mt0) cc_final: 0.8501 (tt0)
REVERT: A 1130 TYR cc_start: 0.7717 (m-10) cc_final: 0.7487 (m-80)
REVERT: A 1138 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7680 (mpp)
REVERT: A 1141 ILE cc_start: 0.7515 (mt) cc_final: 0.7264 (mm)
REVERT: A 1150 GLN cc_start: 0.8571 (tt0) cc_final: 0.7741 (mm110)
REVERT: A 1215 LYS cc_start: 0.9182 (mttt) cc_final: 0.8573 (mmpt)
REVERT: A 1246 ARG cc_start: 0.8497 (tmm-80) cc_final: 0.8212 (ttm-80)
REVERT: A 1344 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7654 (pt0)
REVERT: A 1830 MET cc_start: 0.7092 (ptt) cc_final: 0.6626 (ptt)
REVERT: A 1834 ASP cc_start: 0.8759 (m-30) cc_final: 0.8489 (p0)
REVERT: A 1849 LYS cc_start: 0.8669 (mtpp) cc_final: 0.8227 (mttt)
REVERT: A 2263 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8049 (pp20)
REVERT: A 2319 GLU cc_start: 0.7795 (mp0) cc_final: 0.7424 (tt0)
REVERT: A 2463 MET cc_start: 0.8352 (mtp) cc_final: 0.7661 (mtm)
REVERT: A 2646 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7930 (tt0)
REVERT: A 2785 ASN cc_start: 0.7599 (m-40) cc_final: 0.7360 (p0)
REVERT: A 2901 GLN cc_start: 0.8625 (mt0) cc_final: 0.8089 (mp10)
REVERT: A 3011 HIS cc_start: 0.8109 (m-70) cc_final: 0.7468 (p90)
REVERT: A 3097 GLU cc_start: 0.8591 (mm-30) cc_final: 0.7839 (pp20)
REVERT: A 3127 ASP cc_start: 0.8579 (t0) cc_final: 0.8192 (t0)
REVERT: A 3133 LYS cc_start: 0.8320 (mppt) cc_final: 0.8087 (pptt)
  outliers start: 24
  outliers final: 17
  residues processed: 161
  average time/residue: 0.6962
  time to fit residues: 121.7072
Evaluate side-chains
  164 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 145
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  935 LEU
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1138 MET
Chi-restraints excluded: chain A residue 1376 SER
Chi-restraints excluded: chain A residue 1491 HIS
Chi-restraints excluded: chain A residue 1522 LEU
Chi-restraints excluded: chain A residue 1585 LEU
Chi-restraints excluded: chain A residue 2345 ASN
Chi-restraints excluded: chain A residue 2398 CYS
Chi-restraints excluded: chain A residue 2621 MET
Chi-restraints excluded: chain A residue 2624 SER
Chi-restraints excluded: chain A residue 2646 GLU
Chi-restraints excluded: chain A residue 2784 CYS
Chi-restraints excluded: chain A residue 2830 ILE
Chi-restraints excluded: chain A residue 2951 ILE
Chi-restraints excluded: chain A residue 2964 LEU
Chi-restraints excluded: chain A residue 3091 LYS
Chi-restraints excluded: chain A residue 3099 VAL
Chi-restraints excluded: chain A residue 3179 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   chunk 128 optimal weight:    2.9990
   chunk 123 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 95 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 165 optimal weight:    4.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A1247 ASN
A1354 ASN
** A2252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.107946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.076623 restraints weight = 21996.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3035 rms_B_bonded: 2.36
r_work: 0.2899 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2776 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  14234  Z= 0.128
  Angle     :  0.526  12.094  19272  Z= 0.272
  Chirality :  0.038   0.180   2233
  Planarity :  0.004   0.045   2376
  Dihedral  : 10.682 178.522   2099
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 13.23 %
    Favored  : 85.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.97 (0.21), residues: 1672
  helix:  2.39 (0.16), residues: 995
  sheet:  0.26 (0.50), residues: 89
  loop : -0.42 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A1246 
 TYR   0.024   0.001   TYR A2262 
 PHE   0.028   0.001   PHE A2633 
 TRP   0.013   0.001   TRP A2542 
 HIS   0.004   0.001   HIS A1776 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (14227)
  covalent geometry    : angle       0.51937 (19266)
  hydrogen bonds       : bond        0.04390 (  775)
  hydrogen bonds       : angle       3.70519 ( 2262)
  metal coordination   : bond        0.00459 (    7)
  metal coordination   : angle       4.81778 (    6)

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

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

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
REVERT: A  932 LYS cc_start: 0.8162 (tttt) cc_final: 0.7760 (mppt)
REVERT: A 1006 GLN cc_start: 0.8757 (mt0) cc_final: 0.8462 (tt0)
REVERT: A 1122 ARG cc_start: 0.7590 (mtt90) cc_final: 0.7344 (mtt90)
REVERT: A 1130 TYR cc_start: 0.7686 (m-10) cc_final: 0.7450 (m-80)
REVERT: A 1138 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7629 (mpp)
REVERT: A 1150 GLN cc_start: 0.8530 (tt0) cc_final: 0.7712 (mm110)
REVERT: A 1215 LYS cc_start: 0.9175 (mttt) cc_final: 0.8560 (mmpt)
REVERT: A 1246 ARG cc_start: 0.8500 (tmm-80) cc_final: 0.8233 (ttm-80)
REVERT: A 1344 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7592 (pt0)
REVERT: A 1830 MET cc_start: 0.6988 (ptt) cc_final: 0.6494 (ptt)
REVERT: A 1834 ASP cc_start: 0.8741 (m-30) cc_final: 0.8490 (p0)
REVERT: A 1849 LYS cc_start: 0.8663 (mtpp) cc_final: 0.8201 (mttt)
REVERT: A 2263 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8043 (pp20)
REVERT: A 2319 GLU cc_start: 0.7743 (mp0) cc_final: 0.7355 (tt0)
REVERT: A 2463 MET cc_start: 0.8330 (mtp) cc_final: 0.7626 (mtm)
REVERT: A 2646 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7906 (tt0)
REVERT: A 2785 ASN cc_start: 0.7502 (m-40) cc_final: 0.7301 (p0)
REVERT: A 2901 GLN cc_start: 0.8623 (mt0) cc_final: 0.8130 (mp10)
REVERT: A 3011 HIS cc_start: 0.8120 (m-70) cc_final: 0.7465 (p90)
REVERT: A 3098 GLN cc_start: 0.8140 (tp40) cc_final: 0.7622 (mm110)
REVERT: A 3127 ASP cc_start: 0.8576 (t0) cc_final: 0.8188 (t0)
REVERT: A 3133 LYS cc_start: 0.8300 (mppt) cc_final: 0.8023 (pptt)
  outliers start: 20
  outliers final: 16
  residues processed: 156
  average time/residue: 0.6793
  time to fit residues: 115.5317
Evaluate side-chains
  158 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  935 LEU
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1138 MET
Chi-restraints excluded: chain A residue 1376 SER
Chi-restraints excluded: chain A residue 1491 HIS
Chi-restraints excluded: chain A residue 1522 LEU
Chi-restraints excluded: chain A residue 1585 LEU
Chi-restraints excluded: chain A residue 2345 ASN
Chi-restraints excluded: chain A residue 2398 CYS
Chi-restraints excluded: chain A residue 2621 MET
Chi-restraints excluded: chain A residue 2624 SER
Chi-restraints excluded: chain A residue 2646 GLU
Chi-restraints excluded: chain A residue 2784 CYS
Chi-restraints excluded: chain A residue 2830 ILE
Chi-restraints excluded: chain A residue 2951 ILE
Chi-restraints excluded: chain A residue 3091 LYS
Chi-restraints excluded: chain A residue 3099 VAL
Chi-restraints excluded: chain A residue 3179 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 82 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 159 optimal weight:   10.0000
   chunk 95 optimal weight:    0.8980
   chunk 47 optimal weight:    0.5980
   chunk 23 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0670
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
A1247 ASN
A1354 ASN
A1886 GLN
** A2252 GLN ** 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 = 0.3571 r_free = 0.3571 target = 0.108169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.077639 restraints weight = 22039.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 2.27
r_work: 0.2958 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  14234  Z= 0.122
  Angle     :  0.521  11.864  19272  Z= 0.269
  Chirality :  0.038   0.172   2233
  Planarity :  0.003   0.044   2376
  Dihedral  : 10.647 178.437   2099
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 13.17 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.03 (0.21), residues: 1672
  helix:  2.45 (0.16), residues: 995
  sheet:  0.31 (0.50), residues: 89
  loop : -0.44 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A1246 
 TYR   0.023   0.001   TYR A2262 
 PHE   0.027   0.001   PHE A2633 
 TRP   0.014   0.001   TRP A2542 
 HIS   0.004   0.001   HIS A1776 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (14227)
  covalent geometry    : angle       0.51418 (19266)
  hydrogen bonds       : bond        0.04229 (  775)
  hydrogen bonds       : angle       3.66493 ( 2262)
  metal coordination   : bond        0.00427 (    7)
  metal coordination   : angle       4.67501 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5880.58 seconds
wall clock time: 100 minutes 46.46 seconds (6046.46 seconds total)