Starting phenix.real_space_refine
on Fri Jul  3 09:22:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9xd5_66755/07_2026/9xd5_66755.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9xd5_66755/07_2026/9xd5_66755.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9xd5_66755/07_2026/9xd5_66755.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9xd5_66755/07_2026/9xd5_66755.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9xd5_66755/07_2026/9xd5_66755.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9xd5_66755/07_2026/9xd5_66755.map"
  }
  resolution = 2.72
  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=   0.001 sd=   0.028
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      1      6.06       5
     P      10      5.49       5
     S      91      5.16       5
     C    8059      2.51       5
     N    2221      2.21       5
     O    2428      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12810
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 12577
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1571, 12577
          Classifications: {'peptide': 1571}
          Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 1525}
          Chain breaks: 14
    Chain: "C"
      Number of atoms: 232
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 232
          Classifications: {'RNA': 11}
          Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna3p_pur': 3, 'rna3p_pyr': 4}
          Link IDs: {'rna2p': 3, 'rna3p': 7}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    816  SG  CYS A1028      53.121  17.087  88.623  1.00 59.72           S
  ATOM    835  SG  CYS A1031      56.892  17.034  89.053  1.00 93.27           S
  ATOM   1078  SG  CYS A1062      55.319  14.302  87.182  1.00 74.60           S
  ATOM   1098  SG  CYS A1065      55.188  17.484  85.456  1.00 83.14           S

  Time building chain proxies: 2.75, per 1000 atoms: 0.21
  Number of scatterers: 12810
  At special positions: 0
  Unit cell: (96.36, 104.244, 127.02, 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      1     29.99
     S      91     16.00
     P      10     15.00
     O    2428      8.00
     N    2221      7.00
     C    8059      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: 1.17
  Conformation dependent library (CDL) restraints added in 590.6 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A4001 "
        pdb="ZN    ZN A4001 " - pdb=" SG  CYS A1062 "
        pdb="ZN    ZN A4001 " - pdb=" SG  CYS A1028 "
        pdb="ZN    ZN A4001 " - pdb=" SG  CYS A1031 "
        pdb="ZN    ZN A4001 " - pdb=" SG  CYS A1065 "
      Number of angles added : 6


  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3010

  Finding SS restraints...
    Secondary structure from input PDB file:
      83 helices and 11 sheets defined
      61.8% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 930 through 941
      removed outlier: 3.503A  pdb=" N   VAL A 934 " --> pdb=" O   SER A 930 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 942 through 947
      removed outlier: 3.559A  pdb=" N   ASN A 947 " --> pdb=" O   GLU A 943 " (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 1006 through 1024
      removed outlier: 3.574A  pdb=" N   THR A1010 " --> pdb=" O   GLN A1006 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   SER A1011 " --> pdb=" O   ASN A1007 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1029 through 1041
      removed outlier: 3.578A  pdb=" N   LYS A1036 " --> pdb=" O   LEU A1032 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1044 through 1056
    Processing helix  chain 'A' and resid 1084 through 1088
      removed outlier: 3.532A  pdb=" N   VAL A1088 " --> pdb=" O   ILE A1085 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1104 through 1111
    Processing helix  chain 'A' and resid 1118 through 1140
      removed outlier: 3.569A  pdb=" N   MET A1138 " --> pdb=" O   LEU A1134 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   GLY A1140 " --> pdb=" O   MET A1136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1170 through 1182
      removed outlier: 4.372A  pdb=" N   ALA A1177 " --> pdb=" O   ASP A1173 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   GLU A1178 " --> pdb=" O   GLN A1174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1182 through 1187
    Processing helix  chain 'A' and resid 1191 through 1196
      removed outlier: 3.743A  pdb=" N   SER A1196 " --> pdb=" O   LYS A1193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1199 through 1204
      removed outlier: 3.545A  pdb=" N   SER A1204 " --> pdb=" O   ARG A1200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1221 through 1232
    Processing helix  chain 'A' and resid 1237 through 1254
      removed outlier: 3.849A  pdb=" N   VAL A1241 " --> pdb=" O   LYS A1237 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU A1242 " --> pdb=" O   ASP A1238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1266 through 1281
      removed outlier: 3.524A  pdb=" N   LEU A1270 " --> pdb=" O   SER A1266 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLN A1277 " --> pdb=" O   CYS A1273 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   PHE A1279 " --> pdb=" O   ASP A1275 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   LYS A1280 " --> pdb=" O   VAL A1276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1291 through 1296
      removed outlier: 3.791A  pdb=" N   ILE A1295 " --> pdb=" O   GLN A1291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1297 through 1307
    Processing helix  chain 'A' and resid 1315 through 1328
    Processing helix  chain 'A' and resid 1330 through 1352
    Processing helix  chain 'A' and resid 1401 through 1409
      removed outlier: 3.891A  pdb=" N   LEU A1407 " --> pdb=" O   ARG A1403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1410 through 1426
      removed outlier: 3.928A  pdb=" N   GLN A1424 " --> pdb=" O   ILE A1420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1429 through 1434
      removed outlier: 3.804A  pdb=" N   ASN A1433 " --> pdb=" O   GLU A1430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1436 through 1463
    Processing helix  chain 'A' and resid 1465 through 1481
      removed outlier: 3.762A  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 1512
    Processing helix  chain 'A' and resid 1515 through 1524
      removed outlier: 3.532A  pdb=" N   MET A1524 " --> pdb=" O   LYS A1520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1524 through 1530
    Processing helix  chain 'A' and resid 1531 through 1534
    Processing helix  chain 'A' and resid 1538 through 1543
    Processing helix  chain 'A' and resid 1544 through 1547
      removed outlier: 3.515A  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 1570
    Processing helix  chain 'A' and resid 1572 through 1581
      removed outlier: 3.939A  pdb=" N   LYS A1581 " --> pdb=" O   VAL A1577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1605 through 1612
    Processing helix  chain 'A' and resid 1613 through 1616
      removed outlier: 3.557A  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 1629 through 1645
    Processing helix  chain 'A' and resid 1661 through 1666
    Processing helix  chain 'A' and resid 1758 through 1772
    Processing helix  chain 'A' and resid 1780 through 1792
      removed outlier: 3.566A  pdb=" N   GLU A1789 " --> pdb=" O   GLN A1785 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1796 through 1806
    Processing helix  chain 'A' and resid 1838 through 1852
    Processing helix  chain 'A' and resid 2295 through 2305
    Processing helix  chain 'A' and resid 2316 through 2335
    Processing helix  chain 'A' and resid 2367 through 2379
      removed outlier: 3.712A  pdb=" N   GLN A2377 " --> pdb=" O   GLY A2373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2382 through 2397
    Processing helix  chain 'A' and resid 2404 through 2419
      removed outlier: 3.568A  pdb=" N   LEU A2415 " --> pdb=" O   ILE A2411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2429 through 2434
    Processing helix  chain 'A' and resid 2435 through 2440
      removed outlier: 3.775A  pdb=" N   ASP A2439 " --> pdb=" O   ARG A2435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2441 through 2445
      removed outlier: 3.697A  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: 4.033A  pdb=" N   VAL A2489 " --> pdb=" O   SER A2485 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   LEU A2490 " --> pdb=" O   LEU A2486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2530 through 2540
      removed outlier: 3.536A  pdb=" N   THR A2540 " --> pdb=" O   GLN A2536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2540 through 2558
      removed outlier: 3.596A  pdb=" N   HIS A2544 " --> pdb=" O   THR A2540 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   CYS A2558 " --> pdb=" O   ALA A2554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2589 through 2594
      removed outlier: 3.658A  pdb=" N   MET A2594 " --> pdb=" O   ILE A2591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2595 through 2600
      removed outlier: 3.584A  pdb=" N   ILE A2599 " --> pdb=" O   PHE A2595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2607 through 2623
    Processing helix  chain 'A' and resid 2626 through 2645
      removed outlier: 3.693A  pdb=" N   PHE A2641 " --> pdb=" O   ARG A2637 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   HIS A2644 " --> pdb=" O   ILE A2640 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   VAL A2645 " --> pdb=" O   PHE A2641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2645 through 2652
    Processing helix  chain 'A' and resid 2652 through 2657
      removed outlier: 3.859A  pdb=" N   THR A2656 " --> pdb=" O   TYR A2652 " (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
    Processing helix  chain 'A' and resid 2671 through 2675
      removed outlier: 3.887A  pdb=" N   VAL A2675 " --> 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 2816
    Processing helix  chain 'A' and resid 2818 through 2836
    Processing helix  chain 'A' and resid 2899 through 2910
      removed outlier: 3.540A  pdb=" N   LYS A2906 " --> pdb=" O   LEU A2902 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2950 through 2954
    Processing helix  chain 'A' and resid 2993 through 3003
    Processing helix  chain 'A' and resid 3043 through 3060
      removed outlier: 3.672A  pdb=" N   ASN A3057 " --> pdb=" O   PHE A3053 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3062 through 3073
    Processing helix  chain 'A' and resid 3094 through 3100
      removed outlier: 3.679A  pdb=" N   GLN A3098 " --> pdb=" O   SER A3094 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3104 through 3112
      removed outlier: 3.964A  pdb=" N   LEU A3112 " --> pdb=" O   VAL A3108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3116 through 3120
      removed outlier: 3.624A  pdb=" N   SER A3119 " --> pdb=" O   SER A3116 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   GLU A3120 " --> pdb=" O   ALA A3117 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 3116 through 3120'
    Processing helix  chain 'A' and resid 3130 through 3141
      removed outlier: 3.538A  pdb=" N   GLN A3140 " --> pdb=" O   PHE A3136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3142 through 3157
      removed outlier: 3.596A  pdb=" N   PHE A3146 " --> pdb=" O   PHE A3142 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   SER A3157 " --> pdb=" O   THR A3153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3169 through 3185
      removed outlier: 3.545A  pdb=" N   ARG A3173 " --> pdb=" O   GLN A3169 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   ASN A3176 " --> pdb=" O   ALA A3172 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   MET A3184 " --> pdb=" O   LEU A3180 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ILE A3185 " --> pdb=" O   LEU A3181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3208 through 3217
      removed outlier: 3.704A  pdb=" N   LEU A3212 " --> pdb=" O   THR A3208 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   VAL A3213 " --> pdb=" O   VAL A3209 " (cutoff:3.500A)
      removed outlier: 3.706A  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: 6.929A  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: 3.948A  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: 4.176A  pdb=" N   LEU A1383 " --> pdb=" O   LYS A1373 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   LEU A1386 " --> pdb=" O   GLY A1396 " (cutoff:3.500A)
      removed outlier: 5.469A  pdb=" N   GLY A1396 " --> pdb=" O   LEU A1386 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 2507 through 2511
    Processing sheet with id=AA6, first strand: chain 'A' and resid 2399 through 2400
      removed outlier: 3.508A  pdb=" N   ARG A2399 " --> pdb=" O   SER A2467 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 2574 through 2576
      removed outlier: 4.412A  pdb=" N   PHE A2580 " --> pdb=" O   THR A2587 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 2958 through 2960
      removed outlier: 3.660A  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: 6.246A  pdb=" N   SER A3005 " --> pdb=" O   LEU A3039 " (cutoff:3.500A)
      removed outlier: 7.494A  pdb=" N   VAL A3041 " --> pdb=" O   SER A3005 " (cutoff:3.500A)
      removed outlier: 6.796A  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: 3.912A  pdb=" N   SER A3078 " --> pdb=" O   ARG A3224 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 3086 through 3089

    653 hydrogen bonds defined for protein.
    1884 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.56

  Time building geometry restraints manager: 1.50 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: 4017
        1.34 -     1.46: 1919
        1.46 -     1.58: 6951
        1.58 -     1.69: 20
        1.69 -     1.81: 132
  Bond restraints: 13039
  Sorted by residual:
  bond pdb=" N9    A C   5 "
       pdb=" C4    A C   5 "
    ideal  model  delta    sigma   weight residual
    1.374  1.393 -0.019 6.00e-03 2.78e+04 1.01e+01
  bond pdb=" C8    A C   5 "
       pdb=" N7    A C   5 "
    ideal  model  delta    sigma   weight residual
    1.311  1.301  0.010 7.00e-03 2.04e+04 1.93e+00
  bond pdb=" C   VAL A1288 "
       pdb=" N   PRO A1289 "
    ideal  model  delta    sigma   weight residual
    1.334  1.366 -0.032 2.34e-02 1.83e+03 1.83e+00
  bond pdb=" N7    A C   5 "
       pdb=" C5    A C   5 "
    ideal  model  delta    sigma   weight residual
    1.388  1.381  0.007 6.00e-03 2.78e+04 1.28e+00
  bond pdb=" CG  LEU A2391 "
       pdb=" CD1 LEU A2391 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.035 3.30e-02 9.18e+02 1.14e+00
  ... (remaining 13034 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 17438
        2.38 -     4.75: 157
        4.75 -     7.13: 17
        7.13 -     9.50: 2
        9.50 -    11.88: 2
  Bond angle restraints: 17616
  Sorted by residual:
  angle pdb=" C2    A C   5 "
        pdb=" N3    A C   5 "
        pdb=" C4    A C   5 "
      ideal   model   delta    sigma   weight residual
     110.60  112.80   -2.20 5.00e-01 4.00e+00 1.93e+01
  angle pdb=" N9    A C   5 "
        pdb=" C4    A C   5 "
        pdb=" N3    A C   5 "
      ideal   model   delta    sigma   weight residual
     127.40  130.45   -3.05 8.00e-01 1.56e+00 1.45e+01
  angle pdb=" C5    A C   5 "
        pdb=" C4    A C   5 "
        pdb=" N3    A C   5 "
      ideal   model   delta    sigma   weight residual
     126.80  124.39    2.41 7.00e-01 2.04e+00 1.18e+01
  angle pdb=" CA  LEU A1056 "
        pdb=" CB  LEU A1056 "
        pdb=" CG  LEU A1056 "
      ideal   model   delta    sigma   weight residual
     116.30  128.18  -11.88 3.50e+00 8.16e-02 1.15e+01
  angle pdb=" C1'   A C   5 "
        pdb=" N9    A C   5 "
        pdb=" C4    A C   5 "
      ideal   model   delta    sigma   weight residual
     126.30  132.26   -5.96 1.80e+00 3.09e-01 1.10e+01
  ... (remaining 17611 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 7443
       17.90 -    35.79: 482
       35.79 -    53.69: 62
       53.69 -    71.59: 12
       71.59 -    89.49: 5
  Dihedral angle restraints: 8004
    sinusoidal: 3391
      harmonic: 4613
  Sorted by residual:
  dihedral pdb=" CA  ARG A1027 "
           pdb=" C   ARG A1027 "
           pdb=" N   CYS A1028 "
           pdb=" CA  CYS A1028 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.07  -20.93     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" CA  LEU A1644 "
           pdb=" C   LEU A1644 "
           pdb=" N   ASP A1645 "
           pdb=" CA  ASP A1645 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.98   20.02     0      5.00e+00 4.00e-02 1.60e+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 -160.77  -19.23     0      5.00e+00 4.00e-02 1.48e+01
  ... (remaining 8001 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1438
       0.041 -    0.082: 493
       0.082 -    0.123: 90
       0.123 -    0.164: 15
       0.164 -    0.206: 1
  Chirality restraints: 2037
  Sorted by residual:
  chirality pdb=" CG  LEU A1056 "
            pdb=" CB  LEU A1056 "
            pdb=" CD1 LEU A1056 "
            pdb=" CD2 LEU A1056 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.80    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  PHE A2633 "
            pdb=" N   PHE A2633 "
            pdb=" C   PHE A2633 "
            pdb=" CB  PHE A2633 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.97e-01
  chirality pdb=" CA  ILE A2403 "
            pdb=" N   ILE A2403 "
            pdb=" C   ILE A2403 "
            pdb=" CB  ILE A2403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.21e-01
  ... (remaining 2034 not shown)

  Planarity restraints: 2189
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A2633 "    0.020 2.00e-02 2.50e+03   2.01e-02 7.05e+00
        pdb=" CG  PHE A2633 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 PHE A2633 "    0.013 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 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE A2633 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A3049 "    0.015 2.00e-02 2.50e+03   1.55e-02 4.18e+00
        pdb=" CG  PHE A3049 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 PHE A3049 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE A3049 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE A3049 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A3049 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE A3049 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A1311 "    0.033 5.00e-02 4.00e+02   4.92e-02 3.88e+00
        pdb=" N   PRO A1312 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A1312 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A1312 "    0.027 5.00e-02 4.00e+02
  ... (remaining 2186 not shown)

  Histogram of nonbonded interaction distances:
        2.59 -     3.05: 7848
        3.05 -     3.52: 13210
        3.52 -     3.98: 20696
        3.98 -     4.44: 25517
        4.44 -     4.90: 38356
  Nonbonded interactions: 105627
  Sorted by model distance:
  nonbonded pdb=" O4'   C C   2 "
            pdb=" C6    C C   2 "
     model   vdw
     2.593 2.672
  nonbonded pdb=" N1    G C   8 "
            pdb=" C4    G C   8 "
     model   vdw
     2.604 2.672
  nonbonded pdb=" N   GLY A2337 "
            pdb=" N   LYS A2338 "
     model   vdw
     2.609 2.560
  nonbonded pdb=" N   ILE A1616 "
            pdb=" N   TYR A1617 "
     model   vdw
     2.618 2.560
  nonbonded pdb=" N   THR A1660 "
            pdb=" N   ALA A1661 "
     model   vdw
     2.638 2.560
  ... (remaining 105622 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:             1.870
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     14.610
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
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   0.035  13043  Z= 0.164
  Angle     :  0.597  11.881  17622  Z= 0.317
  Chirality :  0.042   0.206   2037
  Planarity :  0.005   0.049   2189
  Dihedral  : 11.820  89.486   4994
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.07 %
    Favored  : 99.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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: -0.53 (0.21), residues: 1541
  helix:  0.26 (0.17), residues: 879
  sheet:  0.54 (0.72), residues: 69
  loop : -1.31 (0.25), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1184 
 TYR   0.014   0.001   TYR A2994 
 PHE   0.046   0.002   PHE A2633 
 TRP   0.014   0.001   TRP A2542 
 HIS   0.005   0.001   HIS A1491 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.16 (13039)
  covalent geometry    : angle       0.58935 /  0.32 (17616)
  hydrogen bonds       : bond        0.13902 /  8.97 (  653)
  hydrogen bonds       : angle       5.50710 /  3.89 ( 1884)
  metal coordination   : bond        0.00943 /  0.39 (    4)
  metal coordination   : angle       5.22355 /  2.63 (    6)

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

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

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  393 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 393
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  943 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7633 (mm-30)
REVERT: A  975 GLU cc_start: 0.7630 (pt0) cc_final: 0.7403 (pt0)
REVERT: A  982 ASN cc_start: 0.7907 (m-40) cc_final: 0.7620 (m-40)
REVERT: A 1031 CYS cc_start: 0.7340 (m) cc_final: 0.7093 (m)
REVERT: A 1084 LYS cc_start: 0.8482 (mtpt) cc_final: 0.8105 (mtpt)
REVERT: A 1245 ILE cc_start: 0.7984 (pt) cc_final: 0.7743 (mt)
REVERT: A 1277 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7216 (mp10)
REVERT: A 1282 LYS cc_start: 0.8876 (mttt) cc_final: 0.8655 (mttm)
REVERT: A 1379 LYS cc_start: 0.8328 (mttt) cc_final: 0.8108 (mttt)
REVERT: A 1434 SER cc_start: 0.8324 (p) cc_final: 0.7977 (t)
REVERT: A 1448 MET cc_start: 0.8575 (mmt) cc_final: 0.8108 (mpp)
REVERT: A 1452 GLU cc_start: 0.7337 (mt-10) cc_final: 0.7112 (mp0)
REVERT: A 1509 ASP cc_start: 0.8091 (m-30) cc_final: 0.7849 (m-30)
REVERT: A 1519 ASN cc_start: 0.8258 (t0) cc_final: 0.7988 (t0)
REVERT: A 1524 MET cc_start: 0.8398 (mmt) cc_final: 0.8173 (mmm)
REVERT: A 1534 SER cc_start: 0.8727 (t) cc_final: 0.8504 (p)
REVERT: A 1634 GLU cc_start: 0.7724 (tp30) cc_final: 0.7361 (tp30)
REVERT: A 1647 MET cc_start: 0.8166 (ttt) cc_final: 0.7947 (ttm)
REVERT: A 1669 ASN cc_start: 0.8348 (t0) cc_final: 0.8109 (t0)
REVERT: A 1789 GLU cc_start: 0.7861 (tp30) cc_final: 0.7527 (tp30)
REVERT: A 1850 MET cc_start: 0.6247 (mtt) cc_final: 0.5760 (mtt)
REVERT: A 2298 MET cc_start: 0.8008 (ttp) cc_final: 0.7728 (tpp)
REVERT: A 2319 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6990 (mt-10)
REVERT: A 2345 ASN cc_start: 0.8119 (t0) cc_final: 0.7783 (t0)
REVERT: A 2438 THR cc_start: 0.7587 (m) cc_final: 0.7238 (p)
REVERT: A 2459 SER cc_start: 0.8527 (p) cc_final: 0.8280 (m)
REVERT: A 2460 LYS cc_start: 0.8519 (mttt) cc_final: 0.8252 (mttp)
REVERT: A 2493 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7155 (tp30)
REVERT: A 2501 ARG cc_start: 0.8205 (ttp-170) cc_final: 0.8004 (tmm160)
REVERT: A 2538 ASP cc_start: 0.8181 (t0) cc_final: 0.7922 (t0)
REVERT: A 2581 MET cc_start: 0.7874 (tmm) cc_final: 0.7391 (tmm)
REVERT: A 2641 PHE cc_start: 0.8238 (m-80) cc_final: 0.7992 (m-80)
REVERT: A 2663 PHE cc_start: 0.8879 (m-80) cc_final: 0.8653 (m-80)
REVERT: A 2683 ASP cc_start: 0.7612 (m-30) cc_final: 0.7399 (m-30)
REVERT: A 2788 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6959 (mm-30)
REVERT: A 2835 TYR cc_start: 0.8069 (m-80) cc_final: 0.7675 (m-80)
REVERT: A 2993 LYS cc_start: 0.7545 (mttt) cc_final: 0.6989 (mttp)
REVERT: A 3025 ARG cc_start: 0.8028 (mtt180) cc_final: 0.7811 (mpp80)
REVERT: A 3037 ARG cc_start: 0.7945 (mtm180) cc_final: 0.7604 (ttm110)
REVERT: A 3041 VAL cc_start: 0.8196 (t) cc_final: 0.7904 (m)
REVERT: A 3077 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7697 (mt-10)
REVERT: A 3089 LYS cc_start: 0.8382 (ttmt) cc_final: 0.8177 (ttmt)
REVERT: A 3226 SER cc_start: 0.8516 (t) cc_final: 0.8292 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 393
  average time/residue: 0.6001
  time to fit residues: 256.7101
Evaluate side-chains
  319 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 319
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 98 optimal weight:    0.5980
   chunk 107 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0980
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 149 optimal weight:    3.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1006 GLN
A1044 ASN
** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1247 ASN
A1325 ASN
A1424 GLN
A2359 ASN
A2477 HIS
A2505 GLN
A2644 HIS
** A3177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.147076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.126306 restraints weight = 17105.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3656 rms_B_bonded: 1.86
r_work: 0.3552 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3408 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.1386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13043  Z= 0.140
  Angle     :  0.535   9.653  17622  Z= 0.276
  Chirality :  0.040   0.158   2037
  Planarity :  0.004   0.044   2189
  Dihedral  :  7.206  73.270   1840
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 10.02 %
    Favored  : 87.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.12 (0.22), residues: 1541
  helix:  0.94 (0.18), residues: 881
  sheet:  0.51 (0.71), residues: 69
  loop : -1.28 (0.25), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A2418 
 TYR   0.013   0.001   TYR A2994 
 PHE   0.033   0.002   PHE A2633 
 TRP   0.015   0.001   TRP A2542 
 HIS   0.006   0.001   HIS A2477 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.14 (13039)
  covalent geometry    : angle       0.53179 /  0.28 (17616)
  hydrogen bonds       : bond        0.04373 /  2.83 (  653)
  hydrogen bonds       : angle       4.40564 /  3.17 ( 1884)
  metal coordination   : bond        0.00704 /  0.30 (    4)
  metal coordination   : angle       3.41249 /  1.66 (    6)

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

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

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  351 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 320
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  968 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7737 (mp0)
REVERT: A  975 GLU cc_start: 0.7603 (pt0) cc_final: 0.7399 (pt0)
REVERT: A  982 ASN cc_start: 0.7970 (m-40) cc_final: 0.7746 (m-40)
REVERT: A  999 LYS cc_start: 0.8669 (pttp) cc_final: 0.8360 (pttp)
REVERT: A 1031 CYS cc_start: 0.7373 (m) cc_final: 0.7155 (m)
REVERT: A 1037 LYS cc_start: 0.7996 (tttt) cc_final: 0.7765 (tttt)
REVERT: A 1084 LYS cc_start: 0.8160 (mtpt) cc_final: 0.7844 (mtpt)
REVERT: A 1272 LYS cc_start: 0.8032 (mtpp) cc_final: 0.7809 (mttp)
REVERT: A 1277 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7123 (mp10)
REVERT: A 1348 ARG cc_start: 0.8031 (ttm-80) cc_final: 0.7554 (ttm-80)
REVERT: A 1379 LYS cc_start: 0.8267 (mttt) cc_final: 0.8062 (mttt)
REVERT: A 1434 SER cc_start: 0.8234 (p) cc_final: 0.7922 (t)
REVERT: A 1509 ASP cc_start: 0.7897 (m-30) cc_final: 0.7657 (m-30)
REVERT: A 1519 ASN cc_start: 0.8195 (t0) cc_final: 0.7937 (t0)
REVERT: A 1534 SER cc_start: 0.8642 (t) cc_final: 0.8305 (p)
REVERT: A 1541 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7576 (mp0)
REVERT: A 1634 GLU cc_start: 0.7681 (tp30) cc_final: 0.7431 (tp30)
REVERT: A 1647 MET cc_start: 0.8262 (ttt) cc_final: 0.8036 (ttp)
REVERT: A 1669 ASN cc_start: 0.8317 (t0) cc_final: 0.8091 (t0)
REVERT: A 1789 GLU cc_start: 0.7759 (tp30) cc_final: 0.7367 (tp30)
REVERT: A 1850 MET cc_start: 0.6218 (mtt) cc_final: 0.5755 (mtt)
REVERT: A 2298 MET cc_start: 0.8128 (ttp) cc_final: 0.7900 (tpp)
REVERT: A 2319 GLU cc_start: 0.7292 (mt-10) cc_final: 0.7091 (mt-10)
REVERT: A 2345 ASN cc_start: 0.8151 (t0) cc_final: 0.7827 (t0)
REVERT: A 2438 THR cc_start: 0.7584 (m) cc_final: 0.7270 (p)
REVERT: A 2459 SER cc_start: 0.8534 (p) cc_final: 0.8285 (m)
REVERT: A 2460 LYS cc_start: 0.8496 (mttt) cc_final: 0.8256 (mttp)
REVERT: A 2493 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7153 (tp30)
REVERT: A 2538 ASP cc_start: 0.8119 (t0) cc_final: 0.7864 (t0)
REVERT: A 2581 MET cc_start: 0.7867 (tmm) cc_final: 0.7309 (tmm)
REVERT: A 2610 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7763 (ttp)
REVERT: A 2641 PHE cc_start: 0.8171 (m-80) cc_final: 0.7948 (m-80)
REVERT: A 2683 ASP cc_start: 0.7589 (m-30) cc_final: 0.7376 (m-30)
REVERT: A 2788 GLU cc_start: 0.7279 (mm-30) cc_final: 0.7037 (mm-30)
REVERT: A 2835 TYR cc_start: 0.8003 (m-80) cc_final: 0.7723 (m-80)
REVERT: A 2993 LYS cc_start: 0.7422 (mttt) cc_final: 0.6913 (mtmm)
REVERT: A 3037 ARG cc_start: 0.8010 (mtm180) cc_final: 0.7582 (ttm110)
REVERT: A 3203 MET cc_start: 0.6424 (mpp) cc_final: 0.6108 (mpp)
  outliers start: 31
  outliers final: 13
  residues processed: 329
  average time/residue: 0.6327
  time to fit residues: 225.6427
Evaluate side-chains
  314 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 300
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  971 VAL
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1041 GLU
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1113 THR
Chi-restraints excluded: chain A residue 1361 VAL
Chi-restraints excluded: chain A residue 1393 LEU
Chi-restraints excluded: chain A residue 1400 LEU
Chi-restraints excluded: chain A residue 2391 LEU
Chi-restraints excluded: chain A residue 2579 GLU
Chi-restraints excluded: chain A residue 2610 MET
Chi-restraints excluded: chain A residue 2766 LEU
Chi-restraints excluded: chain A residue 3006 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 98 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   chunk 100 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 117 optimal weight:    2.9990
   chunk 149 optimal weight:    0.8980
   chunk 76 optimal weight:    0.6980
   chunk 97 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0050
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.6594

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1044 ASN
** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1424 GLN
A2366 HIS
A2477 HIS
A2505 GLN
A2644 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.146091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.125324 restraints weight = 17376.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 1.88
r_work: 0.3545 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3401 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13043  Z= 0.145
  Angle     :  0.509   6.876  17622  Z= 0.265
  Chirality :  0.039   0.160   2037
  Planarity :  0.004   0.043   2189
  Dihedral  :  7.167  73.277   1840
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 13.61 %
    Favored  : 84.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.34 (0.22), residues: 1541
  helix:  1.18 (0.18), residues: 880
  sheet:  0.50 (0.63), residues: 81
  loop : -1.30 (0.25), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1403 
 TYR   0.013   0.001   TYR A1313 
 PHE   0.033   0.001   PHE A2633 
 TRP   0.015   0.001   TRP A2542 
 HIS   0.006   0.001   HIS A2477 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.15 (13039)
  covalent geometry    : angle       0.50599 /  0.26 (17616)
  hydrogen bonds       : bond        0.04037 /  2.61 (  653)
  hydrogen bonds       : angle       4.22109 /  3.05 ( 1884)
  metal coordination   : bond        0.00714 /  0.31 (    4)
  metal coordination   : angle       3.13019 /  1.46 (    6)

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

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

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 301
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  932 LYS cc_start: 0.7826 (mppt) cc_final: 0.7617 (mppt)
REVERT: A  968 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7796 (mp0)
REVERT: A  975 GLU cc_start: 0.7617 (pt0) cc_final: 0.7395 (pt0)
REVERT: A  982 ASN cc_start: 0.8058 (m-40) cc_final: 0.7854 (m-40)
REVERT: A  999 LYS cc_start: 0.8661 (pttp) cc_final: 0.8381 (pttp)
REVERT: A 1031 CYS cc_start: 0.7310 (m) cc_final: 0.7080 (m)
REVERT: A 1037 LYS cc_start: 0.7997 (tttt) cc_final: 0.7771 (tttt)
REVERT: A 1084 LYS cc_start: 0.8157 (mtpt) cc_final: 0.7877 (mtpt)
REVERT: A 1272 LYS cc_start: 0.7972 (mtpp) cc_final: 0.7761 (mttp)
REVERT: A 1277 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7189 (mp10)
REVERT: A 1348 ARG cc_start: 0.8009 (ttm-80) cc_final: 0.7550 (ttm-80)
REVERT: A 1379 LYS cc_start: 0.8241 (mttt) cc_final: 0.8040 (mttt)
REVERT: A 1434 SER cc_start: 0.8222 (p) cc_final: 0.7922 (t)
REVERT: A 1448 MET cc_start: 0.8461 (mpp) cc_final: 0.7883 (mmt)
REVERT: A 1452 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7244 (mp0)
REVERT: A 1519 ASN cc_start: 0.8210 (t0) cc_final: 0.7936 (t0)
REVERT: A 1534 SER cc_start: 0.8640 (t) cc_final: 0.8324 (p)
REVERT: A 1541 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7602 (mp0)
REVERT: A 1633 GLU cc_start: 0.7744 (tp30) cc_final: 0.7444 (tp30)
REVERT: A 1634 GLU cc_start: 0.7667 (tp30) cc_final: 0.7382 (tp30)
REVERT: A 1647 MET cc_start: 0.8319 (ttt) cc_final: 0.8101 (ttp)
REVERT: A 1789 GLU cc_start: 0.7809 (tp30) cc_final: 0.7390 (tp30)
REVERT: A 1850 MET cc_start: 0.6285 (mtt) cc_final: 0.5839 (mtt)
REVERT: A 2298 MET cc_start: 0.8128 (ttp) cc_final: 0.7875 (tpp)
REVERT: A 2345 ASN cc_start: 0.8157 (t0) cc_final: 0.7893 (t0)
REVERT: A 2438 THR cc_start: 0.7554 (m) cc_final: 0.7224 (p)
REVERT: A 2459 SER cc_start: 0.8531 (p) cc_final: 0.8300 (m)
REVERT: A 2460 LYS cc_start: 0.8510 (mttt) cc_final: 0.8270 (mttp)
REVERT: A 2493 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7230 (tp30)
REVERT: A 2538 ASP cc_start: 0.8148 (t0) cc_final: 0.7898 (t0)
REVERT: A 2581 MET cc_start: 0.7882 (tmm) cc_final: 0.7262 (tmm)
REVERT: A 2622 TYR cc_start: 0.8384 (m-10) cc_final: 0.8170 (m-10)
REVERT: A 2683 ASP cc_start: 0.7637 (m-30) cc_final: 0.7432 (m-30)
REVERT: A 2760 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.8031 (mt)
REVERT: A 2788 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7004 (mm-30)
REVERT: A 2835 TYR cc_start: 0.8054 (m-80) cc_final: 0.7802 (m-80)
REVERT: A 2993 LYS cc_start: 0.7411 (mttt) cc_final: 0.6960 (mttp)
REVERT: A 3037 ARG cc_start: 0.8007 (mtm180) cc_final: 0.7580 (ttm110)
REVERT: A 3108 VAL cc_start: 0.8062 (m) cc_final: 0.7842 (p)
REVERT: A 3203 MET cc_start: 0.6499 (mpp) cc_final: 0.6177 (mpp)
  outliers start: 30
  outliers final: 15
  residues processed: 311
  average time/residue: 0.6699
  time to fit residues: 225.2411
Evaluate side-chains
  306 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 290
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  971 VAL
Chi-restraints excluded: chain A residue 1041 GLU
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1113 THR
Chi-restraints excluded: chain A residue 1241 VAL
Chi-restraints excluded: chain A residue 1378 LYS
Chi-restraints excluded: chain A residue 1393 LEU
Chi-restraints excluded: chain A residue 1400 LEU
Chi-restraints excluded: chain A residue 2391 LEU
Chi-restraints excluded: chain A residue 2475 ILE
Chi-restraints excluded: chain A residue 2579 GLU
Chi-restraints excluded: chain A residue 2760 ILE
Chi-restraints excluded: chain A residue 3006 VAL
Chi-restraints excluded: chain A residue 3091 LYS
Chi-restraints excluded: chain A residue 3138 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 53 optimal weight:    0.0000
   chunk 27 optimal weight:    0.0770
   chunk 136 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 81 optimal weight:    0.3980
   chunk 50 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   overall best weight:    0.4544

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2366 HIS
A2644 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.146489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.125879 restraints weight = 17294.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 1.87
r_work: 0.3554 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3412 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13043  Z= 0.117
  Angle     :  0.483   5.706  17622  Z= 0.251
  Chirality :  0.039   0.159   2037
  Planarity :  0.004   0.043   2189
  Dihedral  :  7.047  73.319   1840
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 13.27 %
    Favored  : 84.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.54 (0.22), residues: 1541
  helix:  1.38 (0.18), residues: 881
  sheet:  0.52 (0.64), residues: 79
  loop : -1.28 (0.25), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1403 
 TYR   0.014   0.001   TYR A2994 
 PHE   0.031   0.001   PHE A2633 
 TRP   0.015   0.001   TRP A2542 
 HIS   0.003   0.001   HIS A2794 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.12 (13039)
  covalent geometry    : angle       0.48051 /  0.25 (17616)
  hydrogen bonds       : bond        0.03673 /  2.39 (  653)
  hydrogen bonds       : angle       4.07729 /  2.94 ( 1884)
  metal coordination   : bond        0.00586 /  0.25 (    4)
  metal coordination   : angle       2.58469 /  1.18 (    6)

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

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

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 301
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  968 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7770 (mp0)
REVERT: A  975 GLU cc_start: 0.7617 (pt0) cc_final: 0.7394 (pt0)
REVERT: A  999 LYS cc_start: 0.8657 (pttp) cc_final: 0.8361 (pttp)
REVERT: A 1272 LYS cc_start: 0.7954 (mtpp) cc_final: 0.7751 (mttp)
REVERT: A 1277 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7133 (mm-40)
REVERT: A 1348 ARG cc_start: 0.8007 (ttm-80) cc_final: 0.7556 (ttm-80)
REVERT: A 1434 SER cc_start: 0.8175 (p) cc_final: 0.7878 (t)
REVERT: A 1448 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7893 (mmp)
REVERT: A 1452 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7217 (mp0)
REVERT: A 1519 ASN cc_start: 0.8124 (t0) cc_final: 0.7879 (t0)
REVERT: A 1534 SER cc_start: 0.8624 (t) cc_final: 0.8298 (p)
REVERT: A 1541 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7607 (mp0)
REVERT: A 1633 GLU cc_start: 0.7881 (tp30) cc_final: 0.7601 (tp30)
REVERT: A 1634 GLU cc_start: 0.7731 (tp30) cc_final: 0.7443 (tp30)
REVERT: A 1647 MET cc_start: 0.8323 (ttt) cc_final: 0.8083 (ttp)
REVERT: A 1669 ASN cc_start: 0.8314 (t0) cc_final: 0.8095 (t0)
REVERT: A 1789 GLU cc_start: 0.7753 (tp30) cc_final: 0.7338 (tp30)
REVERT: A 1850 MET cc_start: 0.6297 (mtt) cc_final: 0.5948 (mtt)
REVERT: A 2298 MET cc_start: 0.8136 (ttp) cc_final: 0.7894 (tpp)
REVERT: A 2338 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8050 (mmtp)
REVERT: A 2345 ASN cc_start: 0.8150 (t0) cc_final: 0.7823 (t0)
REVERT: A 2418 ARG cc_start: 0.8514 (ttt90) cc_final: 0.8243 (tpp80)
REVERT: A 2438 THR cc_start: 0.7561 (m) cc_final: 0.7233 (p)
REVERT: A 2459 SER cc_start: 0.8518 (p) cc_final: 0.8285 (m)
REVERT: A 2460 LYS cc_start: 0.8499 (mttt) cc_final: 0.8259 (mttp)
REVERT: A 2493 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7225 (tp30)
REVERT: A 2538 ASP cc_start: 0.8128 (t0) cc_final: 0.7880 (t0)
REVERT: A 2581 MET cc_start: 0.7907 (tmm) cc_final: 0.7187 (tmm)
REVERT: A 2683 ASP cc_start: 0.7626 (m-30) cc_final: 0.7420 (m-30)
REVERT: A 2744 PHE cc_start: 0.7545 (t80) cc_final: 0.7188 (m-80)
REVERT: A 2788 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6810 (mm-30)
REVERT: A 2993 LYS cc_start: 0.7382 (mttt) cc_final: 0.6928 (mttp)
REVERT: A 3108 VAL cc_start: 0.8008 (m) cc_final: 0.7799 (p)
REVERT: A 3203 MET cc_start: 0.6453 (mpp) cc_final: 0.6144 (mpp)
  outliers start: 36
  outliers final: 23
  residues processed: 317
  average time/residue: 0.6544
  time to fit residues: 224.2948
Evaluate side-chains
  306 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 281
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  971 VAL
Chi-restraints excluded: chain A residue 1041 GLU
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1113 THR
Chi-restraints excluded: chain A residue 1121 GLU
Chi-restraints excluded: chain A residue 1136 MET
Chi-restraints excluded: chain A residue 1241 VAL
Chi-restraints excluded: chain A residue 1306 LYS
Chi-restraints excluded: chain A residue 1361 VAL
Chi-restraints excluded: chain A residue 1378 LYS
Chi-restraints excluded: chain A residue 1393 LEU
Chi-restraints excluded: chain A residue 1400 LEU
Chi-restraints excluded: chain A residue 1448 MET
Chi-restraints excluded: chain A residue 1801 ASP
Chi-restraints excluded: chain A residue 2338 LYS
Chi-restraints excluded: chain A residue 2391 LEU
Chi-restraints excluded: chain A residue 2449 THR
Chi-restraints excluded: chain A residue 2475 ILE
Chi-restraints excluded: chain A residue 2579 GLU
Chi-restraints excluded: chain A residue 2611 GLN
Chi-restraints excluded: chain A residue 3006 VAL
Chi-restraints excluded: chain A residue 3091 LYS
Chi-restraints excluded: chain A residue 3138 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 122 optimal weight:    0.3980
   chunk 48 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 133 optimal weight:    6.9990
   chunk 36 optimal weight:    0.4980
   chunk 41 optimal weight:    1.9990
   chunk 144 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 944 HIS
** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2302 ASN
A2366 HIS
A2477 HIS
A2644 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.146073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.125246 restraints weight = 17391.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 1.88
r_work: 0.3544 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3400 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  13043  Z= 0.144
  Angle     :  0.512   6.966  17622  Z= 0.263
  Chirality :  0.040   0.163   2037
  Planarity :  0.004   0.043   2189
  Dihedral  :  7.074  73.248   1840
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 14.24 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.57 (0.22), residues: 1541
  helix:  1.42 (0.18), residues: 880
  sheet:  0.48 (0.62), residues: 79
  loop : -1.27 (0.26), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1403 
 TYR   0.013   0.001   TYR A1054 
 PHE   0.029   0.001   PHE A2633 
 TRP   0.015   0.001   TRP A2542 
 HIS   0.005   0.001   HIS A2477 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00338 /  0.14 (13039)
  covalent geometry    : angle       0.50747 /  0.26 (17616)
  hydrogen bonds       : bond        0.03730 /  2.42 (  653)
  hydrogen bonds       : angle       4.05054 /  2.92 ( 1884)
  metal coordination   : bond        0.00931 /  0.43 (    4)
  metal coordination   : angle       3.60317 /  1.63 (    6)

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

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

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  333 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 293
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  968 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7779 (mp0)
REVERT: A  975 GLU cc_start: 0.7630 (pt0) cc_final: 0.7408 (pt0)
REVERT: A  999 LYS cc_start: 0.8641 (pttp) cc_final: 0.8394 (pttp)
REVERT: A 1041 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7365 (mt-10)
REVERT: A 1249 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8405 (mm)
REVERT: A 1272 LYS cc_start: 0.7976 (mtpp) cc_final: 0.7768 (mttp)
REVERT: A 1277 GLN cc_start: 0.7679 (mm-40) cc_final: 0.7142 (mp-120)
REVERT: A 1348 ARG cc_start: 0.8022 (ttm-80) cc_final: 0.7491 (ttm-80)
REVERT: A 1434 SER cc_start: 0.8157 (p) cc_final: 0.7874 (t)
REVERT: A 1448 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7965 (mmp)
REVERT: A 1452 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7203 (mp0)
REVERT: A 1519 ASN cc_start: 0.8183 (t0) cc_final: 0.7922 (t0)
REVERT: A 1541 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7615 (mp0)
REVERT: A 1647 MET cc_start: 0.8319 (ttt) cc_final: 0.8079 (ttp)
REVERT: A 1669 ASN cc_start: 0.8325 (t0) cc_final: 0.8087 (t0)
REVERT: A 1789 GLU cc_start: 0.7767 (tp30) cc_final: 0.7353 (tp30)
REVERT: A 1850 MET cc_start: 0.6291 (mtt) cc_final: 0.5884 (mtt)
REVERT: A 2298 MET cc_start: 0.8171 (ttp) cc_final: 0.7913 (tpp)
REVERT: A 2338 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7877 (mmtp)
REVERT: A 2345 ASN cc_start: 0.8164 (t0) cc_final: 0.7833 (t0)
REVERT: A 2418 ARG cc_start: 0.8508 (ttt90) cc_final: 0.8295 (tpp80)
REVERT: A 2438 THR cc_start: 0.7557 (m) cc_final: 0.7223 (p)
REVERT: A 2459 SER cc_start: 0.8529 (p) cc_final: 0.8291 (m)
REVERT: A 2493 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7229 (tp30)
REVERT: A 2538 ASP cc_start: 0.8156 (t0) cc_final: 0.7909 (t0)
REVERT: A 2580 PHE cc_start: 0.8702 (m-80) cc_final: 0.8291 (m-80)
REVERT: A 2581 MET cc_start: 0.7951 (tmm) cc_final: 0.7203 (tmm)
REVERT: A 2683 ASP cc_start: 0.7637 (m-30) cc_final: 0.7431 (m-30)
REVERT: A 2788 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6802 (mm-30)
REVERT: A 2993 LYS cc_start: 0.7411 (mttt) cc_final: 0.6913 (mttp)
REVERT: A 3108 VAL cc_start: 0.7997 (m) cc_final: 0.7782 (p)
REVERT: A 3203 MET cc_start: 0.6521 (mpp) cc_final: 0.6207 (mpp)
  outliers start: 40
  outliers final: 25
  residues processed: 310
  average time/residue: 0.6703
  time to fit residues: 224.5073
Evaluate side-chains
  315 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 286
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  943 GLU
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  971 VAL
Chi-restraints excluded: chain A residue 1041 GLU
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1113 THR
Chi-restraints excluded: chain A residue 1121 GLU
Chi-restraints excluded: chain A residue 1241 VAL
Chi-restraints excluded: chain A residue 1249 LEU
Chi-restraints excluded: chain A residue 1306 LYS
Chi-restraints excluded: chain A residue 1320 LEU
Chi-restraints excluded: chain A residue 1361 VAL
Chi-restraints excluded: chain A residue 1393 LEU
Chi-restraints excluded: chain A residue 1400 LEU
Chi-restraints excluded: chain A residue 1412 LEU
Chi-restraints excluded: chain A residue 1448 MET
Chi-restraints excluded: chain A residue 1458 ILE
Chi-restraints excluded: chain A residue 1801 ASP
Chi-restraints excluded: chain A residue 2338 LYS
Chi-restraints excluded: chain A residue 2391 LEU
Chi-restraints excluded: chain A residue 2439 ASP
Chi-restraints excluded: chain A residue 2449 THR
Chi-restraints excluded: chain A residue 2463 MET
Chi-restraints excluded: chain A residue 2475 ILE
Chi-restraints excluded: chain A residue 2579 GLU
Chi-restraints excluded: chain A residue 3006 VAL
Chi-restraints excluded: chain A residue 3091 LYS
Chi-restraints excluded: chain A residue 3138 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 125 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 11 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 20 optimal weight:    5.9990
   chunk 22 optimal weight:    8.9990
   chunk 145 optimal weight:    2.9990
   chunk 151 optimal weight:    1.9990
   overall best weight:    1.3784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2366 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.143772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.123033 restraints weight = 17182.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3622 rms_B_bonded: 1.85
r_work: 0.3515 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3368 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051  13043  Z= 0.251
  Angle     :  0.574   9.616  17622  Z= 0.295
  Chirality :  0.043   0.182   2037
  Planarity :  0.004   0.067   2189
  Dihedral  :  7.222  73.086   1840
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 15.27 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.42 (0.22), residues: 1541
  helix:  1.30 (0.18), residues: 879
  sheet:  0.37 (0.61), residues: 79
  loop : -1.33 (0.25), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1403 
 TYR   0.018   0.002   TYR A1617 
 PHE   0.033   0.002   PHE A2633 
 TRP   0.017   0.002   TRP A2542 
 HIS   0.004   0.001   HIS A2794 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00592 /  0.25 (13039)
  covalent geometry    : angle       0.56719 /  0.30 (17616)
  hydrogen bonds       : bond        0.04350 /  2.81 (  653)
  hydrogen bonds       : angle       4.18252 /  3.01 ( 1884)
  metal coordination   : bond        0.01771 /  0.81 (    4)
  metal coordination   : angle       4.63499 /  1.93 (    6)

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

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

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 302
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
REVERT: A  968 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7784 (mp0)
REVERT: A  975 GLU cc_start: 0.7650 (pt0) cc_final: 0.7438 (pt0)
REVERT: A 1041 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7389 (mt-10)
REVERT: A 1277 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7177 (mp-120)
REVERT: A 1434 SER cc_start: 0.8152 (p) cc_final: 0.7863 (t)
REVERT: A 1448 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8068 (mpp)
REVERT: A 1452 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7214 (mp0)
REVERT: A 1519 ASN cc_start: 0.8236 (t0) cc_final: 0.7942 (t0)
REVERT: A 1534 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8384 (p)
REVERT: A 1633 GLU cc_start: 0.7885 (tp30) cc_final: 0.7617 (tp30)
REVERT: A 1647 MET cc_start: 0.8348 (ttt) cc_final: 0.8113 (ttp)
REVERT: A 1669 ASN cc_start: 0.8381 (t0) cc_final: 0.8118 (t0)
REVERT: A 1763 LEU cc_start: 0.8392 (tp) cc_final: 0.8159 (tp)
REVERT: A 1789 GLU cc_start: 0.7837 (tp30) cc_final: 0.7432 (tp30)
REVERT: A 1850 MET cc_start: 0.6200 (mtt) cc_final: 0.5824 (mtt)
REVERT: A 2345 ASN cc_start: 0.8172 (t0) cc_final: 0.7891 (t0)
REVERT: A 2418 ARG cc_start: 0.8469 (ttt90) cc_final: 0.8237 (tpp80)
REVERT: A 2459 SER cc_start: 0.8542 (p) cc_final: 0.8314 (m)
REVERT: A 2493 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7258 (tp30)
REVERT: A 2580 PHE cc_start: 0.8700 (m-80) cc_final: 0.8175 (m-80)
REVERT: A 2581 MET cc_start: 0.7953 (tmm) cc_final: 0.7237 (tmm)
REVERT: A 2683 ASP cc_start: 0.7671 (m-30) cc_final: 0.7447 (m-30)
REVERT: A 2744 PHE cc_start: 0.7683 (t80) cc_final: 0.7331 (m-80)
REVERT: A 2788 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6613 (mm-30)
REVERT: A 2993 LYS cc_start: 0.7521 (mttt) cc_final: 0.7045 (mttp)
REVERT: A 3089 LYS cc_start: 0.8359 (ttmt) cc_final: 0.8140 (ttmt)
REVERT: A 3108 VAL cc_start: 0.8016 (m) cc_final: 0.7805 (p)
REVERT: A 3203 MET cc_start: 0.6517 (mpp) cc_final: 0.6196 (mpp)
  outliers start: 39
  outliers final: 25
  residues processed: 319
  average time/residue: 0.6520
  time to fit residues: 224.8281
Evaluate side-chains
  320 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 292
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  971 VAL
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1041 GLU
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1113 THR
Chi-restraints excluded: chain A residue 1241 VAL
Chi-restraints excluded: chain A residue 1306 LYS
Chi-restraints excluded: chain A residue 1320 LEU
Chi-restraints excluded: chain A residue 1361 VAL
Chi-restraints excluded: chain A residue 1393 LEU
Chi-restraints excluded: chain A residue 1400 LEU
Chi-restraints excluded: chain A residue 1412 LEU
Chi-restraints excluded: chain A residue 1448 MET
Chi-restraints excluded: chain A residue 1512 LEU
Chi-restraints excluded: chain A residue 1534 SER
Chi-restraints excluded: chain A residue 1801 ASP
Chi-restraints excluded: chain A residue 2391 LEU
Chi-restraints excluded: chain A residue 2442 ASP
Chi-restraints excluded: chain A residue 2449 THR
Chi-restraints excluded: chain A residue 2462 LEU
Chi-restraints excluded: chain A residue 2463 MET
Chi-restraints excluded: chain A residue 2475 ILE
Chi-restraints excluded: chain A residue 2579 GLU
Chi-restraints excluded: chain A residue 3006 VAL
Chi-restraints excluded: chain A residue 3091 LYS
Chi-restraints excluded: chain A residue 3138 ILE
Chi-restraints excluded: chain A residue 3226 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 122 optimal weight:    0.9980
   chunk 146 optimal weight:    0.3980
   chunk 46 optimal weight:    0.5980
   chunk 51 optimal weight:    0.7980
   chunk 60 optimal weight:    0.3980
   chunk 74 optimal weight:    0.8980
   chunk 82 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2366 HIS
A2476 HIS
A2505 GLN
A2644 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.145415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.124742 restraints weight = 17163.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 1.85
r_work: 0.3540 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3396 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.2284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13043  Z= 0.137
  Angle     :  0.532   7.254  17622  Z= 0.273
  Chirality :  0.040   0.195   2037
  Planarity :  0.004   0.045   2189
  Dihedral  :  7.131  73.274   1840
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.59 %
    Favored  : 81.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.59 (0.22), residues: 1541
  helix:  1.46 (0.18), residues: 877
  sheet:  0.31 (0.60), residues: 79
  loop : -1.27 (0.25), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1805 
 TYR   0.012   0.001   TYR A2417 
 PHE   0.026   0.001   PHE A2633 
 TRP   0.017   0.001   TRP A2542 
 HIS   0.003   0.001   HIS A3045 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.14 (13039)
  covalent geometry    : angle       0.52884 /  0.27 (17616)
  hydrogen bonds       : bond        0.03784 /  2.46 (  653)
  hydrogen bonds       : angle       4.06999 /  2.93 ( 1884)
  metal coordination   : bond        0.00901 /  0.40 (    4)
  metal coordination   : angle       3.06740 /  1.36 (    6)

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

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

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 294
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  932 LYS cc_start: 0.7851 (mppt) cc_final: 0.7648 (mppt)
REVERT: A  968 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7807 (mp0)
REVERT: A  975 GLU cc_start: 0.7630 (pt0) cc_final: 0.7406 (pt0)
REVERT: A 1041 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7365 (mt-10)
REVERT: A 1277 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7127 (mm-40)
REVERT: A 1348 ARG cc_start: 0.7933 (ttm-80) cc_final: 0.7502 (ttm-80)
REVERT: A 1434 SER cc_start: 0.8115 (p) cc_final: 0.7854 (t)
REVERT: A 1448 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7971 (mmp)
REVERT: A 1452 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7222 (mp0)
REVERT: A 1647 MET cc_start: 0.8329 (ttt) cc_final: 0.8085 (ttp)
REVERT: A 1669 ASN cc_start: 0.8349 (t0) cc_final: 0.8083 (t0)
REVERT: A 1763 LEU cc_start: 0.8398 (tp) cc_final: 0.8169 (tp)
REVERT: A 1789 GLU cc_start: 0.7770 (tp30) cc_final: 0.7437 (tp30)
REVERT: A 1850 MET cc_start: 0.6214 (mtt) cc_final: 0.5831 (mtt)
REVERT: A 2345 ASN cc_start: 0.8159 (t0) cc_final: 0.7868 (t0)
REVERT: A 2418 ARG cc_start: 0.8481 (ttt90) cc_final: 0.8261 (tpp80)
REVERT: A 2493 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7295 (tp30)
REVERT: A 2538 ASP cc_start: 0.8163 (t0) cc_final: 0.7914 (t0)
REVERT: A 2580 PHE cc_start: 0.8682 (m-80) cc_final: 0.8298 (m-80)
REVERT: A 2581 MET cc_start: 0.7972 (tmm) cc_final: 0.7226 (tmm)
REVERT: A 2744 PHE cc_start: 0.7639 (t80) cc_final: 0.7257 (m-80)
REVERT: A 2788 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6762 (mm-30)
REVERT: A 2993 LYS cc_start: 0.7417 (mttt) cc_final: 0.6947 (mttp)
REVERT: A 3203 MET cc_start: 0.6607 (mpp) cc_final: 0.6297 (mpp)
  outliers start: 32
  outliers final: 19
  residues processed: 306
  average time/residue: 0.6768
  time to fit residues: 223.3440
Evaluate side-chains
  310 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 289
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  971 VAL
Chi-restraints excluded: chain A residue 1041 GLU
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1113 THR
Chi-restraints excluded: chain A residue 1241 VAL
Chi-restraints excluded: chain A residue 1320 LEU
Chi-restraints excluded: chain A residue 1361 VAL
Chi-restraints excluded: chain A residue 1393 LEU
Chi-restraints excluded: chain A residue 1400 LEU
Chi-restraints excluded: chain A residue 1448 MET
Chi-restraints excluded: chain A residue 2391 LEU
Chi-restraints excluded: chain A residue 2449 THR
Chi-restraints excluded: chain A residue 2475 ILE
Chi-restraints excluded: chain A residue 2579 GLU
Chi-restraints excluded: chain A residue 2611 GLN
Chi-restraints excluded: chain A residue 2793 ARG
Chi-restraints excluded: chain A residue 3006 VAL
Chi-restraints excluded: chain A residue 3091 LYS
Chi-restraints excluded: chain A residue 3138 ILE
Chi-restraints excluded: chain A residue 3226 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 96 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 91 optimal weight:    0.5980
   chunk 117 optimal weight:    0.9990
   chunk 136 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 111 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2366 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.144832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.123996 restraints weight = 17127.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 1.87
r_work: 0.3528 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3385 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.2373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13043  Z= 0.179
  Angle     :  0.549   9.377  17622  Z= 0.281
  Chirality :  0.041   0.165   2037
  Planarity :  0.004   0.049   2189
  Dihedral  :  7.138  73.168   1840
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 16.66 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.56 (0.22), residues: 1541
  helix:  1.43 (0.18), residues: 877
  sheet:  0.36 (0.60), residues: 79
  loop : -1.27 (0.25), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A2815 
 TYR   0.014   0.001   TYR A2994 
 PHE   0.029   0.002   PHE A2633 
 TRP   0.017   0.001   TRP A2542 
 HIS   0.003   0.001   HIS A3045 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00423 /  0.18 (13039)
  covalent geometry    : angle       0.54544 /  0.28 (17616)
  hydrogen bonds       : bond        0.03933 /  2.55 (  653)
  hydrogen bonds       : angle       4.08070 /  2.93 ( 1884)
  metal coordination   : bond        0.01169 /  0.53 (    4)
  metal coordination   : angle       3.42242 /  1.51 (    6)

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

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

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 291
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  932 LYS cc_start: 0.7898 (mppt) cc_final: 0.7668 (mppt)
REVERT: A  968 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7814 (mp0)
REVERT: A  975 GLU cc_start: 0.7647 (pt0) cc_final: 0.7420 (pt0)
REVERT: A 1041 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7361 (mt-10)
REVERT: A 1136 MET cc_start: 0.7444 (mtp) cc_final: 0.6990 (mmm)
REVERT: A 1277 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7146 (mm110)
REVERT: A 1434 SER cc_start: 0.8104 (p) cc_final: 0.7838 (t)
REVERT: A 1448 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7982 (mmp)
REVERT: A 1452 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7209 (mp0)
REVERT: A 1534 SER cc_start: 0.8677 (OUTLIER) cc_final: 0.8325 (p)
REVERT: A 1633 GLU cc_start: 0.7860 (tp30) cc_final: 0.7549 (tp30)
REVERT: A 1647 MET cc_start: 0.8347 (ttt) cc_final: 0.8104 (ttp)
REVERT: A 1763 LEU cc_start: 0.8448 (tp) cc_final: 0.8187 (tp)
REVERT: A 1789 GLU cc_start: 0.7830 (tp30) cc_final: 0.7420 (tp30)
REVERT: A 1850 MET cc_start: 0.6207 (mtt) cc_final: 0.5829 (mtt)
REVERT: A 2345 ASN cc_start: 0.8162 (t0) cc_final: 0.7876 (t0)
REVERT: A 2418 ARG cc_start: 0.8478 (ttt90) cc_final: 0.8256 (tpp80)
REVERT: A 2493 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7308 (tp30)
REVERT: A 2538 ASP cc_start: 0.8182 (t0) cc_final: 0.7918 (t0)
REVERT: A 2580 PHE cc_start: 0.8683 (m-80) cc_final: 0.8315 (m-80)
REVERT: A 2581 MET cc_start: 0.7992 (tmm) cc_final: 0.7243 (tmm)
REVERT: A 2744 PHE cc_start: 0.7657 (t80) cc_final: 0.7321 (m-80)
REVERT: A 2788 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6586 (mm-30)
REVERT: A 2993 LYS cc_start: 0.7444 (mttt) cc_final: 0.6977 (mttp)
REVERT: A 3203 MET cc_start: 0.6629 (mpp) cc_final: 0.6313 (mpp)
  outliers start: 34
  outliers final: 23
  residues processed: 308
  average time/residue: 0.6762
  time to fit residues: 225.0653
Evaluate side-chains
  311 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 285
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  971 VAL
Chi-restraints excluded: chain A residue 1041 GLU
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1113 THR
Chi-restraints excluded: chain A residue 1241 VAL
Chi-restraints excluded: chain A residue 1320 LEU
Chi-restraints excluded: chain A residue 1361 VAL
Chi-restraints excluded: chain A residue 1393 LEU
Chi-restraints excluded: chain A residue 1400 LEU
Chi-restraints excluded: chain A residue 1412 LEU
Chi-restraints excluded: chain A residue 1420 ILE
Chi-restraints excluded: chain A residue 1448 MET
Chi-restraints excluded: chain A residue 1512 LEU
Chi-restraints excluded: chain A residue 1534 SER
Chi-restraints excluded: chain A residue 2391 LEU
Chi-restraints excluded: chain A residue 2449 THR
Chi-restraints excluded: chain A residue 2462 LEU
Chi-restraints excluded: chain A residue 2463 MET
Chi-restraints excluded: chain A residue 2579 GLU
Chi-restraints excluded: chain A residue 2793 ARG
Chi-restraints excluded: chain A residue 3006 VAL
Chi-restraints excluded: chain A residue 3091 LYS
Chi-restraints excluded: chain A residue 3138 ILE
Chi-restraints excluded: chain A residue 3226 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 108 optimal weight:    0.0770
   chunk 5 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 114 optimal weight:    0.7980
   chunk 137 optimal weight:    2.9990
   chunk 147 optimal weight:    0.0370
   chunk 116 optimal weight:    0.6980
   chunk 29 optimal weight:    7.9990
   chunk 144 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.7218

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2366 HIS
A2644 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.145229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.124491 restraints weight = 17214.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 1.86
r_work: 0.3543 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3395 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.2441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13043  Z= 0.157
  Angle     :  0.581  15.149  17622  Z= 0.286
  Chirality :  0.040   0.157   2037
  Planarity :  0.004   0.084   2189
  Dihedral  :  7.128  73.214   1840
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 17.42 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.60 (0.22), residues: 1541
  helix:  1.45 (0.18), residues: 878
  sheet:  0.51 (0.61), residues: 79
  loop : -1.28 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1348 
 TYR   0.016   0.001   TYR A2994 
 PHE   0.027   0.001   PHE A2633 
 TRP   0.017   0.001   TRP A2542 
 HIS   0.004   0.001   HIS A2644 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00369 /  0.16 (13039)
  covalent geometry    : angle       0.56007 /  0.29 (17616)
  hydrogen bonds       : bond        0.03841 /  2.49 (  653)
  hydrogen bonds       : angle       4.08690 /  2.94 ( 1884)
  metal coordination   : bond        0.01790 /  0.72 (    4)
  metal coordination   : angle       8.46137 /  4.54 (    6)

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

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

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 290
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  968 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7811 (mp0)
REVERT: A  975 GLU cc_start: 0.7656 (pt0) cc_final: 0.7435 (pt0)
REVERT: A 1041 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7344 (mt-10)
REVERT: A 1277 GLN cc_start: 0.7640 (mm-40) cc_final: 0.7123 (mm110)
REVERT: A 1350 CYS cc_start: 0.8271 (t) cc_final: 0.8037 (t)
REVERT: A 1373 LYS cc_start: 0.8639 (tttm) cc_final: 0.8418 (tttt)
REVERT: A 1434 SER cc_start: 0.8087 (p) cc_final: 0.7834 (t)
REVERT: A 1448 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7962 (mmp)
REVERT: A 1452 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7221 (mp0)
REVERT: A 1544 LYS cc_start: 0.8582 (mtpp) cc_final: 0.8368 (ttpt)
REVERT: A 1633 GLU cc_start: 0.7888 (tp30) cc_final: 0.7584 (tp30)
REVERT: A 1647 MET cc_start: 0.8348 (ttt) cc_final: 0.8105 (ttp)
REVERT: A 1789 GLU cc_start: 0.7815 (tp30) cc_final: 0.7418 (tp30)
REVERT: A 1850 MET cc_start: 0.6195 (mtt) cc_final: 0.5809 (mtt)
REVERT: A 2338 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.7986 (mmtp)
REVERT: A 2345 ASN cc_start: 0.8164 (t0) cc_final: 0.7877 (t0)
REVERT: A 2418 ARG cc_start: 0.8477 (ttt90) cc_final: 0.8257 (tpp80)
REVERT: A 2538 ASP cc_start: 0.8177 (t0) cc_final: 0.7916 (t0)
REVERT: A 2580 PHE cc_start: 0.8685 (m-80) cc_final: 0.8338 (m-80)
REVERT: A 2581 MET cc_start: 0.8016 (tmm) cc_final: 0.7253 (tmm)
REVERT: A 2744 PHE cc_start: 0.7581 (t80) cc_final: 0.7290 (m-80)
REVERT: A 2788 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6562 (mm-30)
REVERT: A 2993 LYS cc_start: 0.7417 (mttt) cc_final: 0.6959 (mttp)
REVERT: A 3109 MET cc_start: 0.7421 (ptp) cc_final: 0.7096 (mtt)
REVERT: A 3203 MET cc_start: 0.6574 (mpp) cc_final: 0.6263 (mpp)
  outliers start: 27
  outliers final: 22
  residues processed: 300
  average time/residue: 0.6923
  time to fit residues: 223.9299
Evaluate side-chains
  310 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 285
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  971 VAL
Chi-restraints excluded: chain A residue 1041 GLU
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1113 THR
Chi-restraints excluded: chain A residue 1241 VAL
Chi-restraints excluded: chain A residue 1320 LEU
Chi-restraints excluded: chain A residue 1361 VAL
Chi-restraints excluded: chain A residue 1393 LEU
Chi-restraints excluded: chain A residue 1400 LEU
Chi-restraints excluded: chain A residue 1412 LEU
Chi-restraints excluded: chain A residue 1448 MET
Chi-restraints excluded: chain A residue 1458 ILE
Chi-restraints excluded: chain A residue 1534 SER
Chi-restraints excluded: chain A residue 2338 LYS
Chi-restraints excluded: chain A residue 2391 LEU
Chi-restraints excluded: chain A residue 2449 THR
Chi-restraints excluded: chain A residue 2462 LEU
Chi-restraints excluded: chain A residue 2579 GLU
Chi-restraints excluded: chain A residue 2677 SER
Chi-restraints excluded: chain A residue 2793 ARG
Chi-restraints excluded: chain A residue 3006 VAL
Chi-restraints excluded: chain A residue 3091 LYS
Chi-restraints excluded: chain A residue 3226 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 134 optimal weight:    0.6980
   chunk 58 optimal weight:    0.3980
   chunk 146 optimal weight:    6.9990
   chunk 77 optimal weight:    0.4980
   chunk 12 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 156 optimal weight:    1.9990
   chunk 115 optimal weight:    0.9990
   chunk 153 optimal weight:    4.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 987 ASN
** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2366 HIS
A2505 GLN
A2644 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.145717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.124661 restraints weight = 17078.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 1.89
r_work: 0.3541 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3392 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  13043  Z= 0.153
  Angle     :  0.574  12.459  17622  Z= 0.287
  Chirality :  0.040   0.158   2037
  Planarity :  0.004   0.046   2189
  Dihedral  :  7.113  73.220   1840
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 17.69 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.60 (0.22), residues: 1541
  helix:  1.47 (0.18), residues: 878
  sheet:  0.50 (0.61), residues: 79
  loop : -1.30 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A3010 
 TYR   0.011   0.001   TYR A2994 
 PHE   0.027   0.001   PHE A2633 
 TRP   0.017   0.001   TRP A2542 
 HIS   0.004   0.001   HIS A2644 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.15 (13039)
  covalent geometry    : angle       0.55905 /  0.29 (17616)
  hydrogen bonds       : bond        0.03793 /  2.46 (  653)
  hydrogen bonds       : angle       4.09093 /  2.94 ( 1884)
  metal coordination   : bond        0.01581 /  0.65 (    4)
  metal coordination   : angle       7.00159 /  3.75 (    6)

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

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

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 294
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  968 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7770 (mp0)
REVERT: A  975 GLU cc_start: 0.7668 (pt0) cc_final: 0.7452 (pt0)
REVERT: A 1277 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7120 (mm110)
REVERT: A 1350 CYS cc_start: 0.8243 (t) cc_final: 0.8012 (t)
REVERT: A 1373 LYS cc_start: 0.8608 (tttm) cc_final: 0.8388 (tttp)
REVERT: A 1434 SER cc_start: 0.8075 (p) cc_final: 0.7831 (t)
REVERT: A 1448 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7964 (mmp)
REVERT: A 1452 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7269 (mp0)
REVERT: A 1544 LYS cc_start: 0.8613 (mtpp) cc_final: 0.8393 (ttpt)
REVERT: A 1647 MET cc_start: 0.8335 (ttt) cc_final: 0.8076 (ttp)
REVERT: A 1789 GLU cc_start: 0.7773 (tp30) cc_final: 0.7363 (tp30)
REVERT: A 1806 ASP cc_start: 0.7964 (t0) cc_final: 0.7722 (t0)
REVERT: A 1850 MET cc_start: 0.6183 (mtt) cc_final: 0.5794 (mtt)
REVERT: A 2345 ASN cc_start: 0.8129 (t0) cc_final: 0.7836 (t0)
REVERT: A 2375 MET cc_start: 0.8390 (mmt) cc_final: 0.8131 (mmm)
REVERT: A 2418 ARG cc_start: 0.8431 (ttt90) cc_final: 0.8219 (tpp80)
REVERT: A 2477 HIS cc_start: 0.7718 (t-90) cc_final: 0.7391 (t70)
REVERT: A 2538 ASP cc_start: 0.8192 (t0) cc_final: 0.7942 (t0)
REVERT: A 2580 PHE cc_start: 0.8667 (m-80) cc_final: 0.8285 (m-80)
REVERT: A 2581 MET cc_start: 0.7978 (tmm) cc_final: 0.7188 (tmm)
REVERT: A 2744 PHE cc_start: 0.7583 (t80) cc_final: 0.7282 (m-80)
REVERT: A 2788 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6529 (mm-30)
REVERT: A 2993 LYS cc_start: 0.7417 (mttt) cc_final: 0.6954 (mttp)
REVERT: A 3109 MET cc_start: 0.7495 (ptp) cc_final: 0.7161 (mtt)
REVERT: A 3203 MET cc_start: 0.6571 (mpp) cc_final: 0.6082 (mpp)
  outliers start: 29
  outliers final: 23
  residues processed: 305
  average time/residue: 0.6600
  time to fit residues: 217.7333
Evaluate side-chains
  309 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 285
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  971 VAL
Chi-restraints excluded: chain A residue 1041 GLU
Chi-restraints excluded: chain A residue 1056 LEU
Chi-restraints excluded: chain A residue 1070 VAL
Chi-restraints excluded: chain A residue 1113 THR
Chi-restraints excluded: chain A residue 1320 LEU
Chi-restraints excluded: chain A residue 1361 VAL
Chi-restraints excluded: chain A residue 1393 LEU
Chi-restraints excluded: chain A residue 1400 LEU
Chi-restraints excluded: chain A residue 1412 LEU
Chi-restraints excluded: chain A residue 1420 ILE
Chi-restraints excluded: chain A residue 1448 MET
Chi-restraints excluded: chain A residue 1458 ILE
Chi-restraints excluded: chain A residue 1534 SER
Chi-restraints excluded: chain A residue 2391 LEU
Chi-restraints excluded: chain A residue 2449 THR
Chi-restraints excluded: chain A residue 2462 LEU
Chi-restraints excluded: chain A residue 2579 GLU
Chi-restraints excluded: chain A residue 2677 SER
Chi-restraints excluded: chain A residue 2793 ARG
Chi-restraints excluded: chain A residue 3006 VAL
Chi-restraints excluded: chain A residue 3091 LYS
Chi-restraints excluded: chain A residue 3226 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 123 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 134 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   chunk 128 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1247 ASN
A1773 ASN
A2366 HIS
A2505 GLN
A2644 HIS
** A2825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.145071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.124043 restraints weight = 17082.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 1.88
r_work: 0.3536 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3388 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  13043  Z= 0.185
  Angle     :  0.585  11.704  17622  Z= 0.293
  Chirality :  0.041   0.174   2037
  Planarity :  0.004   0.045   2189
  Dihedral  :  7.148  73.143   1840
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 18.18 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.51 (0.22), residues: 1541
  helix:  1.39 (0.18), residues: 879
  sheet:  0.57 (0.61), residues: 79
  loop : -1.37 (0.25), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1348 
 TYR   0.012   0.001   TYR A1617 
 PHE   0.028   0.001   PHE A2633 
 TRP   0.017   0.002   TRP A2542 
 HIS   0.009   0.001   HIS A2644 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00437 /  0.18 (13039)
  covalent geometry    : angle       0.57101 /  0.29 (17616)
  hydrogen bonds       : bond        0.03933 /  2.54 (  653)
  hydrogen bonds       : angle       4.12527 /  2.97 ( 1884)
  metal coordination   : bond        0.01623 /  0.68 (    4)
  metal coordination   : angle       6.81007 /  3.56 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5741.22 seconds
wall clock time: 98 minutes 47.38 seconds (5927.38 seconds total)