Starting phenix.real_space_refine
on Sun Apr  5 18:53:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ybm_72752/04_2026/9ybm_72752.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ybm_72752/04_2026/9ybm_72752.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ybm_72752/04_2026/9ybm_72752.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ybm_72752/04_2026/9ybm_72752.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ybm_72752/04_2026/9ybm_72752.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ybm_72752/04_2026/9ybm_72752.map"
  }
  resolution = 2.62
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.012
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: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      89      5.16       5
     C    7679      2.51       5
     N    2087      2.21       5
     O    2277      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-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12134
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 12132
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1518, 12132
          Classifications: {'peptide': 1518}
          Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 1471}
          Chain breaks: 12
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2550  SG  CYS A1294      53.090  29.102  84.994  1.00 34.97           S
  ATOM    802  SG  CYS A1028      69.571  16.472  34.762  1.00 44.64           S
  ATOM    821  SG  CYS A1031      66.461  14.539  34.370  1.00 56.07           S
  ATOM   1064  SG  CYS A1062      69.181  12.755  36.198  1.00 49.72           S
  ATOM   1084  SG  CYS A1065      67.828  15.491  37.996  1.00 47.63           S

  Time building chain proxies: 2.56, per 1000 atoms: 0.21
  Number of scatterers: 12134
  At special positions: 0
  Unit cell: (115.979, 111.552, 128.373, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      89     16.00
     O    2277      8.00
     N    2087      7.00
     C    7679      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.94
  Conformation dependent library (CDL) restraints added in 715.8 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A6001 "
        pdb="ZN    ZN A6001 " - pdb=" NE2 HIS A1090 "
        pdb="ZN    ZN A6001 " - pdb=" SG  CYS A1294 "
        pdb="ZN    ZN A6001 " - pdb=" ND1 HIS A1365 "
      pdb="  ZN A6002 "
        pdb="ZN    ZN A6002 " - pdb=" SG  CYS A1062 "
        pdb="ZN    ZN A6002 " - pdb=" SG  CYS A1065 "
        pdb="ZN    ZN A6002 " - pdb=" SG  CYS A1031 "
        pdb="ZN    ZN A6002 " - pdb=" SG  CYS A1028 "
      Number of angles added : 6


  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2908

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 11 sheets defined
      61.8% alpha, 6.3% 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 947
      removed outlier: 5.503A  pdb=" N   GLU A 943 " --> pdb=" O   GLU A 939 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   HIS A 944 " --> pdb=" O   LYS A 940 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   ILE A 945 " --> pdb=" O   MET A 941 " (cutoff:3.500A)
      removed outlier: 3.527A  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 1008 through 1024
      removed outlier: 3.690A  pdb=" N   LYS A1024 " --> pdb=" O   SER A1020 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1028 through 1042
      removed outlier: 3.573A  pdb=" N   THR A1042 " --> pdb=" O   ALA A1038 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1044 through 1056
    Processing helix  chain 'A' and resid 1057 through 1061
      removed outlier: 3.759A  pdb=" N   HIS A1061 " --> pdb=" O   LEU A1058 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1103 through 1111
    Processing helix  chain 'A' and resid 1118 through 1140
      removed outlier: 3.807A  pdb=" N   ARG A1126 " --> pdb=" O   ARG A1122 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   GLU A1129 " --> pdb=" O   LYS A1125 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   TYR A1130 " --> pdb=" O   ARG A1126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1173 through 1185
      removed outlier: 4.201A  pdb=" N   VAL A1183 " --> pdb=" O   LYS A1179 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   LYS A1185 " --> pdb=" O   ASP A1181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1196 through 1209
      removed outlier: 4.837A  pdb=" N   VAL A1202 " --> pdb=" O   TYR A1198 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ILE A1203 " --> pdb=" O   ALA A1199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1221 through 1232
    Processing helix  chain 'A' and resid 1266 through 1281
      removed outlier: 3.779A  pdb=" N   VAL A1276 " --> pdb=" O   LYS A1272 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   GLN A1277 " --> pdb=" O   CYS A1273 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   SER A1278 " --> pdb=" O   PHE A1274 " (cutoff:3.500A)
      removed outlier: 4.822A  pdb=" N   PHE A1279 " --> pdb=" O   ASP A1275 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   LYS A1280 " --> pdb=" O   VAL A1276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1291 through 1296
      removed outlier: 3.567A  pdb=" N   ILE A1295 " --> pdb=" O   GLN A1291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1297 through 1309
    Processing helix  chain 'A' and resid 1315 through 1328
    Processing helix  chain 'A' and resid 1330 through 1350
    Processing helix  chain 'A' and resid 1401 through 1426
      removed outlier: 4.914A  pdb=" N   LEU A1412 " --> pdb=" O   GLY A1408 " (cutoff:3.500A)
      removed outlier: 5.310A  pdb=" N   TYR A1413 " --> pdb=" O   SER A1409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1428 through 1434
      removed outlier: 3.665A  pdb=" N   VAL A1431 " --> pdb=" O   CYS A1428 " (cutoff:3.500A)
      removed outlier: 3.604A  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 1480
      removed outlier: 3.798A  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: 3.727A  pdb=" N   MET A1524 " --> pdb=" O   LYS A1520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1524 through 1531
    Processing helix  chain 'A' and resid 1532 through 1534
      No H-bonds generated for 'chain 'A' and resid 1532 through 1534'
    Processing helix  chain 'A' and resid 1538 through 1545
      removed outlier: 3.720A  pdb=" N   LYS A1544 " --> pdb=" O   ASN A1540 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   LYS A1545 " --> pdb=" O   GLU A1541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1552 through 1571
    Processing helix  chain 'A' and resid 1572 through 1581
      removed outlier: 4.154A  pdb=" N   LYS A1581 " --> pdb=" O   VAL A1577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1603 through 1612
      removed outlier: 3.550A  pdb=" N   TYR A1612 " --> pdb=" O   ILE A1608 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1613 through 1616
      removed outlier: 3.546A  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 1633 through 1651
      removed outlier: 3.702A  pdb=" N   CYS A1651 " --> pdb=" O   MET A1647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1658 through 1666
    Processing helix  chain 'A' and resid 1758 through 1773
    Processing helix  chain 'A' and resid 1780 through 1791
    Processing helix  chain 'A' and resid 1792 through 1794
      No H-bonds generated for 'chain 'A' and resid 1792 through 1794'
    Processing helix  chain 'A' and resid 1796 through 1805
    Processing helix  chain 'A' and resid 2297 through 2307
      removed outlier: 3.806A  pdb=" N   THR A2306 " --> pdb=" O   ASN A2302 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   THR A2307 " --> pdb=" O   LEU A2303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2316 through 2336
    Processing helix  chain 'A' and resid 2367 through 2379
      removed outlier: 3.545A  pdb=" N   PHE A2371 " --> pdb=" O   CYS A2367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2382 through 2397
    Processing helix  chain 'A' and resid 2404 through 2419
      removed outlier: 3.593A  pdb=" N   ILE A2408 " --> pdb=" O   PRO A2404 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LEU A2415 " --> pdb=" O   ILE A2411 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU A2419 " --> pdb=" O   LEU A2415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2449 through 2457
    Processing helix  chain 'A' and resid 2476 through 2503
      removed outlier: 4.173A  pdb=" N   VAL A2489 " --> pdb=" O   SER A2485 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   LEU A2490 " --> pdb=" O   LEU A2486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2530 through 2539
    Processing helix  chain 'A' and resid 2540 through 2558
      removed outlier: 3.806A  pdb=" N   CYS A2558 " --> pdb=" O   ALA A2554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2589 through 2594
      removed outlier: 3.643A  pdb=" N   MET A2594 " --> pdb=" O   ILE A2591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2595 through 2600
      removed outlier: 3.611A  pdb=" N   ILE A2599 " --> pdb=" O   PHE A2595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2605 through 2623
      removed outlier: 3.686A  pdb=" N   ASN A2623 " --> pdb=" O   GLN A2619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2626 through 2643
    Processing helix  chain 'A' and resid 2645 through 2657
      removed outlier: 6.743A  pdb=" N   ILE A2654 " --> pdb=" O   ARG A2650 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   LEU A2655 " --> pdb=" O   ARG A2651 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2658 through 2659
      No H-bonds generated for 'chain 'A' and resid 2658 through 2659'
    Processing helix  chain 'A' and resid 2660 through 2664
      removed outlier: 4.234A  pdb=" N   GLY A2664 " --> pdb=" O   SER A2661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2678 through 2697
    Processing helix  chain 'A' and resid 2698 through 2701
      removed outlier: 3.655A  pdb=" N   ILE A2701 " --> pdb=" O   SER A2698 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2698 through 2701'
    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 2816 through 2836
      removed outlier: 3.774A  pdb=" N   VAL A2827 " --> pdb=" O   ARG A2823 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2899 through 2912
    Processing helix  chain 'A' and resid 2944 through 2955
      removed outlier: 3.736A  pdb=" N   MET A2953 " --> pdb=" O   TYR A2949 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2993 through 3003
    Processing helix  chain 'A' and resid 3043 through 3060
      removed outlier: 3.831A  pdb=" N   LYS A3047 " --> pdb=" O   GLN A3043 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   VAL A3048 " --> pdb=" O   SER A3044 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3062 through 3073
    Processing helix  chain 'A' and resid 3095 through 3100
      removed outlier: 4.053A  pdb=" N   VAL A3099 " --> pdb=" O   ALA A3095 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ARG A3100 " --> pdb=" O   THR A3096 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 3095 through 3100'
    Processing helix  chain 'A' and resid 3104 through 3114
    Processing helix  chain 'A' and resid 3115 through 3122
      removed outlier: 4.225A  pdb=" N   SER A3119 " --> pdb=" O   GLU A3115 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   VAL A3121 " --> pdb=" O   ALA A3117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3130 through 3139
    Processing helix  chain 'A' and resid 3142 through 3162
      removed outlier: 3.591A  pdb=" N   PHE A3146 " --> pdb=" O   PHE A3142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3167 through 3185
      removed outlier: 3.976A  pdb=" N   MET A3184 " --> pdb=" O   LEU A3180 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ILE A3185 " --> pdb=" O   LEU A3181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3208 through 3217
      removed outlier: 3.920A  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: 6.893A  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 1144 through 1145
      removed outlier: 3.569A  pdb=" N   ILE A1144 " --> pdb=" O   ILE A1152 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ILE A1152 " --> pdb=" O   ILE A1144 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1357 through 1362
      removed outlier: 4.158A  pdb=" N   LEU A1383 " --> pdb=" O   LYS A1373 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   LEU A1386 " --> pdb=" O   GLY A1396 " (cutoff:3.500A)
      removed outlier: 5.736A  pdb=" N   GLY A1396 " --> pdb=" O   LEU A1386 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 2507 through 2514
    Processing sheet with id=AA6, first strand: chain 'A' and resid 2399 through 2402
      removed outlier: 3.568A  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: 4.541A  pdb=" N   PHE A2580 " --> pdb=" O   THR A2587 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 2958 through 2959
    Processing sheet with id=AA9, first strand: chain 'A' and resid 3005 through 3009
      removed outlier: 6.305A  pdb=" N   SER A3005 " --> pdb=" O   LEU A3039 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   VAL A3041 " --> pdb=" O   SER A3005 " (cutoff:3.500A)
      removed outlier: 6.531A  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: 3.663A  pdb=" N   SER A3078 " --> pdb=" O   ARG A3224 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 3086 through 3090
      removed outlier: 4.171A  pdb=" N   PHE A3195 " --> pdb=" O   THR A3090 " (cutoff:3.500A)

    661 hydrogen bonds defined for protein.
    1932 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: 2.50

  Time building geometry restraints manager: 1.30 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: 3908
        1.34 -     1.46: 2129
        1.46 -     1.58: 6166
        1.58 -     1.70: 0
        1.70 -     1.81: 129
  Bond restraints: 12332
  Sorted by residual:
  bond pdb=" C   LEU A2946 "
       pdb=" N   PRO A2947 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.025 1.28e-02 6.10e+03 3.70e+00
  bond pdb=" CA  VAL A1570 "
       pdb=" C   VAL A1570 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 1.54e-02 4.22e+03 3.49e+00
  bond pdb=" CA  THR A2360 "
       pdb=" C   THR A2360 "
    ideal  model  delta    sigma   weight residual
    1.523  1.544 -0.021 1.34e-02 5.57e+03 2.37e+00
  bond pdb=" N   ASN A1354 "
       pdb=" CA  ASN A1354 "
    ideal  model  delta    sigma   weight residual
    1.461  1.483 -0.022 1.52e-02 4.33e+03 2.00e+00
  bond pdb=" CB  CYS A2398 "
       pdb=" SG  CYS A2398 "
    ideal  model  delta    sigma   weight residual
    1.808  1.762  0.046 3.30e-02 9.18e+02 1.97e+00
  ... (remaining 12327 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 16249
        2.20 -     4.39: 323
        4.39 -     6.59: 39
        6.59 -     8.78: 8
        8.78 -    10.98: 4
  Bond angle restraints: 16623
  Sorted by residual:
  angle pdb=" C   PRO A2364 "
        pdb=" N   ILE A2365 "
        pdb=" CA  ILE A2365 "
      ideal   model   delta    sigma   weight residual
     121.97  130.01   -8.04 1.80e+00 3.09e-01 1.99e+01
  angle pdb=" C   MET A2864 "
        pdb=" N   ILE A2865 "
        pdb=" CA  ILE A2865 "
      ideal   model   delta    sigma   weight residual
     121.70  129.21   -7.51 1.80e+00 3.09e-01 1.74e+01
  angle pdb=" C   PHE A1353 "
        pdb=" N   ASN A1354 "
        pdb=" CA  ASN A1354 "
      ideal   model   delta    sigma   weight residual
     122.07  127.60   -5.53 1.43e+00 4.89e-01 1.50e+01
  angle pdb=" OG1 THR A2360 "
        pdb=" CB  THR A2360 "
        pdb=" CG2 THR A2360 "
      ideal   model   delta    sigma   weight residual
     109.30  101.60    7.70 2.00e+00 2.50e-01 1.48e+01
  angle pdb=" CA  VAL A1570 "
        pdb=" CB  VAL A1570 "
        pdb=" CG1 VAL A1570 "
      ideal   model   delta    sigma   weight residual
     110.40  116.87   -6.47 1.70e+00 3.46e-01 1.45e+01
  ... (remaining 16618 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.23: 7049
       17.23 -    34.46: 445
       34.46 -    51.70: 69
       51.70 -    68.93: 9
       68.93 -    86.16: 2
  Dihedral angle restraints: 7574
    sinusoidal: 3114
      harmonic: 4460
  Sorted by residual:
  dihedral pdb=" CA  GLU A3120 "
           pdb=" C   GLU A3120 "
           pdb=" N   VAL A3121 "
           pdb=" CA  VAL A3121 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.04  -22.96     0      5.00e+00 4.00e-02 2.11e+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 -159.14  -20.86     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  PRO A3123 "
           pdb=" C   PRO A3123 "
           pdb=" N   THR A3124 "
           pdb=" CA  THR A3124 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.24  -20.76     0      5.00e+00 4.00e-02 1.72e+01
  ... (remaining 7571 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1684
       0.073 -    0.146: 215
       0.146 -    0.219: 17
       0.219 -    0.292: 0
       0.292 -    0.365: 1
  Chirality restraints: 1917
  Sorted by residual:
  chirality pdb=" CB  THR A1153 "
            pdb=" CA  THR A1153 "
            pdb=" OG1 THR A1153 "
            pdb=" CG2 THR A1153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.19    0.37 2.00e-01 2.50e+01 3.34e+00
  chirality pdb=" CB  THR A2360 "
            pdb=" CA  THR A2360 "
            pdb=" OG1 THR A2360 "
            pdb=" CG2 THR A2360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.77   -0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CA  THR A1153 "
            pdb=" N   THR A1153 "
            pdb=" C   THR A1153 "
            pdb=" CB  THR A1153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.32    0.21 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 1914 not shown)

  Planarity restraints: 2105
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A1146 "   -0.051 5.00e-02 4.00e+02   7.78e-02 9.68e+00
        pdb=" N   PRO A1147 "    0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO A1147 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A1147 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A2633 "   -0.022 2.00e-02 2.50e+03   2.23e-02 8.68e+00
        pdb=" CG  PHE A2633 "    0.052 2.00e-02 2.50e+03
        pdb=" CD1 PHE A2633 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE A2633 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE A2633 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A2633 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A2633 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 954 "    0.045 5.00e-02 4.00e+02   6.75e-02 7.30e+00
        pdb=" N   PRO A 955 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A 955 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 955 "    0.037 5.00e-02 4.00e+02
  ... (remaining 2102 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 35
        2.56 -     3.15: 8857
        3.15 -     3.73: 18064
        3.73 -     4.32: 26416
        4.32 -     4.90: 43851
  Nonbonded interactions: 97223
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A2788 "
            pdb="ZN    ZN A6001 "
     model   vdw
     1.976 2.230
  nonbonded pdb=" O   MET A1135 "
            pdb=" OG  SER A1139 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" OG1 THR A2507 "
            pdb=" OG1 THR A2526 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" NH2 ARG A1526 "
            pdb=" OE2 GLU A2575 "
     model   vdw
     2.338 3.120
  nonbonded pdb=" OH  TYR A1755 "
            pdb=" OE1 GLN A1785 "
     model   vdw
     2.338 3.040
  ... (remaining 97218 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             5.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     14.280
  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:7.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
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   0.050  12339  Z= 0.200
  Angle     :  0.780  10.981  16629  Z= 0.424
  Chirality :  0.049   0.365   1917
  Planarity :  0.007   0.078   2105
  Dihedral  : 11.442  86.159   4666
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.19), residues: 1492
  helix: -0.38 (0.15), residues: 859
  sheet:  0.97 (0.50), residues: 99
  loop : -1.42 (0.22), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 948 
 TYR   0.032   0.002   TYR A2994 
 PHE   0.052   0.003   PHE A2633 
 TRP   0.019   0.002   TRP A2542 
 HIS   0.008   0.002   HIS A1491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (12332)
  covalent geometry    : angle       0.76895 (16623)
  hydrogen bonds       : bond        0.13957 (  661)
  hydrogen bonds       : angle       5.66058 ( 1932)
  metal coordination   : bond        0.00722 (    7)
  metal coordination   : angle       7.03850 (    6)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1775 SER cc_start: 0.8797 (p) cc_final: 0.8586 (t)
REVERT: A 2298 MET cc_start: 0.8644 (tpp) cc_final: 0.8046 (pmt)
  outliers start: 0
  outliers final: 1
  residues processed: 236
  average time/residue: 0.7818
  time to fit residues: 196.2751
Evaluate side-chains
  119 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 118
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3132 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9980
   chunk 149 optimal weight:    6.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A1284 ASN
A1286 GLN
A1381 ASN
A1421 GLN
A1424 GLN
A1556 ASN
A2644 HIS
A2770 GLN
A2857 ASN
** A3045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A3064 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.119073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.081549 restraints weight = 19342.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 2.55
r_work: 0.3031 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  12339  Z= 0.178
  Angle     :  0.579   8.838  16629  Z= 0.304
  Chirality :  0.042   0.181   1917
  Planarity :  0.005   0.051   2105
  Dihedral  :  4.428  19.861   1637
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  8.02 %
    Favored  : 90.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    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:  0.40 (0.20), residues: 1492
  helix:  1.12 (0.17), residues: 866
  sheet:  0.82 (0.49), residues: 99
  loop : -1.28 (0.23), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1551 
 TYR   0.020   0.001   TYR A2994 
 PHE   0.035   0.002   PHE A2633 
 TRP   0.022   0.002   TRP A2542 
 HIS   0.008   0.001   HIS A3045 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 (12332)
  covalent geometry    : angle       0.56927 (16623)
  hydrogen bonds       : bond        0.05469 (  661)
  hydrogen bonds       : angle       4.15505 ( 1932)
  metal coordination   : bond        0.00843 (    7)
  metal coordination   : angle       5.52134 (    6)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
REVERT: A  990 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7924 (ttt90)
REVERT: A 1362 LYS cc_start: 0.8791 (tttt) cc_final: 0.8502 (tttm)
REVERT: A 1364 ARG cc_start: 0.8249 (mtt90) cc_final: 0.7913 (mtt90)
REVERT: A 2298 MET cc_start: 0.8229 (tpp) cc_final: 0.7146 (pmt)
REVERT: A 2342 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8355 (mp0)
REVERT: A 3100 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.6857 (mtt-85)
REVERT: A 3139 MET cc_start: 0.8408 (ptt) cc_final: 0.7956 (pmm)
  outliers start: 20
  outliers final: 5
  residues processed: 133
  average time/residue: 0.6970
  time to fit residues: 99.3483
Evaluate side-chains
  110 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  990 ARG
Chi-restraints excluded: chain A residue 1216 SER
Chi-restraints excluded: chain A residue 2467 SER
Chi-restraints excluded: chain A residue 2865 ILE
Chi-restraints excluded: chain A residue 3005 SER
Chi-restraints excluded: chain A residue 3100 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 122 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 146 optimal weight:    0.7980
   chunk 149 optimal weight:    0.0000
   chunk 83 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 82 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 106 optimal weight:    0.9980
   overall best weight:    0.5984

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

Flipped N/Q/H residues before XYZ refinement:
A1060 ASN
A1381 ASN
A1485 ASN
A1523 GLN
** A3045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.120583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.082973 restraints weight = 19546.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 2.59
r_work: 0.3069 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2940 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.2611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  12339  Z= 0.117
  Angle     :  0.513  13.086  16629  Z= 0.265
  Chirality :  0.039   0.151   1917
  Planarity :  0.004   0.040   2105
  Dihedral  :  4.036  18.590   1635
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  :  8.73 %
    Favored  : 89.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.21), residues: 1492
  helix:  1.72 (0.18), residues: 875
  sheet:  0.95 (0.51), residues: 97
  loop : -1.12 (0.24), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1551 
 TYR   0.012   0.001   TYR A2994 
 PHE   0.031   0.001   PHE A2633 
 TRP   0.017   0.001   TRP A2542 
 HIS   0.007   0.001   HIS A3045 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (12332)
  covalent geometry    : angle       0.50519 (16623)
  hydrogen bonds       : bond        0.04167 (  661)
  hydrogen bonds       : angle       3.82672 ( 1932)
  metal coordination   : bond        0.00480 (    7)
  metal coordination   : angle       4.59614 (    6)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
REVERT: A  990 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7871 (ttt90)
REVERT: A 1362 LYS cc_start: 0.8779 (tttt) cc_final: 0.8492 (tttm)
REVERT: A 1364 ARG cc_start: 0.8187 (mtt180) cc_final: 0.7747 (mtt90)
REVERT: A 2298 MET cc_start: 0.8216 (tpp) cc_final: 0.7207 (pmt)
REVERT: A 2561 MET cc_start: 0.9036 (mtp) cc_final: 0.8768 (mtp)
REVERT: A 2957 PHE cc_start: 0.7570 (m-80) cc_final: 0.6533 (m-80)
REVERT: A 3132 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8827 (tp)
REVERT: A 3139 MET cc_start: 0.8150 (ptt) cc_final: 0.7789 (ptt)
REVERT: A 3150 LYS cc_start: 0.7742 (tppt) cc_final: 0.7461 (mtmt)
REVERT: A 3183 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7724 (mpp-170)
  outliers start: 23
  outliers final: 8
  residues processed: 127
  average time/residue: 0.6545
  time to fit residues: 89.4909
Evaluate side-chains
  113 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  990 ARG
Chi-restraints excluded: chain A residue 2579 GLU
Chi-restraints excluded: chain A residue 2785 ASN
Chi-restraints excluded: chain A residue 2859 ILE
Chi-restraints excluded: chain A residue 2865 ILE
Chi-restraints excluded: chain A residue 3005 SER
Chi-restraints excluded: chain A residue 3092 LEU
Chi-restraints excluded: chain A residue 3132 LEU
Chi-restraints excluded: chain A residue 3183 ARG
Chi-restraints excluded: chain A residue 3202 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 88 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 142 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 114 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 84 optimal weight:    0.5980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A1381 ASN
A1485 ASN
A1523 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.117708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.079996 restraints weight = 19422.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 2.54
r_work: 0.2973 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.2852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  12339  Z= 0.162
  Angle     :  0.533   7.110  16629  Z= 0.279
  Chirality :  0.041   0.167   1917
  Planarity :  0.004   0.038   2105
  Dihedral  :  4.081  19.403   1635
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  :  8.80 %
    Favored  : 89.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.22), residues: 1492
  helix:  1.80 (0.18), residues: 874
  sheet:  0.63 (0.48), residues: 104
  loop : -1.06 (0.25), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1257 
 TYR   0.014   0.001   TYR A2994 
 PHE   0.029   0.001   PHE A2633 
 TRP   0.017   0.001   TRP A2542 
 HIS   0.008   0.001   HIS A3045 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (12332)
  covalent geometry    : angle       0.52695 (16623)
  hydrogen bonds       : bond        0.05000 (  661)
  hydrogen bonds       : angle       3.91112 ( 1932)
  metal coordination   : bond        0.00716 (    7)
  metal coordination   : angle       4.07403 (    6)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 109
  time to evaluate  : 0.466 
Fit side-chains
REVERT: A  990 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7896 (ttt90)
REVERT: A 1071 ASN cc_start: 0.8325 (m-40) cc_final: 0.7562 (p0)
REVERT: A 1362 LYS cc_start: 0.8819 (tttt) cc_final: 0.8494 (tttm)
REVERT: A 1399 TYR cc_start: 0.9019 (m-80) cc_final: 0.8809 (m-80)
REVERT: A 2298 MET cc_start: 0.8168 (tpp) cc_final: 0.7128 (pmt)
REVERT: A 2463 MET cc_start: 0.7202 (mmp) cc_final: 0.6893 (tpt)
REVERT: A 3132 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8839 (tp)
REVERT: A 3139 MET cc_start: 0.7957 (ptt) cc_final: 0.7752 (ptt)
  outliers start: 30
  outliers final: 9
  residues processed: 127
  average time/residue: 0.6644
  time to fit residues: 90.9264
Evaluate side-chains
  110 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  990 ARG
Chi-restraints excluded: chain A residue 1203 ILE
Chi-restraints excluded: chain A residue 1216 SER
Chi-restraints excluded: chain A residue 1351 THR
Chi-restraints excluded: chain A residue 2360 THR
Chi-restraints excluded: chain A residue 2467 SER
Chi-restraints excluded: chain A residue 2865 ILE
Chi-restraints excluded: chain A residue 3005 SER
Chi-restraints excluded: chain A residue 3092 LEU
Chi-restraints excluded: chain A residue 3132 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 150 optimal weight:    0.6980
   chunk 70 optimal weight:    0.8980
   chunk 123 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 125 optimal weight:    0.0270
   chunk 21 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    0.7038

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

Flipped N/Q/H residues before XYZ refinement:
A1523 GLN
A2785 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.118043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.080415 restraints weight = 19549.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 2.63
r_work: 0.2944 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2819 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.2990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  12339  Z= 0.123
  Angle     :  0.497   7.770  16629  Z= 0.258
  Chirality :  0.040   0.153   1917
  Planarity :  0.003   0.034   2105
  Dihedral  :  3.881  19.143   1635
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 10.02 %
    Favored  : 88.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.22), residues: 1492
  helix:  2.05 (0.18), residues: 867
  sheet:  0.60 (0.48), residues: 104
  loop : -1.03 (0.25), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1805 
 TYR   0.010   0.001   TYR A1413 
 PHE   0.029   0.001   PHE A2633 
 TRP   0.016   0.001   TRP A2542 
 HIS   0.006   0.001   HIS A3045 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (12332)
  covalent geometry    : angle       0.49175 (16623)
  hydrogen bonds       : bond        0.04188 (  661)
  hydrogen bonds       : angle       3.73213 ( 1932)
  metal coordination   : bond        0.00530 (    7)
  metal coordination   : angle       3.93291 (    6)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 0.503 
Fit side-chains
REVERT: A  990 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7847 (ttt90)
REVERT: A 1071 ASN cc_start: 0.8368 (m-40) cc_final: 0.7622 (p0)
REVERT: A 1362 LYS cc_start: 0.8831 (tttt) cc_final: 0.8503 (tttm)
REVERT: A 2298 MET cc_start: 0.8130 (tpp) cc_final: 0.7129 (pmt)
REVERT: A 2463 MET cc_start: 0.7202 (mmp) cc_final: 0.6952 (tpt)
REVERT: A 3135 ARG cc_start: 0.8161 (ttt-90) cc_final: 0.7814 (tmm-80)
REVERT: A 3139 MET cc_start: 0.7930 (ptt) cc_final: 0.7513 (ptm)
  outliers start: 17
  outliers final: 4
  residues processed: 122
  average time/residue: 0.7036
  time to fit residues: 92.3513
Evaluate side-chains
  107 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  990 ARG
Chi-restraints excluded: chain A residue 2865 ILE
Chi-restraints excluded: chain A residue 3005 SER
Chi-restraints excluded: chain A residue 3092 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 117 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 150 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9990
   chunk 120 optimal weight:    2.9990
   chunk 122 optimal weight:    4.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A1424 GLN
A1523 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.117015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.079334 restraints weight = 19458.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 2.63
r_work: 0.2955 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.3077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  12339  Z= 0.143
  Angle     :  0.516   7.946  16629  Z= 0.268
  Chirality :  0.040   0.159   1917
  Planarity :  0.003   0.033   2105
  Dihedral  :  3.911  19.444   1635
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 10.38 %
    Favored  : 88.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.22), residues: 1492
  helix:  2.08 (0.18), residues: 865
  sheet:  0.63 (0.48), residues: 103
  loop : -1.06 (0.24), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1805 
 TYR   0.010   0.001   TYR A2994 
 PHE   0.028   0.001   PHE A2633 
 TRP   0.016   0.001   TRP A2542 
 HIS   0.007   0.001   HIS A3045 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (12332)
  covalent geometry    : angle       0.51124 (16623)
  hydrogen bonds       : bond        0.04614 (  661)
  hydrogen bonds       : angle       3.79294 ( 1932)
  metal coordination   : bond        0.00659 (    7)
  metal coordination   : angle       3.77908 (    6)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A  990 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7860 (ttt90)
REVERT: A 1071 ASN cc_start: 0.8432 (m-40) cc_final: 0.7670 (p0)
REVERT: A 1368 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8254 (pt)
REVERT: A 2298 MET cc_start: 0.8137 (tpp) cc_final: 0.7113 (pmt)
REVERT: A 2463 MET cc_start: 0.7246 (mmp) cc_final: 0.7007 (tpt)
REVERT: A 3132 LEU cc_start: 0.9295 (tp) cc_final: 0.9079 (tt)
REVERT: A 3136 PHE cc_start: 0.8322 (t80) cc_final: 0.7989 (m-10)
REVERT: A 3139 MET cc_start: 0.8319 (ptt) cc_final: 0.7802 (ptt)
REVERT: A 3173 ARG cc_start: 0.8313 (ttp-170) cc_final: 0.8041 (ptp-170)
REVERT: A 3184 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7900 (mmp)
  outliers start: 18
  outliers final: 9
  residues processed: 120
  average time/residue: 0.6799
  time to fit residues: 87.7023
Evaluate side-chains
  114 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  990 ARG
Chi-restraints excluded: chain A residue 1203 ILE
Chi-restraints excluded: chain A residue 1216 SER
Chi-restraints excluded: chain A residue 1368 ILE
Chi-restraints excluded: chain A residue 2360 THR
Chi-restraints excluded: chain A residue 2467 SER
Chi-restraints excluded: chain A residue 2865 ILE
Chi-restraints excluded: chain A residue 3005 SER
Chi-restraints excluded: chain A residue 3092 LEU
Chi-restraints excluded: chain A residue 3184 MET
Chi-restraints excluded: chain A residue 3202 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 143 optimal weight:    0.9990
   chunk 11 optimal weight:    0.3980
   chunk 61 optimal weight:    2.9990
   chunk 147 optimal weight:    7.9990
   chunk 2 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 139 optimal weight:    0.0020
   chunk 85 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   chunk 109 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   overall best weight:    0.6390

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

Flipped N/Q/H residues before XYZ refinement:
A1424 GLN
A1523 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.118120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.080629 restraints weight = 19554.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 2.60
r_work: 0.2977 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.3155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  12339  Z= 0.118
  Angle     :  0.496   8.332  16629  Z= 0.258
  Chirality :  0.040   0.158   1917
  Planarity :  0.003   0.035   2105
  Dihedral  :  3.796  19.365   1635
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 10.74 %
    Favored  : 87.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.22), residues: 1492
  helix:  2.17 (0.18), residues: 863
  sheet:  0.55 (0.48), residues: 104
  loop : -1.02 (0.24), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1805 
 TYR   0.009   0.001   TYR A1413 
 PHE   0.028   0.001   PHE A2633 
 TRP   0.016   0.001   TRP A2542 
 HIS   0.005   0.001   HIS A3045 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (12332)
  covalent geometry    : angle       0.49105 (16623)
  hydrogen bonds       : bond        0.04083 (  661)
  hydrogen bonds       : angle       3.73283 ( 1932)
  metal coordination   : bond        0.00495 (    7)
  metal coordination   : angle       3.72651 (    6)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  990 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7826 (ttt90)
REVERT: A 1071 ASN cc_start: 0.8441 (m-40) cc_final: 0.7719 (p0)
REVERT: A 1215 LYS cc_start: 0.7403 (mmtt) cc_final: 0.6685 (tptp)
REVERT: A 2298 MET cc_start: 0.8086 (tpp) cc_final: 0.7090 (pmt)
REVERT: A 3139 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7741 (ptm)
REVERT: A 3173 ARG cc_start: 0.8190 (ttp-170) cc_final: 0.7946 (ptp-170)
REVERT: A 3184 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7871 (mmp)
  outliers start: 19
  outliers final: 10
  residues processed: 117
  average time/residue: 0.6715
  time to fit residues: 84.3940
Evaluate side-chains
  114 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  990 ARG
Chi-restraints excluded: chain A residue 1216 SER
Chi-restraints excluded: chain A residue 2360 THR
Chi-restraints excluded: chain A residue 2467 SER
Chi-restraints excluded: chain A residue 2859 ILE
Chi-restraints excluded: chain A residue 2865 ILE
Chi-restraints excluded: chain A residue 3005 SER
Chi-restraints excluded: chain A residue 3092 LEU
Chi-restraints excluded: chain A residue 3139 MET
Chi-restraints excluded: chain A residue 3151 MET
Chi-restraints excluded: chain A residue 3184 MET
Chi-restraints excluded: chain A residue 3202 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 78 optimal weight:    0.0170
   chunk 142 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   chunk 116 optimal weight:    0.6980
   chunk 98 optimal weight:    2.9990
   chunk 101 optimal weight:    0.7980
   chunk 114 optimal weight:    0.3980
   chunk 3 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
A1424 GLN
A1523 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.118277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.080752 restraints weight = 19520.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3105 rms_B_bonded: 2.63
r_work: 0.2982 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2861 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.3233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  12339  Z= 0.113
  Angle     :  0.504   8.511  16629  Z= 0.259
  Chirality :  0.039   0.155   1917
  Planarity :  0.003   0.039   2105
  Dihedral  :  3.721  18.686   1635
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 11.17 %
    Favored  : 87.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.56 (0.22), residues: 1492
  helix:  2.25 (0.18), residues: 863
  sheet:  0.56 (0.49), residues: 103
  loop : -0.99 (0.25), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1805 
 TYR   0.010   0.001   TYR A1413 
 PHE   0.026   0.001   PHE A2633 
 TRP   0.016   0.001   TRP A2542 
 HIS   0.005   0.001   HIS A3045 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (12332)
  covalent geometry    : angle       0.49931 (16623)
  hydrogen bonds       : bond        0.03926 (  661)
  hydrogen bonds       : angle       3.67503 ( 1932)
  metal coordination   : bond        0.00506 (    7)
  metal coordination   : angle       3.62763 (    6)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.472 
Fit side-chains
REVERT: A  990 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7833 (ttt90)
REVERT: A 1071 ASN cc_start: 0.8440 (m-40) cc_final: 0.7737 (p0)
REVERT: A 1108 ARG cc_start: 0.7707 (mtt-85) cc_final: 0.7026 (mpp-170)
REVERT: A 1215 LYS cc_start: 0.7364 (mmtt) cc_final: 0.6641 (tptp)
REVERT: A 2298 MET cc_start: 0.8091 (tpp) cc_final: 0.7107 (pmt)
REVERT: A 3132 LEU cc_start: 0.9249 (tt) cc_final: 0.9026 (tp)
REVERT: A 3173 ARG cc_start: 0.8128 (ttp-170) cc_final: 0.7885 (ptp-170)
REVERT: A 3184 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7912 (mmp)
  outliers start: 17
  outliers final: 10
  residues processed: 116
  average time/residue: 0.7062
  time to fit residues: 88.0793
Evaluate side-chains
  111 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  990 ARG
Chi-restraints excluded: chain A residue 1216 SER
Chi-restraints excluded: chain A residue 2360 THR
Chi-restraints excluded: chain A residue 2467 SER
Chi-restraints excluded: chain A residue 2859 ILE
Chi-restraints excluded: chain A residue 2865 ILE
Chi-restraints excluded: chain A residue 3005 SER
Chi-restraints excluded: chain A residue 3092 LEU
Chi-restraints excluded: chain A residue 3151 MET
Chi-restraints excluded: chain A residue 3184 MET
Chi-restraints excluded: chain A residue 3202 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 139 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   chunk 141 optimal weight:    4.9990
   chunk 13 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 83 optimal weight:    0.5980
   chunk 101 optimal weight:    0.8980
   chunk 120 optimal weight:    0.4980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A1424 GLN
A1523 GLN
A1556 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.118103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.080461 restraints weight = 19352.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 2.62
r_work: 0.2931 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2805 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.3265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  12339  Z= 0.125
  Angle     :  0.526  10.577  16629  Z= 0.270
  Chirality :  0.040   0.155   1917
  Planarity :  0.003   0.045   2105
  Dihedral  :  3.749  19.264   1635
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 11.74 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.22), residues: 1492
  helix:  2.21 (0.18), residues: 865
  sheet:  0.53 (0.49), residues: 103
  loop : -0.99 (0.25), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A1805 
 TYR   0.009   0.001   TYR A1413 
 PHE   0.027   0.001   PHE A2633 
 TRP   0.016   0.001   TRP A2542 
 HIS   0.005   0.001   HIS A3045 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (12332)
  covalent geometry    : angle       0.52204 (16623)
  hydrogen bonds       : bond        0.04196 (  661)
  hydrogen bonds       : angle       3.73970 ( 1932)
  metal coordination   : bond        0.00535 (    7)
  metal coordination   : angle       3.57902 (    6)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.304 
Fit side-chains
REVERT: A  990 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7835 (ttt90)
REVERT: A 1071 ASN cc_start: 0.8447 (m-40) cc_final: 0.7739 (p0)
REVERT: A 1108 ARG cc_start: 0.7655 (mtt-85) cc_final: 0.6983 (mpp-170)
REVERT: A 1127 ASN cc_start: 0.8643 (m-40) cc_final: 0.8081 (p0)
REVERT: A 1215 LYS cc_start: 0.7308 (mmtt) cc_final: 0.6580 (tptp)
REVERT: A 2298 MET cc_start: 0.8063 (tpp) cc_final: 0.7086 (pmt)
REVERT: A 3139 MET cc_start: 0.7658 (ptt) cc_final: 0.7371 (pmt)
REVERT: A 3173 ARG cc_start: 0.8109 (ttp-170) cc_final: 0.7887 (ptp-170)
REVERT: A 3184 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7886 (mmp)
  outliers start: 15
  outliers final: 11
  residues processed: 111
  average time/residue: 0.6900
  time to fit residues: 82.3928
Evaluate side-chains
  113 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  990 ARG
Chi-restraints excluded: chain A residue 1216 SER
Chi-restraints excluded: chain A residue 2360 THR
Chi-restraints excluded: chain A residue 2467 SER
Chi-restraints excluded: chain A residue 2830 ILE
Chi-restraints excluded: chain A residue 2859 ILE
Chi-restraints excluded: chain A residue 2865 ILE
Chi-restraints excluded: chain A residue 3005 SER
Chi-restraints excluded: chain A residue 3092 LEU
Chi-restraints excluded: chain A residue 3151 MET
Chi-restraints excluded: chain A residue 3184 MET
Chi-restraints excluded: chain A residue 3202 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 2 optimal weight:    0.0870
   chunk 19 optimal weight:    4.9990
   chunk 91 optimal weight:    1.9990
   chunk 118 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0030
   chunk 86 optimal weight:   20.0000
   chunk 98 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 22 optimal weight:    6.9990
   chunk 146 optimal weight:    0.8980
   overall best weight:    0.7370

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

Flipped N/Q/H residues before XYZ refinement:
A1424 GLN
A1523 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.117532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.079911 restraints weight = 19401.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 2.60
r_work: 0.2970 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.3304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  12339  Z= 0.130
  Angle     :  0.535  11.785  16629  Z= 0.275
  Chirality :  0.040   0.157   1917
  Planarity :  0.003   0.048   2105
  Dihedral  :  3.775  19.349   1635
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 11.88 %
    Favored  : 86.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.22), residues: 1492
  helix:  2.21 (0.18), residues: 862
  sheet:  0.60 (0.48), residues: 105
  loop : -1.00 (0.25), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A1805 
 TYR   0.009   0.001   TYR A1413 
 PHE   0.027   0.001   PHE A2633 
 TRP   0.016   0.001   TRP A2542 
 HIS   0.005   0.001   HIS A3045 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (12332)
  covalent geometry    : angle       0.53054 (16623)
  hydrogen bonds       : bond        0.04271 (  661)
  hydrogen bonds       : angle       3.79859 ( 1932)
  metal coordination   : bond        0.00562 (    7)
  metal coordination   : angle       3.59432 (    6)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.402 
Fit side-chains
REVERT: A  990 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7811 (ttt90)
REVERT: A 1071 ASN cc_start: 0.8468 (m-40) cc_final: 0.7776 (p0)
REVERT: A 1108 ARG cc_start: 0.7682 (mtt-85) cc_final: 0.6891 (mpp-170)
REVERT: A 1127 ASN cc_start: 0.8649 (m-40) cc_final: 0.8082 (p0)
REVERT: A 1215 LYS cc_start: 0.7361 (mmtt) cc_final: 0.6647 (tptp)
REVERT: A 2298 MET cc_start: 0.8056 (tpp) cc_final: 0.7079 (pmt)
REVERT: A 2539 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7711 (mm-30)
REVERT: A 3139 MET cc_start: 0.7708 (ptt) cc_final: 0.7396 (pmt)
REVERT: A 3173 ARG cc_start: 0.8116 (ttp-170) cc_final: 0.7897 (ptp-170)
REVERT: A 3184 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7882 (mmp)
  outliers start: 16
  outliers final: 13
  residues processed: 114
  average time/residue: 0.6612
  time to fit residues: 81.3485
Evaluate side-chains
  117 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  990 ARG
Chi-restraints excluded: chain A residue 1153 THR
Chi-restraints excluded: chain A residue 1216 SER
Chi-restraints excluded: chain A residue 2360 THR
Chi-restraints excluded: chain A residue 2467 SER
Chi-restraints excluded: chain A residue 2539 GLU
Chi-restraints excluded: chain A residue 2830 ILE
Chi-restraints excluded: chain A residue 2859 ILE
Chi-restraints excluded: chain A residue 2865 ILE
Chi-restraints excluded: chain A residue 3005 SER
Chi-restraints excluded: chain A residue 3056 LEU
Chi-restraints excluded: chain A residue 3092 LEU
Chi-restraints excluded: chain A residue 3151 MET
Chi-restraints excluded: chain A residue 3184 MET
Chi-restraints excluded: chain A residue 3202 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 128 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   chunk 143 optimal weight:    0.9980
   chunk 138 optimal weight:    0.0570
   chunk 45 optimal weight:    0.7980
   chunk 93 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0770
   chunk 126 optimal weight:    0.9990
   chunk 147 optimal weight:    6.9990
   overall best weight:    0.5656

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

Flipped N/Q/H residues before XYZ refinement:
A1424 GLN
A1523 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.118853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.081254 restraints weight = 19461.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3070 rms_B_bonded: 2.63
r_work: 0.2942 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2815 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.3349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  12339  Z= 0.116
  Angle     :  0.530  11.869  16629  Z= 0.271
  Chirality :  0.039   0.157   1917
  Planarity :  0.003   0.048   2105
  Dihedral  :  3.688  18.819   1635
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 12.10 %
    Favored  : 86.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.22), residues: 1492
  helix:  2.26 (0.18), residues: 862
  sheet:  0.62 (0.49), residues: 105
  loop : -0.98 (0.25), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A1805 
 TYR   0.009   0.001   TYR A1413 
 PHE   0.026   0.001   PHE A2633 
 TRP   0.016   0.001   TRP A2542 
 HIS   0.004   0.001   HIS A3045 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (12332)
  covalent geometry    : angle       0.52583 (16623)
  hydrogen bonds       : bond        0.03906 (  661)
  hydrogen bonds       : angle       3.74725 ( 1932)
  metal coordination   : bond        0.00469 (    7)
  metal coordination   : angle       3.58501 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4897.87 seconds
wall clock time: 83 minutes 57.26 seconds (5037.26 seconds total)