Starting phenix.real_space_refine
on Tue Jul 29 02:17:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pw6_13676/07_2025/7pw6_13676.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pw6_13676/07_2025/7pw6_13676.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pw6_13676/07_2025/7pw6_13676.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pw6_13676/07_2025/7pw6_13676.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pw6_13676/07_2025/7pw6_13676.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pw6_13676/07_2025/7pw6_13676.cif"
  }
  resolution = 3.05
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.003 sd=   0.073
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
     P       6      5.49       5
     S      53      5.16       5
     Cl      1      4.86       5
     C    6645      2.51       5
     N    1851      2.21       5
     O    1837      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10393
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 5740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 767, 5740
          Classifications: {'peptide': 767}
          Incomplete info: {'truncation_to_alanine': 105}
          Link IDs: {'PTRANS': 25, 'TRANS': 741}
          Chain breaks: 12
          Unresolved non-hydrogen bonds: 329
          Unresolved non-hydrogen angles: 407
          Unresolved non-hydrogen dihedrals: 253
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 19, 'ASN:plan1': 9, 'HIS:plan': 1, 'GLU:plan': 30, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 226
    Chain: "A"
      Number of atoms: 1439
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1439
          Classifications: {'peptide': 216}
          Incomplete info: {'truncation_to_alanine': 95}
          Link IDs: {'PTRANS': 7, 'TRANS': 208}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 268
          Unresolved non-hydrogen angles: 358
          Unresolved non-hydrogen dihedrals: 190
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'UNK:plan-1': 42, 'TRP:plan': 1, 'ASP:plan': 6, 'GLU:plan': 6, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 150
    Chain: "A"
      Number of atoms: 196
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 196
          Classifications: {'peptide': 38}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 1, 'TRANS': 36}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 144
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'TYR:plan': 1, 'UNK:plan-1': 16, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 66
    Chain: "A"
      Number of atoms: 2943
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 395, 2943
          Classifications: {'peptide': 395}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 67}
          Link IDs: {'PTRANS': 18, 'TRANS': 376}
          Chain breaks: 4
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 200
          Unresolved non-hydrogen angles: 257
          Unresolved non-hydrogen dihedrals: 144
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'UNK:plan-1': 16, 'ASP:plan': 6, 'GLU:plan': 16, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 124
    Chain: "A"
      Number of atoms: 75
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 75
          Unusual residues: {'88C': 1, 'IHP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 10.90, per 1000 atoms: 1.05
  Number of scatterers: 10393
  At special positions: 0
  Unit cell: (120.87, 105.549, 107.251, 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)
     Cl      1     17.00
     S      53     16.00
     P       6     15.00
     O    1837      8.00
     N    1851      7.00
     C    6645      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: 2.70
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2718

  Finding SS restraints...
    Secondary structure from input PDB file:
      75 helices and 3 sheets defined
      76.8% alpha, 3.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 792 through 806
      removed outlier: 3.652A  pdb=" N   ARG A 797 " --> pdb=" O   ASP A 793 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 810 through 823
      removed outlier: 3.560A  pdb=" N   LYS A 819 " --> pdb=" O   GLN A 815 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU A 820 " --> pdb=" O   ALA A 816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 825 through 830
    Processing helix  chain 'A' and resid 835 through 851
      removed outlier: 3.530A  pdb=" N   ILE A 841 " --> pdb=" O   GLU A 837 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 858 through 872
    Processing helix  chain 'A' and resid 882 through 891
    Processing helix  chain 'A' and resid 902 through 907
      removed outlier: 4.041A  pdb=" N   LYS A 907 " --> pdb=" O   ASN A 904 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 908 through 927
    Processing helix  chain 'A' and resid 935 through 956
      removed outlier: 3.638A  pdb=" N   THR A 939 " --> pdb=" O   ARG A 935 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   PHE A 940 " --> pdb=" O   ALA A 936 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 969 through 999
      removed outlier: 3.831A  pdb=" N   HIS A 973 " --> pdb=" O   ASN A 969 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLY A 974 " --> pdb=" O   ASP A 970 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLN A 977 " --> pdb=" O   HIS A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1009 through 1019
      removed outlier: 3.567A  pdb=" N   THR A1018 " --> pdb=" O   THR A1014 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1019 through 1041
      removed outlier: 4.446A  pdb=" N   LEU A1032 " --> pdb=" O   THR A1028 " (cutoff:3.500A)
      removed outlier: 5.127A  pdb=" N   SER A1033 " --> pdb=" O   ARG A1029 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ARG A1036 " --> pdb=" O   LEU A1032 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1043 through 1058
      removed outlier: 3.778A  pdb=" N   THR A1047 " --> pdb=" O   GLN A1043 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1068 through 1084
    Processing helix  chain 'A' and resid 1085 through 1097
    Processing helix  chain 'A' and resid 1106 through 1115
      removed outlier: 3.550A  pdb=" N   GLN A1113 " --> pdb=" O   SER A1109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1118 through 1134
    Processing helix  chain 'A' and resid 1143 through 1151
      removed outlier: 3.677A  pdb=" N   LEU A1149 " --> pdb=" O   SER A1145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1179 through 1197
      removed outlier: 3.833A  pdb=" N   ASN A1184 " --> pdb=" O   PRO A1180 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ILE A1197 " --> pdb=" O   CYS A1193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1199 through 1218
    Processing helix  chain 'A' and resid 1227 through 1239
    Processing helix  chain 'A' and resid 1242 through 1250
    Processing helix  chain 'A' and resid 1281 through 1305
      removed outlier: 3.511A  pdb=" N   LEU A1285 " --> pdb=" O   ASP A1281 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ASN A1305 " --> pdb=" O   ALA A1301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1317 through 1332
      removed outlier: 3.615A  pdb=" N   ILE A1332 " --> pdb=" O   SER A1328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1332 through 1341
      removed outlier: 3.781A  pdb=" N   THR A1341 " --> pdb=" O   LEU A1337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1347 through 1367
    Processing helix  chain 'A' and resid 1370 through 1374
      removed outlier: 3.680A  pdb=" N   LEU A1374 " --> pdb=" O   GLU A1371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1378 through 1384
      removed outlier: 3.619A  pdb=" N   ARG A1383 " --> pdb=" O   GLU A1380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1390 through 1407
      removed outlier: 3.738A  pdb=" N   TYR A1399 " --> pdb=" O   GLN A1395 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   TYR A1402 " --> pdb=" O   ARG A1398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1408 through 1410
      No H-bonds generated for 'chain 'A' and resid 1408 through 1410'
    Processing helix  chain 'A' and resid 1417 through 1434
    Processing helix  chain 'A' and resid 1437 through 1450
    Processing helix  chain 'A' and resid 1458 through 1466
      removed outlier: 3.766A  pdb=" N   LEU A1462 " --> pdb=" O   THR A1458 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   VAL A1463 " --> pdb=" O   ALA A1459 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLN A1464 " --> pdb=" O   GLN A1460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1479 through 1494
    Processing helix  chain 'A' and resid 1496 through 1512
    Processing helix  chain 'A' and resid 1518 through 1535
      removed outlier: 4.016A  pdb=" N   ALA A1522 " --> pdb=" O   GLU A1518 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LYS A1523 " --> pdb=" O   TYR A1519 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   LEU A1528 " --> pdb=" O   SER A1524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1535 through 1551
      removed outlier: 5.052A  pdb=" N   GLY A1541 " --> pdb=" O   LYS A1537 " (cutoff:3.500A)
      removed outlier: 5.213A  pdb=" N   GLN A1542 " --> pdb=" O   GLU A1538 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   HIS A1551 " --> pdb=" O   TYR A1547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1559 through 1570
      removed outlier: 3.504A  pdb=" N   THR A1567 " --> pdb=" O   LYS A1563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1595 through 1612
      removed outlier: 3.571A  pdb=" N   PHE A1599 " --> pdb=" O   GLY A1595 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ILE A1600 " --> pdb=" O   GLU A1596 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LEU A1601 " --> pdb=" O   PRO A1597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1615 through 1637
      removed outlier: 3.823A  pdb=" N   TRP A1619 " --> pdb=" O   VAL A1615 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LEU A1622 " --> pdb=" O   SER A1618 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LYS A1632 " --> pdb=" O   ARG A1628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1647 through 1656
    Processing helix  chain 'A' and resid 1664 through 1674
    Processing helix  chain 'A' and resid 1704 through 1717
    Processing helix  chain 'A' and resid 1728 through 1741
      removed outlier: 3.714A  pdb=" N   VAL A1732 " --> pdb=" O   GLY A1728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1741 through 1757
    Processing helix  chain 'A' and resid 1781 through 1799
      removed outlier: 3.813A  pdb=" N   ALA A1788 " --> pdb=" O   MET A1784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1804 through 1812
      removed outlier: 3.909A  pdb=" N   HIS A1809 " --> pdb=" O   GLN A1805 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLU A1812 " --> pdb=" O   GLU A1808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1816 through 1820
      removed outlier: 3.727A  pdb=" N   ARG A1820 " --> pdb=" O   ALA A1817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1822 through 1829
    Processing helix  chain 'A' and resid 1834 through 1850
      removed outlier: 3.834A  pdb=" N   ARG A1838 " --> pdb=" O   GLU A1834 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLN A1850 " --> pdb=" O   CYS A1846 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1856 through 1865
      removed outlier: 3.618A  pdb=" N   ALA A1860 " --> pdb=" O   ILE A1856 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ILE A1865 " --> pdb=" O   ILE A1861 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1924 through 1939
      removed outlier: 4.382A  pdb=" N   CYS A1929 " --> pdb=" O   MET A1925 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   TYR A1930 " --> pdb=" O   MET A1926 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1941 through 1958
    Processing helix  chain 'A' and resid 1963 through 1976
    Processing helix  chain 'A' and resid 2007 through 2020
    Processing helix  chain 'A' and resid 2036 through 2045
    Processing helix  chain 'A' and resid 2046 through 2056
      removed outlier: 3.973A  pdb=" N   LYS A2056 " --> pdb=" O   LEU A2052 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2069 through 2083
      removed outlier: 3.689A  pdb=" N   UNK A2083 " --> pdb=" O   UNK A2079 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2160 through 2176
      removed outlier: 3.668A  pdb=" N   GLU A2164 " --> pdb=" O   LEU A2160 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ARG A2165 " --> pdb=" O   HIS A2161 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   MET A2176 " --> pdb=" O   ILE A2172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2177 through 2178
      No H-bonds generated for 'chain 'A' and resid 2177 through 2178'
    Processing helix  chain 'A' and resid 2179 through 2183
      removed outlier: 3.672A  pdb=" N   GLN A2183 " --> pdb=" O   ILE A2180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2214 through 2232
      removed outlier: 3.760A  pdb=" N   TYR A2218 " --> pdb=" O   LEU A2214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2250 through 2265
      removed outlier: 3.584A  pdb=" N   LYS A2256 " --> pdb=" O   LEU A2252 " (cutoff:3.500A)
      Proline residue:  A2259  - end of helix
      removed outlier: 3.661A  pdb=" N   VAL A2264 " --> pdb=" O   ALA A2260 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLY A2265 " --> pdb=" O   LEU A2261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2276 through 2289
      removed outlier: 3.555A  pdb=" N   MET A2280 " --> pdb=" O   PRO A2276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2294 through 2304
    Processing helix  chain 'A' and resid 2306 through 2332
    Processing helix  chain 'A' and resid 2337 through 2339
      No H-bonds generated for 'chain 'A' and resid 2337 through 2339'
    Processing helix  chain 'A' and resid 2361 through 2365
    Processing helix  chain 'A' and resid 2376 through 2382
    Processing helix  chain 'A' and resid 2390 through 2406
    Processing helix  chain 'A' and resid 2406 through 2419
      removed outlier: 3.813A  pdb=" N   LEU A2410 " --> pdb=" O   GLY A2406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3608 through 3622
    Processing helix  chain 'A' and resid 3632 through 3646
    Processing helix  chain 'A' and resid 3646 through 3652
      removed outlier: 3.694A  pdb=" N   LEU A3650 " --> pdb=" O   ASN A3646 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   GLN A3652 " --> pdb=" O   ASP A3648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3654 through 3658
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2089 through 2091
      removed outlier: 3.576A  pdb=" N   ILE A2128 " --> pdb=" O   LEU A2090 " (cutoff:3.500A)
      removed outlier: 7.471A  pdb=" N   THR A2127 " --> pdb=" O   LEU A2141 " (cutoff:3.500A)
      removed outlier: 5.301A  pdb=" N   LEU A2141 " --> pdb=" O   THR A2127 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   LEU A2141 " --> pdb=" O   VAL A2124 " (cutoff:3.500A)
      removed outlier: 5.094A  pdb=" N   VAL A2124 " --> pdb=" O   LEU A2141 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   LEU A2143 " --> pdb=" O   HIS A2122 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 2089 through 2091
      removed outlier: 3.576A  pdb=" N   ILE A2128 " --> pdb=" O   LEU A2090 " (cutoff:3.500A)
      removed outlier: 7.471A  pdb=" N   THR A2127 " --> pdb=" O   LEU A2141 " (cutoff:3.500A)
      removed outlier: 5.301A  pdb=" N   LEU A2141 " --> pdb=" O   THR A2127 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 2211 through 2213

    696 hydrogen bonds defined for protein.
    2043 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: 6.51

  Time building geometry restraints manager: 3.44 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: 3009
        1.34 -     1.45: 1536
        1.45 -     1.57: 5952
        1.57 -     1.69: 7
        1.69 -     1.81: 80
  Bond restraints: 10584
  Sorted by residual:
  bond pdb=" C13 88C A3702 "
       pdb=" N35 88C A3702 "
    ideal  model  delta    sigma   weight residual
    1.325  1.398 -0.073 2.00e-02 2.50e+03 1.33e+01
  bond pdb=" C28 88C A3702 "
       pdb=" N30 88C A3702 "
    ideal  model  delta    sigma   weight residual
    1.352  1.424 -0.072 2.00e-02 2.50e+03 1.28e+01
  bond pdb=" C26 88C A3702 "
       pdb=" N27 88C A3702 "
    ideal  model  delta    sigma   weight residual
    1.391  1.462 -0.071 2.00e-02 2.50e+03 1.26e+01
  bond pdb=" C28 88C A3702 "
       pdb=" N27 88C A3702 "
    ideal  model  delta    sigma   weight residual
    1.376  1.443 -0.067 2.00e-02 2.50e+03 1.13e+01
  bond pdb=" C13 88C A3702 "
       pdb=" N12 88C A3702 "
    ideal  model  delta    sigma   weight residual
    1.364  1.417 -0.053 2.00e-02 2.50e+03 7.14e+00
  ... (remaining 10579 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 14160
        1.82 -     3.64: 213
        3.64 -     5.46: 54
        5.46 -     7.27: 10
        7.27 -     9.09: 10
  Bond angle restraints: 14447
  Sorted by residual:
  angle pdb=" C   ALA A1002 "
        pdb=" N   ASN A1003 "
        pdb=" CA  ASN A1003 "
      ideal   model   delta    sigma   weight residual
     121.54  128.41   -6.87 1.91e+00 2.74e-01 1.29e+01
  angle pdb=" N   VAL A1390 "
        pdb=" CA  VAL A1390 "
        pdb=" C   VAL A1390 "
      ideal   model   delta    sigma   weight residual
     112.83  109.30    3.53 9.90e-01 1.02e+00 1.27e+01
  angle pdb=" O12 IHP A3701 "
        pdb=" P2  IHP A3701 "
        pdb=" O32 IHP A3701 "
      ideal   model   delta    sigma   weight residual
     100.47  109.56   -9.09 3.00e+00 1.11e-01 9.19e+00
  angle pdb=" C09 88C A3702 "
        pdb=" S06 88C A3702 "
        pdb=" N03 88C A3702 "
      ideal   model   delta    sigma   weight residual
     102.09  110.79   -8.70 3.00e+00 1.11e-01 8.42e+00
  angle pdb=" O16 IHP A3701 "
        pdb=" P6  IHP A3701 "
        pdb=" O36 IHP A3701 "
      ideal   model   delta    sigma   weight residual
     101.25  109.51   -8.26 3.00e+00 1.11e-01 7.58e+00
  ... (remaining 14442 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.03: 6175
       33.03 -    66.06: 116
       66.06 -    99.09: 23
       99.09 -   132.12: 4
      132.12 -   165.16: 3
  Dihedral angle restraints: 6321
    sinusoidal: 2175
      harmonic: 4146
  Sorted by residual:
  dihedral pdb=" C6  IHP A3701 "
           pdb=" C1  IHP A3701 "
           pdb=" C2  IHP A3701 "
           pdb=" O12 IHP A3701 "
      ideal   model   delta sinusoidal    sigma   weight residual
      61.05 -104.11  165.16     1      3.00e+01 1.11e-03 2.10e+01
  dihedral pdb=" C4  IHP A3701 "
           pdb=" C2  IHP A3701 "
           pdb=" C3  IHP A3701 "
           pdb=" O12 IHP A3701 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.90 -159.10 -140.00     1      3.00e+01 1.11e-03 1.88e+01
  dihedral pdb=" O12 IHP A3701 "
           pdb=" C2  IHP A3701 "
           pdb=" C3  IHP A3701 "
           pdb=" O13 IHP A3701 "
      ideal   model   delta sinusoidal    sigma   weight residual
      64.08  -72.56  136.64     1      3.00e+01 1.11e-03 1.84e+01
  ... (remaining 6318 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.005: 1751
       1.005 -    2.010: 0
       2.010 -    3.015: 0
       3.015 -    4.020: 0
       4.020 -    5.026: 3
  Chirality restraints: 1754
  Sorted by residual:
  chirality pdb=" C2  IHP A3701 "
            pdb=" C1  IHP A3701 "
            pdb=" C3  IHP A3701 "
            pdb=" O12 IHP A3701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52    2.51   -5.03 2.00e-01 2.50e+01 6.31e+02
  chirality pdb=" C4  IHP A3701 "
            pdb=" C3  IHP A3701 "
            pdb=" C5  IHP A3701 "
            pdb=" O14 IHP A3701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48   -2.52    5.00 2.00e-01 2.50e+01 6.26e+02
  chirality pdb=" C1  IHP A3701 "
            pdb=" C2  IHP A3701 "
            pdb=" C6  IHP A3701 "
            pdb=" O11 IHP A3701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.32   -2.48    4.80 2.00e-01 2.50e+01 5.75e+02
  ... (remaining 1751 not shown)

  Planarity restraints: 1790
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A2246 "    0.049 5.00e-02 4.00e+02   7.48e-02 8.95e+00
        pdb=" N   PRO A2247 "   -0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO A2247 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A2247 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A1333 "   -0.029 5.00e-02 4.00e+02   4.42e-02 3.13e+00
        pdb=" N   PRO A1334 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A1334 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A1334 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A1281 "   -0.027 5.00e-02 4.00e+02   4.02e-02 2.58e+00
        pdb=" N   PRO A1282 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A1282 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A1282 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1787 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 134
        2.70 -     3.25: 10175
        3.25 -     3.80: 16100
        3.80 -     4.35: 19688
        4.35 -     4.90: 34247
  Nonbonded interactions: 80344
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A2193 "
            pdb=" O   ILE A2353 "
     model   vdw
     2.146 3.040
  nonbonded pdb=" O   TRP A1106 "
            pdb=" OG  SER A1109 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" O   GLU A1068 "
            pdb=" OG1 THR A1072 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   GLN A 963 "
            pdb=" NH2 ARG A 979 "
     model   vdw
     2.285 3.120
  nonbonded pdb=" OE1 GLU A 991 "
            pdb=" NH2 ARG A1049 "
     model   vdw
     2.298 3.120
  ... (remaining 80339 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:             68.160
  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:             0.030
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     38.220
  Find NCS groups from input model:        0.500
  Set up NCS constraints:                  0.110
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  111.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073  10584  Z= 0.169
  Angle     :  0.647   9.093  14447  Z= 0.346
  Chirality :  0.208   5.026   1754
  Planarity :  0.004   0.075   1790
  Dihedral  : 15.204 165.156   3603
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.10 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.24), residues: 1298
  helix:  2.42 (0.18), residues: 878
  sheet: -0.27 (0.80), residues: 36
  loop : -1.28 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1393 
 HIS   0.007   0.001   HIS A2352 
 PHE   0.012   0.001   PHE A1827 
 TYR   0.020   0.001   TYR A 998 
 ARG   0.003   0.000   ARG A 930 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13375 (  693)
  hydrogen bonds       : angle       4.46328 ( 2043)
  covalent geometry    : bond        0.00333 (10584)
  covalent geometry    : angle       0.64687 (14447)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 1.070 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 114
  average time/residue: 0.2577
  time to fit residues: 40.4683
Evaluate side-chains
  81 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 114 optimal weight:    0.5980
   chunk 103 optimal weight:    1.9990
   chunk 57 optimal weight:    0.1980
   chunk 35 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   chunk 106 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 64 optimal weight:    0.7980
   chunk 79 optimal weight:   20.0000
   chunk 123 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A1344 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.141426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.124325 restraints weight = 14174.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.24
r_work: 0.3311 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.1073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10584  Z= 0.121
  Angle     :  0.517  13.249  14447  Z= 0.245
  Chirality :  0.037   0.244   1754
  Planarity :  0.004   0.059   1790
  Dihedral  :  8.651 100.265   1564
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  7.26 %
    Favored  : 92.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.24 (0.24), residues: 1298
  helix:  2.54 (0.18), residues: 886
  sheet:  0.28 (0.88), residues: 38
  loop : -1.09 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A2221 
 HIS   0.004   0.001   HIS A2337 
 PHE   0.011   0.001   PHE A 940 
 TYR   0.023   0.001   TYR A 998 
 ARG   0.003   0.000   ARG A1329 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04116 (  693)
  hydrogen bonds       : angle       3.41885 ( 2043)
  covalent geometry    : bond        0.00281 (10584)
  covalent geometry    : angle       0.51733 (14447)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 5
  residues processed: 87
  average time/residue: 0.2676
  time to fit residues: 33.5204
Evaluate side-chains
  84 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  807 VAL
Chi-restraints excluded: chain A residue  854 SER
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue 1056 THR
Chi-restraints excluded: chain A residue 1130 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0970
   chunk 62 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 55 optimal weight:    0.4980
   chunk 113 optimal weight:    0.6980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.139701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.123498 restraints weight = 14296.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.12
r_work: 0.3294 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.1332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10584  Z= 0.114
  Angle     :  0.480  11.110  14447  Z= 0.232
  Chirality :  0.037   0.224   1754
  Planarity :  0.004   0.053   1790
  Dihedral  :  7.629  93.248   1564
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 2.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  7.47 %
    Favored  : 91.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.31 (0.24), residues: 1298
  helix:  2.60 (0.18), residues: 881
  sheet:  0.33 (0.86), residues: 38
  loop : -1.05 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A2207 
 HIS   0.004   0.001   HIS A2337 
 PHE   0.012   0.001   PHE A1016 
 TYR   0.021   0.001   TYR A 998 
 ARG   0.003   0.000   ARG A1329 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04014 (  693)
  hydrogen bonds       : angle       3.28048 ( 2043)
  covalent geometry    : bond        0.00265 (10584)
  covalent geometry    : angle       0.47970 (14447)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 1.167 
Fit side-chains
REVERT: A 1784 MET cc_start: 0.8011 (ttt) cc_final: 0.7628 (ttt)
REVERT: A 2196 THR cc_start: 0.9296 (OUTLIER) cc_final: 0.9000 (p)
  outliers start: 14
  outliers final: 10
  residues processed: 98
  average time/residue: 0.2401
  time to fit residues: 33.8478
Evaluate side-chains
  89 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  807 VAL
Chi-restraints excluded: chain A residue  854 SER
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue 1056 THR
Chi-restraints excluded: chain A residue 1130 CYS
Chi-restraints excluded: chain A residue 1533 GLN
Chi-restraints excluded: chain A residue 1744 TYR
Chi-restraints excluded: chain A residue 2196 THR
Chi-restraints excluded: chain A residue 2288 MET
Chi-restraints excluded: chain A residue 3625 VAL
Chi-restraints excluded: chain A residue 3661 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 124 optimal weight:    2.9990
   chunk 10 optimal weight:    0.4980
   chunk 98 optimal weight:    9.9990
   chunk 70 optimal weight:    0.8980
   chunk 79 optimal weight:   20.0000
   chunk 119 optimal weight:    0.9980
   chunk 126 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.136305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.119466 restraints weight = 14189.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 1.32
r_work: 0.3224 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10584  Z= 0.172
  Angle     :  0.550  10.730  14447  Z= 0.268
  Chirality :  0.040   0.206   1754
  Planarity :  0.005   0.052   1790
  Dihedral  :  7.890  89.352   1564
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  8.40 %
    Favored  : 90.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.24), residues: 1298
  helix:  2.31 (0.18), residues: 878
  sheet:  0.37 (0.82), residues: 38
  loop : -1.08 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A2207 
 HIS   0.006   0.001   HIS A2337 
 PHE   0.013   0.002   PHE A1016 
 TYR   0.021   0.001   TYR A 998 
 ARG   0.003   0.000   ARG A2374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05251 (  693)
  hydrogen bonds       : angle       3.49711 ( 2043)
  covalent geometry    : bond        0.00419 (10584)
  covalent geometry    : angle       0.54964 (14447)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 1.149 
Fit side-chains
REVERT: A 2196 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.9041 (p)
  outliers start: 14
  outliers final: 11
  residues processed: 93
  average time/residue: 0.2624
  time to fit residues: 34.4042
Evaluate side-chains
  90 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 1.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  807 VAL
Chi-restraints excluded: chain A residue  854 SER
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue 1047 THR
Chi-restraints excluded: chain A residue 1056 THR
Chi-restraints excluded: chain A residue 1130 CYS
Chi-restraints excluded: chain A residue 1563 LYS
Chi-restraints excluded: chain A residue 1744 TYR
Chi-restraints excluded: chain A residue 2196 THR
Chi-restraints excluded: chain A residue 2288 MET
Chi-restraints excluded: chain A residue 3625 VAL
Chi-restraints excluded: chain A residue 3661 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 77 optimal weight:   20.0000
   chunk 12 optimal weight:    0.5980
   chunk 101 optimal weight:    6.9990
   chunk 47 optimal weight:    4.9990
   chunk 9 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.136899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.119815 restraints weight = 14171.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 1.22
r_work: 0.3253 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10584  Z= 0.141
  Angle     :  0.501   9.584  14447  Z= 0.246
  Chirality :  0.038   0.225   1754
  Planarity :  0.005   0.049   1790
  Dihedral  :  7.726  86.214   1564
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  :  9.54 %
    Favored  : 88.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.24), residues: 1298
  helix:  2.37 (0.17), residues: 880
  sheet:  0.38 (0.82), residues: 38
  loop : -1.05 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A2207 
 HIS   0.005   0.001   HIS A2337 
 PHE   0.011   0.001   PHE A1016 
 TYR   0.021   0.001   TYR A 998 
 ARG   0.002   0.000   ARG A1794 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04589 (  693)
  hydrogen bonds       : angle       3.38384 ( 2043)
  covalent geometry    : bond        0.00336 (10584)
  covalent geometry    : angle       0.50084 (14447)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 1.203 
Fit side-chains
REVERT: A  959 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6919 (tt0)
REVERT: A 2136 LYS cc_start: 0.8685 (mmpt) cc_final: 0.8482 (mmtp)
REVERT: A 2196 THR cc_start: 0.9286 (OUTLIER) cc_final: 0.9039 (p)
  outliers start: 15
  outliers final: 11
  residues processed: 93
  average time/residue: 0.2272
  time to fit residues: 30.6458
Evaluate side-chains
  91 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  807 VAL
Chi-restraints excluded: chain A residue  854 SER
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue  959 GLN
Chi-restraints excluded: chain A residue 1047 THR
Chi-restraints excluded: chain A residue 1056 THR
Chi-restraints excluded: chain A residue 1130 CYS
Chi-restraints excluded: chain A residue 1463 VAL
Chi-restraints excluded: chain A residue 1744 TYR
Chi-restraints excluded: chain A residue 2196 THR
Chi-restraints excluded: chain A residue 2228 LEU
Chi-restraints excluded: chain A residue 3625 VAL
Chi-restraints excluded: chain A residue 3661 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 120 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 118 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 82 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0980
   chunk 107 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.137702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.120687 restraints weight = 14312.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 1.33
r_work: 0.3253 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3156 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10584  Z= 0.122
  Angle     :  0.472   8.084  14447  Z= 0.233
  Chirality :  0.037   0.209   1754
  Planarity :  0.004   0.047   1790
  Dihedral  :  7.559  84.648   1564
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  9.23 %
    Favored  : 89.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.21 (0.24), residues: 1298
  helix:  2.46 (0.17), residues: 888
  sheet:  0.37 (0.82), residues: 38
  loop : -0.96 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A2207 
 HIS   0.004   0.001   HIS A2337 
 PHE   0.010   0.001   PHE A1016 
 TYR   0.021   0.001   TYR A 998 
 ARG   0.002   0.000   ARG A2336 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04139 (  693)
  hydrogen bonds       : angle       3.28339 ( 2043)
  covalent geometry    : bond        0.00288 (10584)
  covalent geometry    : angle       0.47226 (14447)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 1.350 
Fit side-chains
REVERT: A  959 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6899 (tt0)
REVERT: A 1784 MET cc_start: 0.8184 (ttt) cc_final: 0.7928 (ttt)
REVERT: A 2196 THR cc_start: 0.9275 (OUTLIER) cc_final: 0.9045 (p)
  outliers start: 17
  outliers final: 12
  residues processed: 96
  average time/residue: 0.2271
  time to fit residues: 31.5486
Evaluate side-chains
  91 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  807 VAL
Chi-restraints excluded: chain A residue  854 SER
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue  959 GLN
Chi-restraints excluded: chain A residue 1047 THR
Chi-restraints excluded: chain A residue 1056 THR
Chi-restraints excluded: chain A residue 1130 CYS
Chi-restraints excluded: chain A residue 1463 VAL
Chi-restraints excluded: chain A residue 1744 TYR
Chi-restraints excluded: chain A residue 2196 THR
Chi-restraints excluded: chain A residue 2288 MET
Chi-restraints excluded: chain A residue 3625 VAL
Chi-restraints excluded: chain A residue 3657 TRP
Chi-restraints excluded: chain A residue 3661 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 109 optimal weight:    3.9990
   chunk 135 optimal weight:    0.3980
   chunk 85 optimal weight:    0.6980
   chunk 126 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 101 optimal weight:    7.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.137490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.120948 restraints weight = 14407.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 1.39
r_work: 0.3243 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3146 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10584  Z= 0.125
  Angle     :  0.471   7.762  14447  Z= 0.234
  Chirality :  0.037   0.188   1754
  Planarity :  0.004   0.046   1790
  Dihedral  :  7.706  85.571   1564
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  9.34 %
    Favored  : 88.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.24 (0.24), residues: 1298
  helix:  2.47 (0.17), residues: 889
  sheet:  0.52 (0.85), residues: 38
  loop : -0.95 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A2207 
 HIS   0.004   0.001   HIS A2352 
 PHE   0.011   0.001   PHE A 817 
 TYR   0.021   0.001   TYR A 998 
 ARG   0.002   0.000   ARG A2336 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04232 (  693)
  hydrogen bonds       : angle       3.28184 ( 2043)
  covalent geometry    : bond        0.00295 (10584)
  covalent geometry    : angle       0.47083 (14447)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 1.112 
Fit side-chains
REVERT: A  959 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6899 (tt0)
REVERT: A 2196 THR cc_start: 0.9281 (OUTLIER) cc_final: 0.9045 (p)
  outliers start: 17
  outliers final: 14
  residues processed: 95
  average time/residue: 0.2326
  time to fit residues: 32.7466
Evaluate side-chains
  92 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  807 VAL
Chi-restraints excluded: chain A residue  854 SER
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue  959 GLN
Chi-restraints excluded: chain A residue 1047 THR
Chi-restraints excluded: chain A residue 1056 THR
Chi-restraints excluded: chain A residue 1130 CYS
Chi-restraints excluded: chain A residue 1463 VAL
Chi-restraints excluded: chain A residue 1744 TYR
Chi-restraints excluded: chain A residue 1811 LEU
Chi-restraints excluded: chain A residue 2196 THR
Chi-restraints excluded: chain A residue 2228 LEU
Chi-restraints excluded: chain A residue 2288 MET
Chi-restraints excluded: chain A residue 3625 VAL
Chi-restraints excluded: chain A residue 3657 TRP
Chi-restraints excluded: chain A residue 3661 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 79 optimal weight:   20.0000
   chunk 5 optimal weight:    0.6980
   chunk 66 optimal weight:    0.3980
   chunk 121 optimal weight:    0.0570
   chunk 108 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 101 optimal weight:    5.9990
   chunk 55 optimal weight:    0.5980
   chunk 94 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
A 922 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.139049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.120222 restraints weight = 14279.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 1.41
r_work: 0.3259 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.1835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10584  Z= 0.106
  Angle     :  0.445   8.004  14447  Z= 0.223
  Chirality :  0.036   0.176   1754
  Planarity :  0.004   0.046   1790
  Dihedral  :  7.727  87.059   1564
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  9.75 %
    Favored  : 88.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.40 (0.24), residues: 1298
  helix:  2.59 (0.17), residues: 890
  sheet:  0.61 (0.86), residues: 38
  loop : -0.90 (0.34), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A2221 
 HIS   0.004   0.001   HIS A2352 
 PHE   0.010   0.001   PHE A 817 
 TYR   0.021   0.001   TYR A 998 
 ARG   0.002   0.000   ARG A1794 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03734 (  693)
  hydrogen bonds       : angle       3.19892 ( 2043)
  covalent geometry    : bond        0.00242 (10584)
  covalent geometry    : angle       0.44451 (14447)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 1.240 
Fit side-chains
REVERT: A  959 GLN cc_start: 0.7147 (OUTLIER) cc_final: 0.6937 (tt0)
REVERT: A 2196 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.9027 (p)
  outliers start: 17
  outliers final: 12
  residues processed: 95
  average time/residue: 0.2325
  time to fit residues: 32.0672
Evaluate side-chains
  94 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  807 VAL
Chi-restraints excluded: chain A residue  854 SER
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue  959 GLN
Chi-restraints excluded: chain A residue 1047 THR
Chi-restraints excluded: chain A residue 1056 THR
Chi-restraints excluded: chain A residue 1130 CYS
Chi-restraints excluded: chain A residue 1463 VAL
Chi-restraints excluded: chain A residue 1744 TYR
Chi-restraints excluded: chain A residue 2196 THR
Chi-restraints excluded: chain A residue 2228 LEU
Chi-restraints excluded: chain A residue 2288 MET
Chi-restraints excluded: chain A residue 3657 TRP
Chi-restraints excluded: chain A residue 3661 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 123 optimal weight:    0.2980
   chunk 111 optimal weight:    0.5980
   chunk 120 optimal weight:    0.5980
   chunk 60 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 57 optimal weight:    0.0570
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.4298

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.139387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.121166 restraints weight = 14304.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 1.25
r_work: 0.3289 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  10584  Z= 0.098
  Angle     :  0.428   8.076  14447  Z= 0.214
  Chirality :  0.036   0.187   1754
  Planarity :  0.004   0.046   1790
  Dihedral  :  7.550  86.791   1564
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 10.48 %
    Favored  : 87.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.52 (0.24), residues: 1298
  helix:  2.68 (0.17), residues: 890
  sheet:  0.72 (0.87), residues: 38
  loop : -0.87 (0.34), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A2221 
 HIS   0.004   0.001   HIS A2352 
 PHE   0.009   0.001   PHE A 817 
 TYR   0.020   0.001   TYR A 998 
 ARG   0.003   0.000   ARG A1794 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03501 (  693)
  hydrogen bonds       : angle       3.14313 ( 2043)
  covalent geometry    : bond        0.00221 (10584)
  covalent geometry    : angle       0.42819 (14447)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 1.188 
Fit side-chains
REVERT: A 1784 MET cc_start: 0.8098 (ttt) cc_final: 0.7826 (ttt)
  outliers start: 15
  outliers final: 13
  residues processed: 95
  average time/residue: 0.2293
  time to fit residues: 31.7641
Evaluate side-chains
  95 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  807 VAL
Chi-restraints excluded: chain A residue  854 SER
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue 1047 THR
Chi-restraints excluded: chain A residue 1056 THR
Chi-restraints excluded: chain A residue 1130 CYS
Chi-restraints excluded: chain A residue 1463 VAL
Chi-restraints excluded: chain A residue 1744 TYR
Chi-restraints excluded: chain A residue 2228 LEU
Chi-restraints excluded: chain A residue 2288 MET
Chi-restraints excluded: chain A residue 3625 VAL
Chi-restraints excluded: chain A residue 3657 TRP
Chi-restraints excluded: chain A residue 3661 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 118 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0370
   chunk 23 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 104 optimal weight:    0.9990
   chunk 40 optimal weight:    0.1980
   chunk 36 optimal weight:    0.5980
   chunk 131 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.139061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.119757 restraints weight = 14220.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 1.41
r_work: 0.3283 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  10584  Z= 0.103
  Angle     :  0.440   8.147  14447  Z= 0.220
  Chirality :  0.036   0.191   1754
  Planarity :  0.004   0.046   1790
  Dihedral  :  7.468  85.945   1564
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 10.68 %
    Favored  : 87.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.52 (0.24), residues: 1298
  helix:  2.68 (0.17), residues: 890
  sheet:  0.69 (0.87), residues: 38
  loop : -0.86 (0.34), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A2221 
 HIS   0.004   0.001   HIS A2352 
 PHE   0.010   0.001   PHE A 817 
 TYR   0.021   0.001   TYR A 998 
 ARG   0.003   0.000   ARG A1794 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03616 (  693)
  hydrogen bonds       : angle       3.13825 ( 2043)
  covalent geometry    : bond        0.00236 (10584)
  covalent geometry    : angle       0.43996 (14447)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 1.193 
Fit side-chains
REVERT: A 1784 MET cc_start: 0.8167 (ttt) cc_final: 0.7941 (ttt)
  outliers start: 14
  outliers final: 13
  residues processed: 93
  average time/residue: 0.2451
  time to fit residues: 32.6062
Evaluate side-chains
  94 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  807 VAL
Chi-restraints excluded: chain A residue  854 SER
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue 1047 THR
Chi-restraints excluded: chain A residue 1056 THR
Chi-restraints excluded: chain A residue 1130 CYS
Chi-restraints excluded: chain A residue 1463 VAL
Chi-restraints excluded: chain A residue 1744 TYR
Chi-restraints excluded: chain A residue 2228 LEU
Chi-restraints excluded: chain A residue 2288 MET
Chi-restraints excluded: chain A residue 3625 VAL
Chi-restraints excluded: chain A residue 3657 TRP
Chi-restraints excluded: chain A residue 3661 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 101 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   chunk 124 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 110 optimal weight:    1.9990
   chunk 127 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 96 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.136635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.117029 restraints weight = 14127.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 1.35
r_work: 0.3223 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.2005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10584  Z= 0.158
  Angle     :  0.506   8.113  14447  Z= 0.253
  Chirality :  0.039   0.197   1754
  Planarity :  0.005   0.046   1790
  Dihedral  :  7.698  86.957   1564
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 11.00 %
    Favored  : 87.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.24), residues: 1298
  helix:  2.40 (0.17), residues: 891
  sheet:  0.72 (0.89), residues: 38
  loop : -0.97 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A2207 
 HIS   0.006   0.001   HIS A2337 
 PHE   0.013   0.002   PHE A1228 
 TYR   0.021   0.001   TYR A 998 
 ARG   0.005   0.000   ARG A1794 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04923 (  693)
  hydrogen bonds       : angle       3.38458 ( 2043)
  covalent geometry    : bond        0.00378 (10584)
  covalent geometry    : angle       0.50633 (14447)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5778.05 seconds
wall clock time: 100 minutes 17.70 seconds (6017.70 seconds total)