Starting phenix.real_space_refine
on Sat Aug 23 11:48:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sg4_40451/08_2025/8sg4_40451.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sg4_40451/08_2025/8sg4_40451.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sg4_40451/08_2025/8sg4_40451.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sg4_40451/08_2025/8sg4_40451.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sg4_40451/08_2025/8sg4_40451.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sg4_40451/08_2025/8sg4_40451.map"
  }
  resolution = 3.11
  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=   0.067
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    7571      2.51       5
     N    1972      2.21       5
     O    2119      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11715
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 11715
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1469, 11703
          Classifications: {'peptide': 1469}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1425}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 10
      Conformer: "B"
        Number of residues, atoms: 1469, 11703
          Classifications: {'peptide': 1469}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1425}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 10
          bond proxies already assigned to first conformer: 11934
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG A1048 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A1048 " occ=0.50
  Time building chain proxies: 4.10, per 1000 atoms: 0.35
  Number of scatterers: 11715
  At special positions: 0
  Unit cell: (108.009, 128.328, 133.675, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      53     16.00
     O    2119      8.00
     N    1972      7.00
     C    7571      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: 0.91
  Conformation dependent library (CDL) restraints added in 824.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2786

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 6 sheets defined
      72.5% alpha, 7.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 13
      removed outlier: 3.784A  pdb=" N   TRP A   8 " --> pdb=" O   ASN A   4 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ALA A   9 " --> pdb=" O   LEU A   5 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 36
    Processing helix  chain 'A' and resid 36 through 58
      removed outlier: 3.924A  pdb=" N   ILE A  50 " --> pdb=" O   ILE A  46 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   CYS A  57 " --> pdb=" O   LEU A  53 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LYS A  58 " --> pdb=" O   VAL A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 92
      removed outlier: 3.785A  pdb=" N   VAL A  73 " --> pdb=" O   ASN A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 100
      removed outlier: 3.547A  pdb=" N   GLU A  99 " --> pdb=" O   LYS A  95 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   ASN A 100 " --> pdb=" O   GLU A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 128
      removed outlier: 4.006A  pdb=" N   VAL A 104 " --> pdb=" O   ASN A 100 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   TRP A 122 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ASP A 126 " --> pdb=" O   TRP A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 161
    Processing helix  chain 'A' and resid 166 through 189
    Processing helix  chain 'A' and resid 195 through 202
      removed outlier: 3.994A  pdb=" N   HIS A 199 " --> pdb=" O   MET A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 215
      removed outlier: 3.581A  pdb=" N   ASP A 213 " --> pdb=" O   ASN A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 223
    Processing helix  chain 'A' and resid 226 through 236
    Processing helix  chain 'A' and resid 251 through 270
    Processing helix  chain 'A' and resid 274 through 327
      removed outlier: 5.953A  pdb=" N   SER A 285 " --> pdb=" O   ARG A 281 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   LYS A 286 " --> pdb=" O   THR A 282 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   MET A 287 " --> pdb=" O   PHE A 283 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLN A 304 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
      Proline residue:  A 305  - end of helix
    Processing helix  chain 'A' and resid 342 through 392
      removed outlier: 3.607A  pdb=" N   PHE A 346 " --> pdb=" O   ILE A 342 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLN A 365 " --> pdb=" O   SER A 361 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU A 390 " --> pdb=" O   TYR A 386 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   VAL A 391 " --> pdb=" O   GLN A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 399
    Processing helix  chain 'A' and resid 401 through 411
    Processing helix  chain 'A' and resid 411 through 424
      removed outlier: 4.086A  pdb=" N   THR A 420 " --> pdb=" O   LEU A 416 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   GLN A 421 " --> pdb=" O   GLN A 417 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   TRP A 422 " --> pdb=" O   ASP A 418 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   ASN A 424 " --> pdb=" O   THR A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 445
      Proline residue:  A 430  - end of helix
    Processing helix  chain 'A' and resid 447 through 493
      removed outlier: 4.249A  pdb=" N   GLY A 451 " --> pdb=" O   SER A 447 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU A 455 " --> pdb=" O   GLY A 451 " (cutoff:3.500A)
      Proline residue:  A 460  - end of helix
    Processing helix  chain 'A' and resid 493 through 501
    Processing helix  chain 'A' and resid 502 through 517
      removed outlier: 3.601A  pdb=" N   LYS A 517 " --> pdb=" O   VAL A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 555
      Proline residue:  A 540  - end of helix
      removed outlier: 3.684A  pdb=" N   SER A 544 " --> pdb=" O   PRO A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 579
      Proline residue:  A 566  - end of helix
      removed outlier: 3.858A  pdb=" N   ASN A 572 " --> pdb=" O   LEU A 568 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LEU A 573 " --> pdb=" O   THR A 569 " (cutoff:3.500A)
      Proline residue:  A 577  - end of helix
    Processing helix  chain 'A' and resid 580 through 603
    Processing helix  chain 'A' and resid 668 through 677
      removed outlier: 3.736A  pdb=" N   LEU A 673 " --> pdb=" O   LYS A 669 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   MET A 676 " --> pdb=" O   LEU A 672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 707 through 713
    Processing helix  chain 'A' and resid 718 through 729
    Processing helix  chain 'A' and resid 731 through 738
    Processing helix  chain 'A' and resid 740 through 743
    Processing helix  chain 'A' and resid 754 through 770
      removed outlier: 3.710A  pdb=" N   ARG A 770 " --> pdb=" O   ALA A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 779 through 783
      removed outlier: 3.810A  pdb=" N   ALA A 782 " --> pdb=" O   PRO A 779 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 784 through 795
    Processing helix  chain 'A' and resid 800 through 805
      removed outlier: 4.364A  pdb=" N   THR A 804 " --> pdb=" O   LEU A 801 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 813 through 819
      removed outlier: 4.065A  pdb=" N   ILE A 819 " --> pdb=" O   SER A 815 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 836 through 842
    Processing helix  chain 'A' and resid 846 through 854
    Processing helix  chain 'A' and resid 900 through 913
    Processing helix  chain 'A' and resid 923 through 929
      removed outlier: 3.534A  pdb=" N   GLU A 927 " --> pdb=" O   ALA A 924 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 935 through 946
      removed outlier: 3.948A  pdb=" N   TYR A 939 " --> pdb=" O   LYS A 935 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 947 through 983
    Processing helix  chain 'A' and resid 987 through 1016
    Processing helix  chain 'A' and resid 1017 through 1035
      removed outlier: 3.807A  pdb=" N   ARG A1035 " --> pdb=" O   ASN A1031 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1037 through 1044
      removed outlier: 3.801A  pdb=" N   PHE A1041 " --> pdb=" O   PRO A1037 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1045 through 1063
      removed outlier: 3.607A  pdb=" N  AILE A1049 " --> pdb=" O   PRO A1045 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ASP A1056 " --> pdb=" O   ARG A1052 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ILE A1057 " --> pdb=" O   PHE A1053 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1063 through 1089
      removed outlier: 3.600A  pdb=" N   ASN A1074 " --> pdb=" O   GLN A1070 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1092 through 1137
      Proline residue:  A1098  - end of helix
      removed outlier: 3.954A  pdb=" N   SER A1126 " --> pdb=" O   SER A1122 " (cutoff:3.500A)
      Proline residue:  A1127  - end of helix
    Processing helix  chain 'A' and resid 1138 through 1146
    Processing helix  chain 'A' and resid 1147 through 1202
      removed outlier: 3.728A  pdb=" N   ALA A1165 " --> pdb=" O   ASN A1161 " (cutoff:3.500A)
      Proline residue:  A1168  - end of helix
      removed outlier: 4.113A  pdb=" N   ASN A1173 " --> pdb=" O   SER A1169 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ARG A1174 " --> pdb=" O   ILE A1170 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ARG A1179 " --> pdb=" O   TRP A1175 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLN A1201 " --> pdb=" O   PHE A1197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1205 through 1218
      removed outlier: 3.830A  pdb=" N   VAL A1209 " --> pdb=" O   THR A1205 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   GLN A1218 " --> pdb=" O   SER A1214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1218 through 1237
      removed outlier: 4.381A  pdb=" N   THR A1222 " --> pdb=" O   GLN A1218 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ASN A1224 " --> pdb=" O   THR A1220 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   VAL A1227 " --> pdb=" O   LEU A1223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1237 through 1248
    Processing helix  chain 'A' and resid 1257 through 1261
      removed outlier: 4.105A  pdb=" N   ARG A1261 " --> pdb=" O   GLU A1258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1313 through 1320
      removed outlier: 3.779A  pdb=" N   LEU A1317 " --> pdb=" O   SER A1313 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   PHE A1320 " --> pdb=" O   THR A1316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1341 through 1347
    Processing helix  chain 'A' and resid 1363 through 1368
    Processing helix  chain 'A' and resid 1374 through 1385
    Processing helix  chain 'A' and resid 1387 through 1395
      removed outlier: 4.003A  pdb=" N   SER A1395 " --> pdb=" O   VAL A1391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1397 through 1400
    Processing helix  chain 'A' and resid 1404 through 1408
      removed outlier: 3.534A  pdb=" N   GLY A1408 " --> pdb=" O   GLU A1405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1411 through 1426
      removed outlier: 3.658A  pdb=" N   VAL A1426 " --> pdb=" O   ARG A1422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1442 through 1455
      removed outlier: 3.597A  pdb=" N   VAL A1447 " --> pdb=" O   GLU A1443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1467 through 1471
    Processing helix  chain 'A' and resid 1490 through 1497
      removed outlier: 3.616A  pdb=" N   ASP A1497 " --> pdb=" O   GLN A1493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1500 through 1509
    Processing sheet with id=AA1, first strand: chain 'A' and resid 613 through 615
      removed outlier: 4.640A  pdb=" N   ARG A 682 " --> pdb=" O   THR A 633 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   THR A 633 " --> pdb=" O   ARG A 682 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   LYS A 684 " --> pdb=" O   ASP A 631 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   ASP A 631 " --> pdb=" O   LYS A 684 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   ALA A 625 " --> pdb=" O   HIS A 690 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   ASP A 630 " --> pdb=" O   ILE A 649 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   ILE A 649 " --> pdb=" O   ASP A 630 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA A 632 " --> pdb=" O   LYS A 647 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   LYS A 647 " --> pdb=" O   ALA A 632 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   PHE A 634 " --> pdb=" O   ALA A 645 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   LYS A 643 " --> pdb=" O   TRP A 636 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 693 through 696
      removed outlier: 6.601A  pdb=" N   ALA A 694 " --> pdb=" O   LEU A 775 " (cutoff:3.500A)
      removed outlier: 7.210A  pdb=" N   ASP A 777 " --> pdb=" O   ALA A 694 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   VAL A 696 " --> pdb=" O   ASP A 777 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   CYS A 660 " --> pdb=" O   ALA A 824 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   LEU A 826 " --> pdb=" O   CYS A 660 " (cutoff:3.500A)
      removed outlier: 5.731A  pdb=" N   VAL A 662 " --> pdb=" O   LEU A 826 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLN A 833 " --> pdb=" O   LEU A 825 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   ASP A 827 " --> pdb=" O   ILE A 831 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   ILE A 831 " --> pdb=" O   ASP A 827 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 705 through 706
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1287 through 1296
      removed outlier: 6.163A  pdb=" N   VAL A1288 " --> pdb=" O   ARG A1280 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   ARG A1280 " --> pdb=" O   VAL A1288 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   LYS A1290 " --> pdb=" O   SER A1278 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   SER A1278 " --> pdb=" O   LYS A1290 " (cutoff:3.500A)
      removed outlier: 5.062A  pdb=" N   ILE A1292 " --> pdb=" O   ASN A1276 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   TYR A1277 " --> pdb=" O   GLU A1327 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   GLU A1327 " --> pdb=" O   TYR A1277 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1350 through 1352
      removed outlier: 6.693A  pdb=" N   LYS A1301 " --> pdb=" O   ARG A1476 " (cutoff:3.500A)
      removed outlier: 8.141A  pdb=" N   ILE A1478 " --> pdb=" O   LYS A1301 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   GLY A1303 " --> pdb=" O   ILE A1478 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   LEU A1480 " --> pdb=" O   GLY A1303 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   VAL A1305 " --> pdb=" O   LEU A1480 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   ASP A1481 " --> pdb=" O   VAL A1485 " (cutoff:3.500A)
      removed outlier: 5.478A  pdb=" N   VAL A1485 " --> pdb=" O   ASP A1481 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1361 through 1362

    778 hydrogen bonds defined for protein.
    2271 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: 1.84

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3717
        1.34 -     1.46: 2128
        1.46 -     1.58: 6029
        1.58 -     1.69: 0
        1.69 -     1.81: 86
  Bond restraints: 11960
  Sorted by residual:
  bond pdb=" N   ASP A 325 "
       pdb=" CA  ASP A 325 "
    ideal  model  delta    sigma   weight residual
    1.459  1.484 -0.025 1.19e-02 7.06e+03 4.34e+00
  bond pdb=" CA  ASP A 778 "
       pdb=" CB  ASP A 778 "
    ideal  model  delta    sigma   weight residual
    1.522  1.533 -0.011 7.00e-03 2.04e+04 2.43e+00
  bond pdb=" C   MET A 459 "
       pdb=" N   PRO A 460 "
    ideal  model  delta    sigma   weight residual
    1.335  1.352 -0.016 1.36e-02 5.41e+03 1.43e+00
  bond pdb=" CA  MET A 459 "
       pdb=" C   MET A 459 "
    ideal  model  delta    sigma   weight residual
    1.520  1.535 -0.015 1.23e-02 6.61e+03 1.41e+00
  bond pdb=" CB  VAL A1209 "
       pdb=" CG2 VAL A1209 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.32e+00
  ... (remaining 11955 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 15538
        1.46 -     2.92: 564
        2.92 -     4.39: 82
        4.39 -     5.85: 18
        5.85 -     7.31: 10
  Bond angle restraints: 16212
  Sorted by residual:
  angle pdb=" N   ALA A1465 "
        pdb=" CA  ALA A1465 "
        pdb=" C   ALA A1465 "
      ideal   model   delta    sigma   weight residual
     109.46  115.33   -5.87 1.66e+00 3.63e-01 1.25e+01
  angle pdb=" C   ASN A 898 "
        pdb=" N   SER A 899 "
        pdb=" CA  SER A 899 "
      ideal   model   delta    sigma   weight residual
     122.35  127.25   -4.90 1.46e+00 4.69e-01 1.13e+01
  angle pdb=" N   ASP A 325 "
        pdb=" CA  ASP A 325 "
        pdb=" C   ASP A 325 "
      ideal   model   delta    sigma   weight residual
     111.07  107.50    3.57 1.07e+00 8.73e-01 1.12e+01
  angle pdb=" CA  TYR A1105 "
        pdb=" CB  TYR A1105 "
        pdb=" CG  TYR A1105 "
      ideal   model   delta    sigma   weight residual
     113.90  119.44   -5.54 1.80e+00 3.09e-01 9.47e+00
  angle pdb=" N   PHE A 576 "
        pdb=" CA  PHE A 576 "
        pdb=" C   PHE A 576 "
      ideal   model   delta    sigma   weight residual
     109.81  116.38   -6.57 2.21e+00 2.05e-01 8.83e+00
  ... (remaining 16207 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.57: 6679
       17.57 -    35.13: 395
       35.13 -    52.70: 65
       52.70 -    70.26: 6
       70.26 -    87.83: 8
  Dihedral angle restraints: 7153
    sinusoidal: 2846
      harmonic: 4307
  Sorted by residual:
  dihedral pdb=" CA  ASP A1061 "
           pdb=" C   ASP A1061 "
           pdb=" N   ALA A1062 "
           pdb=" CA  ALA A1062 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.12  -19.88     0      5.00e+00 4.00e-02 1.58e+01
  dihedral pdb=" CA  ILE A1471 "
           pdb=" C   ILE A1471 "
           pdb=" N   MET A1472 "
           pdb=" CA  MET A1472 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.60  -19.40     0      5.00e+00 4.00e-02 1.51e+01
  dihedral pdb=" CA  ARG A 929 "
           pdb=" C   ARG A 929 "
           pdb=" N   GLU A 930 "
           pdb=" CA  GLU A 930 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.27   18.73     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 7150 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1233
       0.038 -    0.077: 482
       0.077 -    0.115: 118
       0.115 -    0.153: 40
       0.153 -    0.192: 6
  Chirality restraints: 1879
  Sorted by residual:
  chirality pdb=" CA  VAL A 239 "
            pdb=" N   VAL A 239 "
            pdb=" C   VAL A 239 "
            pdb=" CB  VAL A 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 9.17e-01
  chirality pdb=" CA  TYR A 159 "
            pdb=" N   TYR A 159 "
            pdb=" C   TYR A 159 "
            pdb=" CB  TYR A 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.75e-01
  chirality pdb=" CA  PHE A 576 "
            pdb=" N   PHE A 576 "
            pdb=" C   PHE A 576 "
            pdb=" CB  PHE A 576 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.65e-01
  ... (remaining 1876 not shown)

  Planarity restraints: 2027
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A1054 "   -0.012 2.00e-02 2.50e+03   2.48e-02 6.13e+00
        pdb=" C   SER A1054 "    0.043 2.00e-02 2.50e+03
        pdb=" O   SER A1054 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ASN A1055 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 597 "   -0.195 9.50e-02 1.11e+02   8.80e-02 6.09e+00
        pdb=" NE  ARG A 597 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 597 "   -0.018 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 597 "    0.009 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 597 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A1228 "    0.012 2.00e-02 2.50e+03   2.46e-02 6.05e+00
        pdb=" C   ARG A1228 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   ARG A1228 "    0.016 2.00e-02 2.50e+03
        pdb=" N   MET A1229 "    0.014 2.00e-02 2.50e+03
  ... (remaining 2024 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 3161
        2.82 -     3.34: 11811
        3.34 -     3.86: 19402
        3.86 -     4.38: 22216
        4.38 -     4.90: 38821
  Nonbonded interactions: 95411
  Sorted by model distance:
  nonbonded pdb=" O   VAL A1227 "
            pdb=" OG1 THR A1230 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O   TYR A 837 "
            pdb=" OG1 THR A 841 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" OD2 ASP A 734 "
            pdb=" NH2 ARG A 760 "
     model   vdw
     2.369 3.120
  nonbonded pdb=" OE2 GLU A 605 "
            pdb=" NH2 ARG A 638 "
     model   vdw
     2.372 3.120
  nonbonded pdb=" NZ  LYS A 655 "
            pdb=" O   THR A 804 "
     model   vdw
     2.384 3.120
  ... (remaining 95406 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=0.50 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:             2.880
  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:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     12.090
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
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   0.042  11960  Z= 0.170
  Angle     :  0.656   7.309  16212  Z= 0.371
  Chirality :  0.045   0.192   1879
  Planarity :  0.006   0.088   2027
  Dihedral  : 12.028  87.826   4367
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 0.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    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 aren not related in a simple way.
  whole:  0.44 (0.21), residues: 1466
  helix:  0.71 (0.16), residues: 963
  sheet: -0.58 (0.59), residues: 72
  loop : -0.26 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG A 906 
 TYR   0.023   0.002   TYR A1105 
 PHE   0.023   0.002   PHE A 292 
 TRP   0.026   0.002   TRP A 422 
 HIS   0.004   0.001   HIS A 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (11960)
  covalent geometry    : angle       0.65600 (16212)
  hydrogen bonds       : bond        0.12263 (  778)
  hydrogen bonds       : angle       5.58427 ( 2271)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A  520 LYS cc_start: 0.7554 (mmtt) cc_final: 0.6579 (mtpt)
REVERT: A  521 ASN cc_start: 0.7780 (t0) cc_final: 0.7296 (t0)
REVERT: A  657 ASN cc_start: 0.6901 (m110) cc_final: 0.5537 (p0)
REVERT: A  670 THR cc_start: 0.8295 (p) cc_final: 0.7934 (t)
REVERT: A  698 GLN cc_start: 0.8780 (tt0) cc_final: 0.8079 (tm-30)
REVERT: A  717 TYR cc_start: 0.7823 (t80) cc_final: 0.7495 (t80)
REVERT: A  744 THR cc_start: 0.8231 (m) cc_final: 0.7971 (p)
REVERT: A  777 ASP cc_start: 0.6896 (t0) cc_final: 0.6424 (t0)
REVERT: A  789 ARG cc_start: 0.8625 (ttt180) cc_final: 0.8318 (ptm-80)
REVERT: A 1149 LYS cc_start: 0.8307 (ttmt) cc_final: 0.8056 (tptt)
REVERT: A 1215 TYR cc_start: 0.8904 (m-80) cc_final: 0.7962 (m-80)
REVERT: A 1282 ARG cc_start: 0.8209 (mtt180) cc_final: 0.7773 (mtt180)
REVERT: A 1285 LEU cc_start: 0.8079 (mt) cc_final: 0.6944 (mt)
REVERT: A 1323 ILE cc_start: 0.7616 (mt) cc_final: 0.7236 (pt)
REVERT: A 1327 GLU cc_start: 0.7273 (tt0) cc_final: 0.6800 (tt0)
REVERT: A 1493 GLN cc_start: 0.7493 (tt0) cc_final: 0.7207 (tm-30)
REVERT: A 1505 LEU cc_start: 0.7887 (mt) cc_final: 0.7564 (mt)
REVERT: A 1508 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7494 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.1083
  time to fit residues: 28.8299
Evaluate side-chains
  114 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 469 GLN
** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 648 ASN
A 812 ASN
A 969 ASN
A1371 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.144258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.111225 restraints weight = 21778.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 2.40
r_work: 0.3373 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3374
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3374 r_free = 0.3374    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3374 r_free = 0.3374    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3374
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.1279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11960  Z= 0.159
  Angle     :  0.564   6.873  16212  Z= 0.304
  Chirality :  0.042   0.165   1879
  Planarity :  0.004   0.060   2027
  Dihedral  :  4.705  21.922   1589
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  6.50 %
    Favored  : 92.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    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 aren not related in a simple way.
  whole:  1.26 (0.22), residues: 1466
  helix:  1.37 (0.16), residues: 973
  sheet: -0.57 (0.58), residues: 70
  loop :  0.02 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 926 
 TYR   0.021   0.002   TYR A1105 
 PHE   0.018   0.002   PHE A 954 
 TRP   0.020   0.002   TRP A 422 
 HIS   0.007   0.001   HIS A1347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (11960)
  covalent geometry    : angle       0.56379 (16212)
  hydrogen bonds       : bond        0.05382 (  778)
  hydrogen bonds       : angle       4.57821 ( 2271)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 127
  time to evaluate  : 0.386 
Fit side-chains
REVERT: A  120 LEU cc_start: 0.8586 (tp) cc_final: 0.8382 (tp)
REVERT: A  520 LYS cc_start: 0.8079 (mmtt) cc_final: 0.7125 (mtpt)
REVERT: A  657 ASN cc_start: 0.7242 (m110) cc_final: 0.5846 (p0)
REVERT: A  670 THR cc_start: 0.8421 (p) cc_final: 0.8139 (t)
REVERT: A  698 GLN cc_start: 0.8828 (tt0) cc_final: 0.8216 (tm-30)
REVERT: A  744 THR cc_start: 0.8826 (m) cc_final: 0.8549 (p)
REVERT: A  777 ASP cc_start: 0.6933 (t0) cc_final: 0.6530 (t0)
REVERT: A  967 MET cc_start: 0.8358 (mmm) cc_final: 0.8154 (mmt)
REVERT: A 1327 GLU cc_start: 0.7488 (tt0) cc_final: 0.7159 (tt0)
REVERT: A 1505 LEU cc_start: 0.8188 (mt) cc_final: 0.7930 (mp)
REVERT: A 1507 MET cc_start: 0.8052 (mmm) cc_final: 0.7626 (tpt)
  outliers start: 8
  outliers final: 5
  residues processed: 130
  average time/residue: 0.1126
  time to fit residues: 20.8067
Evaluate side-chains
  111 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 106
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 GLU
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain A residue 1019 ILE
Chi-restraints excluded: chain A residue 1235 THR
Chi-restraints excluded: chain A residue 1451 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 9 optimal weight:    0.2980
   chunk 14 optimal weight:    2.9990
   chunk 108 optimal weight:    0.7980
   chunk 104 optimal weight:    0.7980
   chunk 122 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 111 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 476 GLN
A1371 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.148091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.115196 restraints weight = 21742.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 2.50
r_work: 0.3388 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3389
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3389
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11960  Z= 0.138
  Angle     :  0.530   7.372  16212  Z= 0.284
  Chirality :  0.040   0.167   1879
  Planarity :  0.004   0.098   2027
  Dihedral  :  4.466  21.788   1589
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  7.74 %
    Favored  : 91.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    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 aren not related in a simple way.
  whole:  1.59 (0.22), residues: 1466
  helix:  1.67 (0.16), residues: 969
  sheet: -0.61 (0.57), residues: 70
  loop :  0.04 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 926 
 TYR   0.021   0.001   TYR A1105 
 PHE   0.017   0.001   PHE A1132 
 TRP   0.016   0.001   TRP A 422 
 HIS   0.007   0.001   HIS A1347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (11960)
  covalent geometry    : angle       0.53039 (16212)
  hydrogen bonds       : bond        0.04904 (  778)
  hydrogen bonds       : angle       4.30686 ( 2271)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
REVERT: A  520 LYS cc_start: 0.8014 (mmtt) cc_final: 0.7091 (mtpt)
REVERT: A  657 ASN cc_start: 0.7305 (m110) cc_final: 0.5930 (p0)
REVERT: A  698 GLN cc_start: 0.8803 (tt0) cc_final: 0.8274 (tm-30)
REVERT: A  744 THR cc_start: 0.8797 (m) cc_final: 0.8200 (p)
REVERT: A  777 ASP cc_start: 0.6952 (t0) cc_final: 0.6552 (t0)
REVERT: A 1058 TYR cc_start: 0.8164 (t80) cc_final: 0.7722 (t80)
REVERT: A 1282 ARG cc_start: 0.8092 (ptp-110) cc_final: 0.7840 (ptp-170)
REVERT: A 1327 GLU cc_start: 0.7272 (tt0) cc_final: 0.6940 (tt0)
REVERT: A 1507 MET cc_start: 0.8095 (mmm) cc_final: 0.7688 (tpt)
  outliers start: 10
  outliers final: 5
  residues processed: 115
  average time/residue: 0.0969
  time to fit residues: 16.4836
Evaluate side-chains
  110 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain A residue  662 VAL
Chi-restraints excluded: chain A residue 1235 THR
Chi-restraints excluded: chain A residue 1451 THR
Chi-restraints excluded: chain A residue 1468 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 93 optimal weight:    0.8980
   chunk 108 optimal weight:    0.1980
   chunk 10 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 473 GLN
A 928 HIS
A 974 HIS
A1371 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.149295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.116997 restraints weight = 27405.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 2.87
r_work: 0.3371 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3371
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3371 r_free = 0.3371    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3371 r_free = 0.3371    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3371
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11960  Z= 0.125
  Angle     :  0.496   6.495  16212  Z= 0.265
  Chirality :  0.040   0.151   1879
  Planarity :  0.004   0.068   2027
  Dihedral  :  4.298  21.800   1589
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  8.13 %
    Favored  : 91.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    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 aren not related in a simple way.
  whole:  1.85 (0.22), residues: 1466
  helix:  1.92 (0.16), residues: 970
  sheet: -0.76 (0.55), residues: 72
  loop :  0.07 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 926 
 TYR   0.022   0.001   TYR A1105 
 PHE   0.015   0.001   PHE A 954 
 TRP   0.015   0.001   TRP A 422 
 HIS   0.007   0.001   HIS A1347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (11960)
  covalent geometry    : angle       0.49594 (16212)
  hydrogen bonds       : bond        0.04559 (  778)
  hydrogen bonds       : angle       4.15381 ( 2271)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.371 
Fit side-chains
REVERT: A  520 LYS cc_start: 0.7987 (mmtt) cc_final: 0.7082 (mtpt)
REVERT: A  657 ASN cc_start: 0.7314 (m110) cc_final: 0.5991 (p0)
REVERT: A  662 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7792 (m)
REVERT: A  698 GLN cc_start: 0.8833 (tt0) cc_final: 0.8286 (tm-30)
REVERT: A  716 ARG cc_start: 0.8015 (tmt170) cc_final: 0.7791 (tmt170)
REVERT: A  740 ASP cc_start: 0.7838 (t0) cc_final: 0.7520 (p0)
REVERT: A  777 ASP cc_start: 0.7028 (t0) cc_final: 0.6605 (t0)
REVERT: A 1058 TYR cc_start: 0.8119 (t80) cc_final: 0.7790 (t80)
REVERT: A 1327 GLU cc_start: 0.7192 (tt0) cc_final: 0.6875 (tt0)
REVERT: A 1507 MET cc_start: 0.8088 (mmm) cc_final: 0.7703 (tpt)
  outliers start: 8
  outliers final: 4
  residues processed: 116
  average time/residue: 0.1119
  time to fit residues: 18.6469
Evaluate side-chains
  109 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain A residue  473 GLN
Chi-restraints excluded: chain A residue  662 VAL
Chi-restraints excluded: chain A residue 1235 THR
Chi-restraints excluded: chain A residue 1370 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9990
   chunk 82 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 88 optimal weight:    9.9990
   chunk 23 optimal weight:    0.7980
   chunk 120 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 125 optimal weight:    0.0070
   chunk 131 optimal weight:    0.9990
   chunk 128 optimal weight:    0.9980
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
A 473 GLN
A 690 HIS
A 812 ASN
A1371 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.146193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.113025 restraints weight = 25702.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 2.85
r_work: 0.3371 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3399
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3399 r_free = 0.3399    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3399 r_free = 0.3399    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3399
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.1965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11960  Z= 0.125
  Angle     :  0.486   6.277  16212  Z= 0.260
  Chirality :  0.039   0.162   1879
  Planarity :  0.004   0.055   2027
  Dihedral  :  4.212  21.491   1589
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  8.51 %
    Favored  : 90.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    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 aren not related in a simple way.
  whole:  1.89 (0.22), residues: 1466
  helix:  1.95 (0.16), residues: 972
  sheet: -0.86 (0.55), residues: 72
  loop :  0.09 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 789 
 TYR   0.021   0.001   TYR A1105 
 PHE   0.026   0.001   PHE A 576 
 TRP   0.015   0.001   TRP A 422 
 HIS   0.006   0.001   HIS A1347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (11960)
  covalent geometry    : angle       0.48611 (16212)
  hydrogen bonds       : bond        0.04485 (  778)
  hydrogen bonds       : angle       4.10435 ( 2271)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.432 
Fit side-chains
REVERT: A  592 SER cc_start: 0.7594 (t) cc_final: 0.7040 (p)
REVERT: A  657 ASN cc_start: 0.7318 (m110) cc_final: 0.5999 (p0)
REVERT: A  662 VAL cc_start: 0.8042 (OUTLIER) cc_final: 0.7789 (m)
REVERT: A  698 GLN cc_start: 0.8839 (tt0) cc_final: 0.8293 (tm-30)
REVERT: A  716 ARG cc_start: 0.8063 (tmt170) cc_final: 0.7803 (tmt170)
REVERT: A  740 ASP cc_start: 0.8081 (t0) cc_final: 0.7770 (t0)
REVERT: A  744 THR cc_start: 0.8707 (m) cc_final: 0.8376 (m)
REVERT: A  777 ASP cc_start: 0.7026 (t0) cc_final: 0.6594 (t0)
REVERT: A 1058 TYR cc_start: 0.8116 (t80) cc_final: 0.7768 (t80)
REVERT: A 1327 GLU cc_start: 0.7172 (tt0) cc_final: 0.6846 (tt0)
REVERT: A 1394 MET cc_start: 0.6333 (mtp) cc_final: 0.5632 (ptm)
REVERT: A 1507 MET cc_start: 0.8079 (mmm) cc_final: 0.7696 (tpt)
  outliers start: 11
  outliers final: 6
  residues processed: 118
  average time/residue: 0.1039
  time to fit residues: 17.6064
Evaluate side-chains
  113 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  473 GLN
Chi-restraints excluded: chain A residue  662 VAL
Chi-restraints excluded: chain A residue  675 CYS
Chi-restraints excluded: chain A residue 1235 THR
Chi-restraints excluded: chain A residue 1350 SER
Chi-restraints excluded: chain A residue 1370 ILE
Chi-restraints excluded: chain A residue 1451 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 136 optimal weight:    6.9990
   chunk 15 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0070
   chunk 14 optimal weight:    0.7980
   chunk 122 optimal weight:    0.9990
   chunk 138 optimal weight:    3.9990
   chunk 119 optimal weight:    0.9980
   chunk 110 optimal weight:    0.9980
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
A 432 GLN
A 473 GLN
A1371 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.146040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.108226 restraints weight = 36137.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 3.45
r_work: 0.3346 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3358
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3358 r_free = 0.3358    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3358 r_free = 0.3358    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3358
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11960  Z= 0.125
  Angle     :  0.485   6.918  16212  Z= 0.259
  Chirality :  0.039   0.157   1879
  Planarity :  0.004   0.046   2027
  Dihedral  :  4.152  20.984   1589
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  8.67 %
    Favored  : 90.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    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 aren not related in a simple way.
  whole:  1.96 (0.22), residues: 1466
  helix:  2.01 (0.16), residues: 972
  sheet: -0.87 (0.55), residues: 72
  loop :  0.12 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 789 
 TYR   0.021   0.001   TYR A1105 
 PHE   0.015   0.001   PHE A 954 
 TRP   0.015   0.001   TRP A 422 
 HIS   0.005   0.001   HIS A1347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (11960)
  covalent geometry    : angle       0.48533 (16212)
  hydrogen bonds       : bond        0.04435 (  778)
  hydrogen bonds       : angle       4.06868 ( 2271)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.449 
Fit side-chains
REVERT: A  657 ASN cc_start: 0.7304 (m110) cc_final: 0.6030 (p0)
REVERT: A  662 VAL cc_start: 0.8049 (OUTLIER) cc_final: 0.7791 (m)
REVERT: A  698 GLN cc_start: 0.8848 (tt0) cc_final: 0.8306 (tm-30)
REVERT: A  716 ARG cc_start: 0.8108 (tmt170) cc_final: 0.7862 (tmt170)
REVERT: A  740 ASP cc_start: 0.8191 (t0) cc_final: 0.7833 (t0)
REVERT: A 1058 TYR cc_start: 0.8135 (t80) cc_final: 0.7786 (t80)
REVERT: A 1203 THR cc_start: 0.9122 (p) cc_final: 0.8645 (t)
REVERT: A 1314 SER cc_start: 0.8298 (m) cc_final: 0.8087 (t)
REVERT: A 1327 GLU cc_start: 0.7285 (tt0) cc_final: 0.6943 (tt0)
REVERT: A 1394 MET cc_start: 0.6420 (mtp) cc_final: 0.5990 (mtm)
REVERT: A 1507 MET cc_start: 0.8072 (mmm) cc_final: 0.7692 (tpt)
  outliers start: 10
  outliers final: 6
  residues processed: 120
  average time/residue: 0.0847
  time to fit residues: 15.1930
Evaluate side-chains
  111 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  473 GLN
Chi-restraints excluded: chain A residue  662 VAL
Chi-restraints excluded: chain A residue  675 CYS
Chi-restraints excluded: chain A residue 1235 THR
Chi-restraints excluded: chain A residue 1350 SER
Chi-restraints excluded: chain A residue 1370 ILE
Chi-restraints excluded: chain A residue 1451 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 143 optimal weight:    6.9990
   chunk 137 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 76 optimal weight:    0.7980
   chunk 131 optimal weight:    4.9990
   chunk 94 optimal weight:    0.8980
   chunk 115 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 9 optimal weight:    5.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 473 GLN
A1371 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.145328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.106790 restraints weight = 41393.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 3.69
r_work: 0.3331 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3328
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3328 r_free = 0.3328    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3328
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11960  Z= 0.136
  Angle     :  0.490   7.853  16212  Z= 0.260
  Chirality :  0.040   0.169   1879
  Planarity :  0.004   0.040   2027
  Dihedral  :  4.123  20.647   1589
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  8.98 %
    Favored  : 90.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    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 aren not related in a simple way.
  whole:  1.94 (0.22), residues: 1466
  helix:  1.98 (0.16), residues: 974
  sheet: -0.89 (0.56), residues: 72
  loop :  0.15 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 789 
 TYR   0.028   0.001   TYR A 722 
 PHE   0.016   0.001   PHE A 954 
 TRP   0.018   0.001   TRP A1379 
 HIS   0.005   0.001   HIS A1347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (11960)
  covalent geometry    : angle       0.48985 (16212)
  hydrogen bonds       : bond        0.04503 (  778)
  hydrogen bonds       : angle       4.06977 ( 2271)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A  657 ASN cc_start: 0.7296 (m110) cc_final: 0.6192 (p0)
REVERT: A  662 VAL cc_start: 0.8031 (OUTLIER) cc_final: 0.7780 (m)
REVERT: A  698 GLN cc_start: 0.8856 (tt0) cc_final: 0.8324 (tm-30)
REVERT: A  716 ARG cc_start: 0.8137 (tmt170) cc_final: 0.7911 (tmt170)
REVERT: A  740 ASP cc_start: 0.8251 (t0) cc_final: 0.7762 (t0)
REVERT: A 1058 TYR cc_start: 0.8160 (t80) cc_final: 0.7807 (t80)
REVERT: A 1203 THR cc_start: 0.9126 (p) cc_final: 0.8661 (t)
REVERT: A 1327 GLU cc_start: 0.7408 (tt0) cc_final: 0.7079 (tt0)
REVERT: A 1394 MET cc_start: 0.6351 (mtp) cc_final: 0.5943 (mtm)
REVERT: A 1507 MET cc_start: 0.8089 (mmm) cc_final: 0.7807 (tpt)
  outliers start: 9
  outliers final: 5
  residues processed: 116
  average time/residue: 0.0971
  time to fit residues: 16.4167
Evaluate side-chains
  111 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  662 VAL
Chi-restraints excluded: chain A residue  675 CYS
Chi-restraints excluded: chain A residue 1235 THR
Chi-restraints excluded: chain A residue 1350 SER
Chi-restraints excluded: chain A residue 1370 ILE
Chi-restraints excluded: chain A residue 1451 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 101 optimal weight:    0.5980
   chunk 63 optimal weight:    0.0980
   chunk 77 optimal weight:    0.3980
   chunk 53 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 105 optimal weight:    0.6980
   chunk 87 optimal weight:    8.9990
   chunk 29 optimal weight:    0.6980
   chunk 131 optimal weight:    0.0000
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 476 GLN
A 979 ASN
A1371 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.151383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.114127 restraints weight = 32726.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 3.53
r_work: 0.3362 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3371
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3371 r_free = 0.3371    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3371 r_free = 0.3371    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3371
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  11960  Z= 0.104
  Angle     :  0.461   7.734  16212  Z= 0.245
  Chirality :  0.038   0.144   1879
  Planarity :  0.003   0.038   2027
  Dihedral  :  3.981  20.421   1589
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  9.37 %
    Favored  : 90.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    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 aren not related in a simple way.
  whole:  2.21 (0.22), residues: 1466
  helix:  2.21 (0.16), residues: 976
  sheet: -0.80 (0.57), residues: 72
  loop :  0.17 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1280 
 TYR   0.020   0.001   TYR A1105 
 PHE   0.014   0.001   PHE A 954 
 TRP   0.012   0.001   TRP A 849 
 HIS   0.004   0.001   HIS A1347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 (11960)
  covalent geometry    : angle       0.46100 (16212)
  hydrogen bonds       : bond        0.04030 (  778)
  hydrogen bonds       : angle       3.94475 ( 2271)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 120
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A  407 ASN cc_start: 0.8022 (t0) cc_final: 0.7488 (t0)
REVERT: A  529 MET cc_start: 0.8116 (mtp) cc_final: 0.7843 (mtt)
REVERT: A  537 ASN cc_start: 0.8938 (t0) cc_final: 0.8713 (t0)
REVERT: A  657 ASN cc_start: 0.7369 (m110) cc_final: 0.6059 (p0)
REVERT: A  662 VAL cc_start: 0.7959 (OUTLIER) cc_final: 0.7715 (m)
REVERT: A  698 GLN cc_start: 0.8843 (tt0) cc_final: 0.8306 (tm-30)
REVERT: A  721 PHE cc_start: 0.7325 (t80) cc_final: 0.7035 (t80)
REVERT: A  763 LEU cc_start: 0.8494 (tp) cc_final: 0.8276 (tt)
REVERT: A  773 THR cc_start: 0.8276 (m) cc_final: 0.7793 (p)
REVERT: A 1058 TYR cc_start: 0.8071 (t80) cc_final: 0.7790 (t80)
REVERT: A 1203 THR cc_start: 0.9123 (p) cc_final: 0.8695 (t)
REVERT: A 1327 GLU cc_start: 0.7018 (tt0) cc_final: 0.6689 (tt0)
REVERT: A 1394 MET cc_start: 0.6377 (mtp) cc_final: 0.6015 (mtm)
REVERT: A 1507 MET cc_start: 0.8062 (mmm) cc_final: 0.7792 (tpt)
  outliers start: 7
  outliers final: 4
  residues processed: 124
  average time/residue: 0.0957
  time to fit residues: 17.3753
Evaluate side-chains
  111 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 106
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  662 VAL
Chi-restraints excluded: chain A residue  675 CYS
Chi-restraints excluded: chain A residue 1235 THR
Chi-restraints excluded: chain A residue 1370 ILE
Chi-restraints excluded: chain A residue 1451 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 110 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9980
   chunk 129 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 77 optimal weight:    7.9990
   chunk 118 optimal weight:    0.6980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A1371 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.149088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.110641 restraints weight = 39347.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 4.02
r_work: 0.3314 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3316
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3316 r_free = 0.3316    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3316 r_free = 0.3316    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3316
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11960  Z= 0.138
  Angle     :  0.495   8.411  16212  Z= 0.263
  Chirality :  0.040   0.166   1879
  Planarity :  0.004   0.041   2027
  Dihedral  :  4.028  24.014   1589
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  9.52 %
    Favored  : 89.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    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 aren not related in a simple way.
  whole:  2.06 (0.22), residues: 1466
  helix:  2.05 (0.16), residues: 976
  sheet: -0.55 (0.64), residues: 62
  loop :  0.14 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 789 
 TYR   0.022   0.001   TYR A1105 
 PHE   0.032   0.001   PHE A 576 
 TRP   0.017   0.001   TRP A 422 
 HIS   0.008   0.001   HIS A1347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (11960)
  covalent geometry    : angle       0.49490 (16212)
  hydrogen bonds       : bond        0.04394 (  778)
  hydrogen bonds       : angle       3.99666 ( 2271)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.490 
Fit side-chains
REVERT: A  529 MET cc_start: 0.8161 (mtp) cc_final: 0.7901 (mtt)
REVERT: A  537 ASN cc_start: 0.8962 (t0) cc_final: 0.8734 (t0)
REVERT: A  592 SER cc_start: 0.7579 (t) cc_final: 0.7022 (p)
REVERT: A  657 ASN cc_start: 0.7441 (m110) cc_final: 0.6304 (p0)
REVERT: A  662 VAL cc_start: 0.7954 (OUTLIER) cc_final: 0.7721 (m)
REVERT: A  698 GLN cc_start: 0.8865 (tt0) cc_final: 0.8320 (tm-30)
REVERT: A  721 PHE cc_start: 0.7411 (t80) cc_final: 0.7066 (t80)
REVERT: A 1058 TYR cc_start: 0.8133 (t80) cc_final: 0.7798 (t80)
REVERT: A 1203 THR cc_start: 0.9169 (p) cc_final: 0.8725 (t)
REVERT: A 1327 GLU cc_start: 0.7424 (tt0) cc_final: 0.7103 (tt0)
REVERT: A 1394 MET cc_start: 0.6371 (mtp) cc_final: 0.5964 (mtm)
REVERT: A 1507 MET cc_start: 0.8060 (mmm) cc_final: 0.7787 (tpt)
  outliers start: 8
  outliers final: 7
  residues processed: 108
  average time/residue: 0.1085
  time to fit residues: 17.3846
Evaluate side-chains
  112 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  662 VAL
Chi-restraints excluded: chain A residue  675 CYS
Chi-restraints excluded: chain A residue  676 MET
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue 1011 ILE
Chi-restraints excluded: chain A residue 1235 THR
Chi-restraints excluded: chain A residue 1370 ILE
Chi-restraints excluded: chain A residue 1451 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 77 optimal weight:    7.9990
   chunk 99 optimal weight:    0.9990
   chunk 72 optimal weight:    6.9990
   chunk 73 optimal weight:    9.9990
   chunk 141 optimal weight:    2.9990
   chunk 44 optimal weight:    0.4980
   chunk 65 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 137 optimal weight:    0.9980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 432 GLN
A1218 GLN
A1371 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.144618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.107957 restraints weight = 29409.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 3.07
r_work: 0.3344 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3354
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3354 r_free = 0.3354    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3354 r_free = 0.3354    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3354
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.2369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11960  Z= 0.158
  Angle     :  0.513   8.545  16212  Z= 0.271
  Chirality :  0.040   0.188   1879
  Planarity :  0.004   0.041   2027
  Dihedral  :  4.107  25.420   1589
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  9.52 %
    Favored  : 89.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    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 aren not related in a simple way.
  whole:  1.86 (0.22), residues: 1466
  helix:  1.90 (0.16), residues: 974
  sheet: -0.22 (0.69), residues: 53
  loop : -0.00 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 789 
 TYR   0.024   0.001   TYR A1105 
 PHE   0.026   0.001   PHE A 576 
 TRP   0.020   0.001   TRP A 422 
 HIS   0.008   0.001   HIS A1347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (11960)
  covalent geometry    : angle       0.51267 (16212)
  hydrogen bonds       : bond        0.04679 (  778)
  hydrogen bonds       : angle       4.07698 ( 2271)

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

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

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2932 Ramachandran restraints generated.
    1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.465 
Fit side-chains
REVERT: A  529 MET cc_start: 0.8148 (mtp) cc_final: 0.7885 (mtt)
REVERT: A  537 ASN cc_start: 0.8938 (t0) cc_final: 0.8728 (t0)
REVERT: A  662 VAL cc_start: 0.7968 (OUTLIER) cc_final: 0.7732 (m)
REVERT: A  698 GLN cc_start: 0.8842 (tt0) cc_final: 0.8313 (tm-30)
REVERT: A  716 ARG cc_start: 0.8037 (tmt170) cc_final: 0.7711 (tmt170)
REVERT: A  721 PHE cc_start: 0.7423 (t80) cc_final: 0.7066 (t80)
REVERT: A 1058 TYR cc_start: 0.8179 (t80) cc_final: 0.7816 (t80)
REVERT: A 1116 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6922 (mt-10)
REVERT: A 1203 THR cc_start: 0.9167 (p) cc_final: 0.8731 (t)
REVERT: A 1218 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.7674 (mp-120)
REVERT: A 1327 GLU cc_start: 0.7480 (tt0) cc_final: 0.7153 (tt0)
REVERT: A 1394 MET cc_start: 0.6513 (mtp) cc_final: 0.6152 (mtm)
REVERT: A 1507 MET cc_start: 0.8073 (mmm) cc_final: 0.7802 (tpt)
  outliers start: 9
  outliers final: 6
  residues processed: 107
  average time/residue: 0.0992
  time to fit residues: 15.8372
Evaluate side-chains
  108 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  662 VAL
Chi-restraints excluded: chain A residue  675 CYS
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue 1011 ILE
Chi-restraints excluded: chain A residue 1116 GLU
Chi-restraints excluded: chain A residue 1218 GLN
Chi-restraints excluded: chain A residue 1235 THR
Chi-restraints excluded: chain A residue 1370 ILE
Chi-restraints excluded: chain A residue 1451 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 104 optimal weight:    0.4980
   chunk 38 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0970
   chunk 95 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 77 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 58 optimal weight:    0.4980
   chunk 99 optimal weight:    0.0570
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.3696

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

Flipped N/Q/H residues before XYZ refinement:
A1218 GLN
A1371 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.145032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.106871 restraints weight = 35522.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 3.41
r_work: 0.3333 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3315
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3315 r_free = 0.3315    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3315 r_free = 0.3315    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3315
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.134  11960  Z= 0.188
  Angle     :  0.865  59.191  16212  Z= 0.495
  Chirality :  0.042   0.643   1879
  Planarity :  0.004   0.042   2027
  Dihedral  :  4.107  25.215   1589
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  9.60 %
    Favored  : 89.71 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    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 aren not related in a simple way.
  whole:  1.87 (0.22), residues: 1466
  helix:  1.91 (0.16), residues: 974
  sheet: -0.22 (0.69), residues: 53
  loop : -0.01 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 789 
 TYR   0.024   0.001   TYR A1105 
 PHE   0.025   0.001   PHE A 576 
 TRP   0.019   0.001   TRP A 422 
 HIS   0.007   0.001   HIS A1347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (11960)
  covalent geometry    : angle       0.86461 (16212)
  hydrogen bonds       : bond        0.04612 (  778)
  hydrogen bonds       : angle       4.07638 ( 2271)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3043.18 seconds
wall clock time: 52 minutes 45.17 seconds (3165.17 seconds total)