Starting phenix.real_space_refine
on Thu Feb 13 22:59:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pmj_17761/02_2025/8pmj_17761.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pmj_17761/02_2025/8pmj_17761.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pmj_17761/02_2025/8pmj_17761.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pmj_17761/02_2025/8pmj_17761.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pmj_17761/02_2025/8pmj_17761.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pmj_17761/02_2025/8pmj_17761.cif"
  }
  resolution = 2.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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: 7
    Type Number    sf(0)   Gaussians
     V       1      8.30       5
     P       5      5.49       5
     Mg      2      5.21       5
     S      52      5.16       5
     C    5774      2.51       5
     N    1503      2.21       5
     O    1648      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8985
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1133, 8805
          Classifications: {'peptide': 1133}
          Link IDs: {'PTRANS': 32, 'TRANS': 1100}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 180
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 180
          Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'CLR': 4, 'VO4': 1}
          Classifications: {'undetermined': 9, 'water': 3}
          Link IDs: {None: 11}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   VAL A 248 " occ=0.96
      ... (5 atoms not shown)
      pdb=" CG2 VAL A 248 " occ=0.68
  Time building chain proxies: 6.08, per 1000 atoms: 0.68
  Number of scatterers: 8985
  At special positions: 0
  Unit cell: (104.94, 100.98, 127.38, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     V       1     22.97
     S      52     16.00
     P       5     15.00
     Mg      2     11.99
     O    1648      8.00
     N    1503      7.00
     C    5774      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.36
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2086

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 5 sheets defined
      70.9% alpha, 8.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 52
      removed outlier: 3.673A  pdb=" N   PHE A  51 " --> pdb=" O   PHE A  48 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ARG A  52 " --> pdb=" O   GLN A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 100
      removed outlier: 4.330A  pdb=" N   GLN A  76 " --> pdb=" O   HIS A  72 " (cutoff:3.500A)
      Proline residue:  A  77  - end of helix
      removed outlier: 3.637A  pdb=" N   ASP A  88 " --> pdb=" O   GLY A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 183
      removed outlier: 3.568A  pdb=" N   ARG A 169 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLN A 170 " --> pdb=" O   ALA A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 191
      removed outlier: 3.747A  pdb=" N   PHE A 190 " --> pdb=" O   GLU A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 214
      removed outlier: 4.772A  pdb=" N   ILE A 206 " --> pdb=" O   PHE A 202 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   ASN A 207 " --> pdb=" O   SER A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 237
      removed outlier: 3.696A  pdb=" N   GLY A 234 " --> pdb=" O   GLY A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 287
      removed outlier: 4.345A  pdb=" N   ILE A 245 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
      Proline residue:  A 250  - end of helix
      removed outlier: 3.807A  pdb=" N   VAL A 280 " --> pdb=" O   LYS A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 295
    Processing helix  chain 'A' and resid 296 through 344
      removed outlier: 3.708A  pdb=" N   PHE A 310 " --> pdb=" O   LYS A 306 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA A 311 " --> pdb=" O   ASN A 307 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   TRP A 314 " --> pdb=" O   PHE A 310 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR A 326 " --> pdb=" O   MET A 322 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   TRP A 330 " --> pdb=" O   THR A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 375
      removed outlier: 3.537A  pdb=" N   VAL A 360 " --> pdb=" O   PRO A 356 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   GLN A 361 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ILE A 367 " --> pdb=" O   PHE A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 398
      removed outlier: 3.509A  pdb=" N   LEU A 380 " --> pdb=" O   ALA A 376 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   THR A 396 " --> pdb=" O   SER A 392 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ILE A 397 " --> pdb=" O   ILE A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 469
      removed outlier: 3.723A  pdb=" N   LEU A 465 " --> pdb=" O   LYS A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 489
      No H-bonds generated for 'chain 'A' and resid 487 through 489'
    Processing helix  chain 'A' and resid 490 through 497
    Processing helix  chain 'A' and resid 511 through 518
    Processing helix  chain 'A' and resid 524 through 535
    Processing helix  chain 'A' and resid 537 through 543
    Processing helix  chain 'A' and resid 553 through 557
    Processing helix  chain 'A' and resid 560 through 574
    Processing helix  chain 'A' and resid 590 through 604
      removed outlier: 3.575A  pdb=" N   VAL A 600 " --> pdb=" O   MET A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 621
    Processing helix  chain 'A' and resid 739 through 748
    Processing helix  chain 'A' and resid 751 through 781
      removed outlier: 4.005A  pdb=" N   THR A 769 " --> pdb=" O   ASN A 765 " (cutoff:3.500A)
      Proline residue:  A 770  - end of helix
      removed outlier: 3.745A  pdb=" N   ALA A 773 " --> pdb=" O   THR A 769 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 792 through 841
      removed outlier: 3.661A  pdb=" N   ASN A 796 " --> pdb=" O   ARG A 792 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   SER A 809 " --> pdb=" O   MET A 805 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   PHE A 814 " --> pdb=" O   LEU A 810 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ALA A 821 " --> pdb=" O   GLY A 817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 843 through 848
      removed outlier: 3.561A  pdb=" N   PHE A 847 " --> pdb=" O   ASP A 843 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 849 through 852
    Processing helix  chain 'A' and resid 853 through 873
      removed outlier: 4.419A  pdb=" N   ALA A 865 " --> pdb=" O   LEU A 861 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   SER A 866 " --> pdb=" O   ALA A 862 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL A 868 " --> pdb=" O   ASP A 864 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 874 through 895
    Processing helix  chain 'A' and resid 897 through 908
      removed outlier: 4.063A  pdb=" N   VAL A 903 " --> pdb=" O   LYS A 899 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ILE A 904 " --> pdb=" O   LEU A 900 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   PHE A 907 " --> pdb=" O   VAL A 903 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   PHE A 908 " --> pdb=" O   ILE A 904 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 908 through 946
      removed outlier: 3.588A  pdb=" N   ALA A 912 " --> pdb=" O   PHE A 908 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   GLY A 924 " --> pdb=" O   ARG A 920 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   PHE A 925 " --> pdb=" O   MET A 921 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ARG A 928 " --> pdb=" O   GLY A 924 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   GLN A 931 " --> pdb=" O   SER A 927 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ALA A 932 " --> pdb=" O   ARG A 928 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 946 through 954
    Processing helix  chain 'A' and resid 955 through 1010
      removed outlier: 4.511A  pdb=" N   LYS A 969 " --> pdb=" O   THR A 965 " (cutoff:3.500A)
      Proline residue:  A 970  - end of helix
      removed outlier: 3.991A  pdb=" N   THR A 973 " --> pdb=" O   LYS A 969 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   ILE A 975 " --> pdb=" O   PHE A 971 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   GLN A 976 " --> pdb=" O   LYS A 972 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLN A 989 " --> pdb=" O   PHE A 985 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   SER A1008 " --> pdb=" O   GLY A1004 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1028
      removed outlier: 4.091A  pdb=" N   VAL A1017 " --> pdb=" O   HIS A1013 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1029 through 1039
      removed outlier: 3.569A  pdb=" N   GLY A1032 " --> pdb=" O   THR A1029 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   ALA A1034 " --> pdb=" O   LEU A1031 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   PHE A1035 " --> pdb=" O   GLY A1032 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   THR A1038 " --> pdb=" O   PHE A1035 " (cutoff:3.500A)
      Proline residue:  A1039  - end of helix
    Processing helix  chain 'A' and resid 1040 through 1056
    Processing helix  chain 'A' and resid 1118 through 1127
      removed outlier: 3.565A  pdb=" N   ILE A1123 " --> pdb=" O   LYS A1119 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU A1126 " --> pdb=" O   SER A1122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1147
      No H-bonds generated for 'chain 'A' and resid 1145 through 1147'
    Processing helix  chain 'A' and resid 1148 through 1155
      removed outlier: 3.671A  pdb=" N   ASN A1155 " --> pdb=" O   PHE A1151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1169 through 1176
    Processing helix  chain 'A' and resid 1184 through 1195
    Processing helix  chain 'A' and resid 1197 through 1203
    Processing helix  chain 'A' and resid 1213 through 1217
    Processing helix  chain 'A' and resid 1220 through 1235
      removed outlier: 4.067A  pdb=" N   ARG A1235 " --> pdb=" O   ARG A1231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1250 through 1265
      removed outlier: 3.649A  pdb=" N   THR A1256 " --> pdb=" O   GLU A1252 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   LYS A1263 " --> pdb=" O   VAL A1259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1276 through 1280
      removed outlier: 3.778A  pdb=" N   ILE A1280 " --> pdb=" O   LEU A1277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1299 through 1306
    Processing helix  chain 'A' and resid 1308 through 1317
      removed outlier: 3.640A  pdb=" N   GLY A1317 " --> pdb=" O   LEU A1313 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 445
      removed outlier: 6.764A  pdb=" N   ILE A 437 " --> pdb=" O   HIS A 428 " (cutoff:3.500A)
      removed outlier: 7.571A  pdb=" N   HIS A 428 " --> pdb=" O   ILE A 437 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   ASN A 439 " --> pdb=" O   THR A 426 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   THR A 426 " --> pdb=" O   ASN A 439 " (cutoff:3.500A)
      removed outlier: 4.947A  pdb=" N   LEU A 441 " --> pdb=" O   ASN A 424 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   MET A 443 " --> pdb=" O   PHE A 422 " (cutoff:3.500A)
      removed outlier: 5.752A  pdb=" N   PHE A 422 " --> pdb=" O   THR A 480 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   THR A 480 " --> pdb=" O   PHE A 422 " (cutoff:3.500A)
      removed outlier: 5.492A  pdb=" N   ASN A 424 " --> pdb=" O   MET A 478 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   MET A 478 " --> pdb=" O   ASN A 424 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 498 through 501
      removed outlier: 6.266A  pdb=" N   THR A 451 " --> pdb=" O   SER A 612 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   MET A 450 " --> pdb=" O   THR A 625 " (cutoff:3.500A)
      removed outlier: 7.687A  pdb=" N   ILE A 627 " --> pdb=" O   MET A 450 " (cutoff:3.500A)
      removed outlier: 6.132A  pdb=" N   ALA A 452 " --> pdb=" O   ILE A 627 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   PHE A 629 " --> pdb=" O   ALA A 452 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   VAL A 454 " --> pdb=" O   PHE A 629 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1096 through 1097
      removed outlier: 3.561A  pdb=" N   LEU A1096 " --> pdb=" O   PHE A1085 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1096 through 1097
      removed outlier: 3.561A  pdb=" N   LEU A1096 " --> pdb=" O   PHE A1085 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LYS A1136 " --> pdb=" O   VAL A1081 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   CYS A1083 " --> pdb=" O   GLN A1134 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   GLN A1134 " --> pdb=" O   CYS A1083 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1159
      removed outlier: 6.266A  pdb=" N   GLY A1157 " --> pdb=" O   LEU A1241 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   ASP A1243 " --> pdb=" O   GLY A1157 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   VAL A1159 " --> pdb=" O   ASP A1243 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   LEU A1109 " --> pdb=" O   VAL A1272 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   THR A1108 " --> pdb=" O   ILE A1285 " (cutoff:3.500A)
      removed outlier: 7.417A  pdb=" N   ALA A1287 " --> pdb=" O   THR A1108 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   ALA A1110 " --> pdb=" O   ALA A1287 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   MET A1289 " --> pdb=" O   ALA A1110 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   VAL A1112 " --> pdb=" O   MET A1289 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   GLU A1296 " --> pdb=" O   VAL A1288 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   ALA A1290 " --> pdb=" O   VAL A1294 " (cutoff:3.500A)
      removed outlier: 5.231A  pdb=" N   VAL A1294 " --> pdb=" O   ALA A1290 " (cutoff:3.500A)

    584 hydrogen bonds defined for protein.
    1698 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: 3.25

  Time building geometry restraints manager: 2.69 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2890
        1.35 -     1.49: 2275
        1.49 -     1.62: 3909
        1.62 -     1.76: 0
        1.76 -     1.90: 89
  Bond restraints: 9163
  Sorted by residual:
  bond pdb=" C4  ADP A1506 "
       pdb=" C5  ADP A1506 "
    ideal  model  delta    sigma   weight residual
    1.490  1.378  0.112 2.00e-02 2.50e+03 3.16e+01
  bond pdb=" C5  ADP A1506 "
       pdb=" C6  ADP A1506 "
    ideal  model  delta    sigma   weight residual
    1.490  1.405  0.085 2.00e-02 2.50e+03 1.80e+01
  bond pdb=" O3B ADP A1506 "
       pdb=" PB  ADP A1506 "
    ideal  model  delta    sigma   weight residual
    1.510  1.463  0.047 2.00e-02 2.50e+03 5.63e+00
  bond pdb=" C8  ADP A1506 "
       pdb=" N7  ADP A1506 "
    ideal  model  delta    sigma   weight residual
    1.350  1.306  0.044 2.00e-02 2.50e+03 4.82e+00
  bond pdb=" N   LYS A 829 "
       pdb=" CA  LYS A 829 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.027 1.26e-02 6.30e+03 4.72e+00
  ... (remaining 9158 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.20: 12343
        3.20 -     6.40: 63
        6.40 -     9.60: 12
        9.60 -    12.79: 0
       12.79 -    15.99: 1
  Bond angle restraints: 12419
  Sorted by residual:
  angle pdb=" PA  ADP A1506 "
        pdb=" O3A ADP A1506 "
        pdb=" PB  ADP A1506 "
      ideal   model   delta    sigma   weight residual
     120.50  136.49  -15.99 3.00e+00 1.11e-01 2.84e+01
  angle pdb=" C   TYR A1037 "
        pdb=" N   THR A1038 "
        pdb=" CA  THR A1038 "
      ideal   model   delta    sigma   weight residual
     120.09  125.08   -4.99 1.25e+00 6.40e-01 1.60e+01
  angle pdb=" CA  MET A  86 "
        pdb=" C   MET A  86 "
        pdb=" O   MET A  86 "
      ideal   model   delta    sigma   weight residual
     120.55  116.61    3.94 1.06e+00 8.90e-01 1.38e+01
  angle pdb=" O   ALA A 739 "
        pdb=" C   ALA A 739 "
        pdb=" N   PRO A 740 "
      ideal   model   delta    sigma   weight residual
     121.37  118.13    3.24 9.00e-01 1.23e+00 1.29e+01
  angle pdb=" C   LYS A 829 "
        pdb=" N   ARG A 830 "
        pdb=" CA  ARG A 830 "
      ideal   model   delta    sigma   weight residual
     120.28  115.75    4.53 1.34e+00 5.57e-01 1.14e+01
  ... (remaining 12414 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.41: 4967
       17.41 -    34.81: 492
       34.81 -    52.22: 148
       52.22 -    69.63: 31
       69.63 -    87.04: 9
  Dihedral angle restraints: 5647
    sinusoidal: 2401
      harmonic: 3246
  Sorted by residual:
  dihedral pdb=" O1B ADP A1506 "
           pdb=" O3A ADP A1506 "
           pdb=" PB  ADP A1506 "
           pdb=" PA  ADP A1506 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   27.03  -87.04     1      2.00e+01 2.50e-03 2.28e+01
  dihedral pdb=" CA  MET A 138 "
           pdb=" C   MET A 138 "
           pdb=" N   ILE A 139 "
           pdb=" CA  ILE A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.21   17.79     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CG  ARG A1050 "
           pdb=" CD  ARG A1050 "
           pdb=" NE  ARG A1050 "
           pdb=" CZ  ARG A1050 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.05   48.95     2      1.50e+01 4.44e-03 1.21e+01
  ... (remaining 5644 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.177: 1417
       0.177 -    0.354: 1
       0.354 -    0.531: 0
       0.531 -    0.708: 0
       0.708 -    0.886: 1
  Chirality restraints: 1419
  Sorted by residual:
  chirality pdb=" V   VO4 A1507 "
            pdb=" O1  VO4 A1507 "
            pdb=" O2  VO4 A1507 "
            pdb=" O4  VO4 A1507 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       5.36    4.48    0.89 2.00e-01 2.50e+01 1.96e+01
  chirality pdb=" C3' ADP A1506 "
            pdb=" C2' ADP A1506 "
            pdb=" C4' ADP A1506 "
            pdb=" O3' ADP A1506 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.70    0.19 2.00e-01 2.50e+01 8.71e-01
  chirality pdb=" CA  MET A 138 "
            pdb=" N   MET A 138 "
            pdb=" C   MET A 138 "
            pdb=" CB  MET A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.87e-01
  ... (remaining 1416 not shown)

  Planarity restraints: 1551
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 828 "   -0.011 2.00e-02 2.50e+03   2.10e-02 4.40e+00
        pdb=" C   THR A 828 "    0.036 2.00e-02 2.50e+03
        pdb=" O   THR A 828 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LYS A 829 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 534 "    0.010 2.00e-02 2.50e+03   2.07e-02 4.27e+00
        pdb=" CD  GLU A 534 "   -0.036 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 534 "    0.013 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 534 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 776 "    0.011 2.00e-02 2.50e+03   1.24e-02 2.70e+00
        pdb=" CG  PHE A 776 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 776 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 776 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 776 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 776 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 776 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1548 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 53
        2.55 -     3.13: 6979
        3.13 -     3.72: 14013
        3.72 -     4.31: 19897
        4.31 -     4.90: 33159
  Nonbonded interactions: 74101
  Sorted by model distance:
  nonbonded pdb="MG    MG A1508 "
            pdb=" O   HOH A1602 "
     model   vdw
     1.958 2.170
  nonbonded pdb=" O3G ATP A1501 "
            pdb="MG    MG A1509 "
     model   vdw
     1.958 2.170
  nonbonded pdb="MG    MG A1509 "
            pdb=" O   HOH A1601 "
     model   vdw
     1.986 2.170
  nonbonded pdb=" OG  SER A 462 "
            pdb="MG    MG A1509 "
     model   vdw
     1.995 2.170
  nonbonded pdb=" OE1 GLN A1161 "
            pdb="MG    MG A1508 "
     model   vdw
     2.017 2.170
  ... (remaining 74096 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=0.00 max=1.00 mean=0.91
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:             3.630
  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:          0.400
  Check model and map are aligned:         0.050
  Set scattering table:                    0.090
  Process input model:                     24.210
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
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   0.112   9163  Z= 0.236
  Angle     :  0.640  15.993  12419  Z= 0.336
  Chirality :  0.047   0.886   1419
  Planarity :  0.003   0.039   1551
  Dihedral  : 15.655  87.036   3561
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.93 %
    Favored  : 87.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.24), residues: 1123
  helix:  1.02 (0.19), residues: 748
  sheet:  0.40 (0.60), residues: 76
  loop : -1.18 (0.32), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1071 
 HIS   0.004   0.001   HIS A 615 
 PHE   0.029   0.001   PHE A 776 
 TYR   0.025   0.001   TYR A 337 
 ARG   0.012   0.000   ARG A1050 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 1.070 
Fit side-chains
   revert: symmetry clash
REVERT: A  594 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8219 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 1.5216
  time to fit residues: 188.4027
Evaluate side-chains
  94 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 45 optimal weight:    6.9990
   chunk 88 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 102 optimal weight:    2.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 307 ASN
A 312 GLN
A 530 GLN
A 885 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.116736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.102293 restraints weight = 12880.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 1.26
r_work: 0.3109 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3004
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      161 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2889 r_free = 0.2889    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      267 |
|-----------------------------------------------------------------------------|
r_final: 0.2889
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.1115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9163  Z= 0.207
  Angle     :  0.563   8.649  12419  Z= 0.295
  Chirality :  0.042   0.161   1419
  Planarity :  0.004   0.039   1551
  Dihedral  :  7.300  71.244   1525
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 13.89 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.24), residues: 1123
  helix:  1.47 (0.19), residues: 759
  sheet:  0.06 (0.56), residues: 74
  loop : -1.36 (0.32), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 314 
 HIS   0.002   0.001   HIS A 428 
 PHE   0.027   0.001   PHE A 776 
 TYR   0.020   0.001   TYR A 337 
 ARG   0.008   0.001   ARG A1050 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 106
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
REVERT: A  468 ILE cc_start: 0.8912 (mt) cc_final: 0.8671 (mt)
REVERT: A  476 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8454 (tp30)
REVERT: A  526 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7979 (tp30)
REVERT: A  778 GLN cc_start: 0.7637 (tt0) cc_final: 0.7122 (mp10)
REVERT: A  957 ARG cc_start: 0.8184 (mpp80) cc_final: 0.7938 (mtt90)
  outliers start: 28
  outliers final: 14
  residues processed: 127
  average time/residue: 1.3642
  time to fit residues: 184.7736
Evaluate side-chains
  112 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  534 GLU
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain A residue  809 SER
Chi-restraints excluded: chain A residue  906 CYS
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  991 ILE
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1233 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 108 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 82 optimal weight:    6.9990
   chunk 56 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 312 GLN
A 530 GLN
A 885 ASN
A 946 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.107644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.092990 restraints weight = 13742.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 1.22
r_work: 0.2991 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2904 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2930
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      267 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2920 r_free = 0.2920    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      322 |
|-----------------------------------------------------------------------------|
r_final: 0.2920
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.1403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9163  Z= 0.167
  Angle     :  0.502   7.153  12419  Z= 0.264
  Chirality :  0.040   0.147   1419
  Planarity :  0.003   0.042   1551
  Dihedral  :  6.784  79.742   1525
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 15.06 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.25), residues: 1123
  helix:  1.81 (0.19), residues: 758
  sheet:  0.14 (0.56), residues: 74
  loop : -1.32 (0.32), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 163 
 HIS   0.002   0.001   HIS A 428 
 PHE   0.023   0.001   PHE A 776 
 TYR   0.020   0.001   TYR A 337 
 ARG   0.009   0.000   ARG A1050 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 107
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  476 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8494 (tp30)
REVERT: A  526 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8060 (tp30)
REVERT: A  778 GLN cc_start: 0.7488 (tt0) cc_final: 0.6896 (mm-40)
REVERT: A  957 ARG cc_start: 0.8162 (mpp80) cc_final: 0.7916 (mtt90)
REVERT: A  989 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.6661 (mm-40)
REVERT: A 1180 THR cc_start: 0.7472 (p) cc_final: 0.7231 (p)
REVERT: A 1186 GLU cc_start: 0.8306 (mp0) cc_final: 0.8103 (tp30)
  outliers start: 27
  outliers final: 15
  residues processed: 128
  average time/residue: 1.5704
  time to fit residues: 212.4253
Evaluate side-chains
  115 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  534 GLU
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain A residue  906 CYS
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  989 GLN
Chi-restraints excluded: chain A residue  991 ILE
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1101 VAL
Chi-restraints excluded: chain A residue 1233 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 95 optimal weight:    4.9990
   chunk 55 optimal weight:    0.3980
   chunk 57 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   chunk 101 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 170 GLN
A 312 GLN
A 530 GLN
A 885 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.109487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.095332 restraints weight = 13442.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 1.15
r_work: 0.3002 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2911
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2911 r_free = 0.2911    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      322 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      338 |
|-----------------------------------------------------------------------------|
r_final: 0.2908
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.1544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9163  Z= 0.179
  Angle     :  0.509   7.476  12419  Z= 0.266
  Chirality :  0.040   0.166   1419
  Planarity :  0.003   0.034   1551
  Dihedral  :  6.662  82.351   1525
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 15.17 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.25), residues: 1123
  helix:  1.84 (0.19), residues: 760
  sheet:  0.20 (0.55), residues: 74
  loop : -1.26 (0.33), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 314 
 HIS   0.002   0.001   HIS A 615 
 PHE   0.023   0.001   PHE A 776 
 TYR   0.015   0.001   TYR A 337 
 ARG   0.009   0.000   ARG A1050 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 101
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 LEU cc_start: 0.4945 (OUTLIER) cc_final: 0.4536 (pp)
REVERT: A  476 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8491 (tp30)
REVERT: A  526 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8062 (tp30)
REVERT: A  554 GLU cc_start: 0.7415 (tp30) cc_final: 0.7043 (tp30)
REVERT: A  594 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8434 (tm-30)
REVERT: A  778 GLN cc_start: 0.7484 (tt0) cc_final: 0.6884 (mm-40)
REVERT: A  957 ARG cc_start: 0.8151 (mpp80) cc_final: 0.7822 (mtt90)
REVERT: A  989 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.6675 (mm-40)
REVERT: A 1180 THR cc_start: 0.7550 (p) cc_final: 0.7300 (p)
  outliers start: 33
  outliers final: 17
  residues processed: 127
  average time/residue: 1.4168
  time to fit residues: 191.2618
Evaluate side-chains
  118 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  534 GLU
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain A residue  809 SER
Chi-restraints excluded: chain A residue  906 CYS
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  989 GLN
Chi-restraints excluded: chain A residue  991 ILE
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1095 VAL
Chi-restraints excluded: chain A residue 1101 VAL
Chi-restraints excluded: chain A residue 1233 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   chunk 95 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 58 optimal weight:    9.9990
   chunk 70 optimal weight:    6.9990
   chunk 90 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
A  72 HIS
A 312 GLN
A 361 GLN
A 530 GLN
A 885 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.103744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.089285 restraints weight = 13581.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 1.15
r_work: 0.2931 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2842
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2842 r_free = 0.2842    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      338 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      344 |
|-----------------------------------------------------------------------------|
r_final: 0.2839
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   9163  Z= 0.318
  Angle     :  0.607   8.492  12419  Z= 0.318
  Chirality :  0.044   0.191   1419
  Planarity :  0.004   0.048   1551
  Dihedral  :  7.150  76.694   1525
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 14.96 %
    Favored  : 81.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.24), residues: 1123
  helix:  1.47 (0.18), residues: 760
  sheet:  0.01 (0.53), residues: 74
  loop : -1.31 (0.33), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 846 
 HIS   0.003   0.001   HIS A 428 
 PHE   0.023   0.002   PHE A 776 
 TYR   0.015   0.002   TYR A 337 
 ARG   0.010   0.001   ARG A1050 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 100
  time to evaluate  : 1.042 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.7942 (t0) cc_final: 0.7676 (t0)
REVERT: A  172 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7935 (tp40)
REVERT: A  243 LEU cc_start: 0.4911 (OUTLIER) cc_final: 0.4548 (pp)
REVERT: A  411 TYR cc_start: 0.7778 (t80) cc_final: 0.7573 (t80)
REVERT: A  476 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8475 (tp30)
REVERT: A  526 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8081 (tp30)
REVERT: A  594 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8429 (tm-30)
REVERT: A  989 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.6894 (mm-40)
  outliers start: 32
  outliers final: 21
  residues processed: 127
  average time/residue: 1.3973
  time to fit residues: 189.2014
Evaluate side-chains
  114 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 88
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  172 GLN
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  534 GLU
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain A residue  809 SER
Chi-restraints excluded: chain A residue  810 LEU
Chi-restraints excluded: chain A residue  906 CYS
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  989 GLN
Chi-restraints excluded: chain A residue  991 ILE
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1095 VAL
Chi-restraints excluded: chain A residue 1101 VAL
Chi-restraints excluded: chain A residue 1233 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0670
   chunk 72 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 111 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 52 optimal weight:    8.9990
   chunk 31 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.7318

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

Flipped N/Q/H residues before XYZ refinement:
A 307 ASN
A 312 GLN
A 530 GLN
A 885 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.107142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.092938 restraints weight = 13563.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 1.17
r_work: 0.2992 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2911
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2911 r_free = 0.2911    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      344 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      361 |
|-----------------------------------------------------------------------------|
r_final: 0.2909
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9163  Z= 0.157
  Angle     :  0.501   6.948  12419  Z= 0.264
  Chirality :  0.040   0.166   1419
  Planarity :  0.003   0.035   1551
  Dihedral  :  6.578  84.041   1525
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 16.24 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.25), residues: 1123
  helix:  1.84 (0.19), residues: 760
  sheet:  0.17 (0.55), residues: 74
  loop : -1.24 (0.33), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 493 
 HIS   0.002   0.001   HIS A 423 
 PHE   0.023   0.001   PHE A 776 
 TYR   0.016   0.001   TYR A 337 
 ARG   0.009   0.000   ARG A1050 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 97
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.7979 (t0) cc_final: 0.7702 (t0)
REVERT: A  243 LEU cc_start: 0.4766 (OUTLIER) cc_final: 0.4414 (pp)
REVERT: A  443 MET cc_start: 0.8800 (mtm) cc_final: 0.8582 (ptt)
REVERT: A  476 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8518 (tp30)
REVERT: A  526 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8035 (tp30)
REVERT: A  554 GLU cc_start: 0.7469 (tp30) cc_final: 0.7108 (tp30)
REVERT: A  594 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8411 (tm-30)
REVERT: A  957 ARG cc_start: 0.8176 (mpp80) cc_final: 0.7850 (mtt90)
REVERT: A  989 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.6680 (mm-40)
REVERT: A 1180 THR cc_start: 0.7570 (p) cc_final: 0.7289 (p)
REVERT: A 1186 GLU cc_start: 0.7971 (tp30) cc_final: 0.7594 (mp0)
REVERT: A 1254 GLU cc_start: 0.7771 (tt0) cc_final: 0.7458 (tt0)
  outliers start: 30
  outliers final: 18
  residues processed: 120
  average time/residue: 1.4745
  time to fit residues: 188.0925
Evaluate side-chains
  113 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  404 ASP
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  534 GLU
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain A residue  809 SER
Chi-restraints excluded: chain A residue  810 LEU
Chi-restraints excluded: chain A residue  906 CYS
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  989 GLN
Chi-restraints excluded: chain A residue  991 ILE
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1101 VAL
Chi-restraints excluded: chain A residue 1233 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 18 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   chunk 3 optimal weight:    0.8980
   chunk 111 optimal weight:    7.9990
   chunk 37 optimal weight:    4.9990
   chunk 80 optimal weight:    6.9990
   chunk 40 optimal weight:    0.0770
   chunk 4 optimal weight:    3.9990
   chunk 69 optimal weight:    6.9990
   overall best weight:    1.5942

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

Flipped N/Q/H residues before XYZ refinement:
A 312 GLN
A 530 GLN
A 885 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.105403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.091308 restraints weight = 13726.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 1.15
r_work: 0.2979 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2896 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2907
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2907 r_free = 0.2907    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      361 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2905 r_free = 0.2905    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      377 |
|-----------------------------------------------------------------------------|
r_final: 0.2905
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9163  Z= 0.222
  Angle     :  0.542   7.416  12419  Z= 0.285
  Chirality :  0.042   0.179   1419
  Planarity :  0.003   0.039   1551
  Dihedral  :  6.727  81.846   1525
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 16.35 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.25), residues: 1123
  helix:  1.74 (0.18), residues: 763
  sheet:  0.07 (0.54), residues: 74
  loop : -1.19 (0.34), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 314 
 HIS   0.002   0.001   HIS A 428 
 PHE   0.023   0.001   PHE A 776 
 TYR   0.018   0.001   TYR A 337 
 ARG   0.010   0.000   ARG A 299 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 95
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.8013 (t0) cc_final: 0.7727 (t0)
REVERT: A  243 LEU cc_start: 0.4711 (OUTLIER) cc_final: 0.4433 (pp)
REVERT: A  476 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8496 (tp30)
REVERT: A  526 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8093 (tp30)
REVERT: A  594 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8422 (tm-30)
REVERT: A  957 ARG cc_start: 0.8191 (mpp80) cc_final: 0.7878 (mtt90)
REVERT: A  989 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.6754 (mm-40)
REVERT: A 1180 THR cc_start: 0.7637 (p) cc_final: 0.7361 (p)
REVERT: A 1186 GLU cc_start: 0.8017 (tp30) cc_final: 0.7627 (mp0)
REVERT: A 1254 GLU cc_start: 0.7832 (tt0) cc_final: 0.7518 (tt0)
  outliers start: 36
  outliers final: 22
  residues processed: 124
  average time/residue: 1.4007
  time to fit residues: 184.9084
Evaluate side-chains
  118 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 92
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  404 ASP
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  534 GLU
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain A residue  809 SER
Chi-restraints excluded: chain A residue  810 LEU
Chi-restraints excluded: chain A residue  906 CYS
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  989 GLN
Chi-restraints excluded: chain A residue  991 ILE
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1095 VAL
Chi-restraints excluded: chain A residue 1101 VAL
Chi-restraints excluded: chain A residue 1233 ILE
Chi-restraints excluded: chain A residue 1295 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0030
   chunk 52 optimal weight:    7.9990
   chunk 15 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9980
   chunk 23 optimal weight:    7.9990
   overall best weight:    1.9996

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

Flipped N/Q/H residues before XYZ refinement:
A 312 GLN
A 530 GLN
A 885 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.104164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.090007 restraints weight = 13951.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 1.17
r_work: 0.2948 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2864 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2860
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2860 r_free = 0.2860    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      377 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2859 r_free = 0.2859    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      377 |
|-----------------------------------------------------------------------------|
r_final: 0.2859
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.1767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9163  Z= 0.261
  Angle     :  0.579   7.949  12419  Z= 0.304
  Chirality :  0.043   0.196   1419
  Planarity :  0.004   0.042   1551
  Dihedral  :  6.951  79.633   1525
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 16.13 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.24), residues: 1123
  helix:  1.60 (0.18), residues: 761
  sheet: -0.04 (0.53), residues: 74
  loop : -1.24 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 846 
 HIS   0.003   0.001   HIS A 428 
 PHE   0.023   0.002   PHE A 776 
 TYR   0.016   0.002   TYR A 337 
 ARG   0.011   0.001   ARG A 299 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 95
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.8003 (t0) cc_final: 0.7721 (t0)
REVERT: A  243 LEU cc_start: 0.4799 (OUTLIER) cc_final: 0.4583 (pp)
REVERT: A  476 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8498 (tp30)
REVERT: A  526 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8076 (tp30)
REVERT: A  554 GLU cc_start: 0.7529 (tp30) cc_final: 0.7163 (tp30)
REVERT: A  594 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8390 (tm-30)
REVERT: A  989 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.6818 (mm-40)
REVERT: A 1007 ILE cc_start: 0.7411 (mt) cc_final: 0.6856 (tt)
REVERT: A 1186 GLU cc_start: 0.8063 (tp30) cc_final: 0.7650 (mp0)
REVERT: A 1254 GLU cc_start: 0.7864 (tt0) cc_final: 0.7538 (tt0)
  outliers start: 36
  outliers final: 23
  residues processed: 124
  average time/residue: 1.4409
  time to fit residues: 189.6833
Evaluate side-chains
  117 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 90
  time to evaluate  : 1.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  404 ASP
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  534 GLU
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain A residue  809 SER
Chi-restraints excluded: chain A residue  810 LEU
Chi-restraints excluded: chain A residue  906 CYS
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  989 GLN
Chi-restraints excluded: chain A residue  991 ILE
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1095 VAL
Chi-restraints excluded: chain A residue 1101 VAL
Chi-restraints excluded: chain A residue 1233 ILE
Chi-restraints excluded: chain A residue 1295 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 32 optimal weight:    0.4980
   chunk 38 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 9 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 109 optimal weight:    6.9990
   chunk 111 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 96 optimal weight:    0.6980
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
A 312 GLN
A 492 GLN
A 530 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.105437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.091501 restraints weight = 13772.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 1.16
r_work: 0.2970 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2880
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      377 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      384 |
|-----------------------------------------------------------------------------|
r_final: 0.2880
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9163  Z= 0.193
  Angle     :  0.541   7.292  12419  Z= 0.285
  Chirality :  0.041   0.183   1419
  Planarity :  0.003   0.048   1551
  Dihedral  :  6.717  82.524   1525
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 16.67 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.25), residues: 1123
  helix:  1.75 (0.19), residues: 761
  sheet:  0.09 (0.54), residues: 74
  loop : -1.25 (0.33), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1071 
 HIS   0.002   0.001   HIS A 428 
 PHE   0.022   0.001   PHE A 776 
 TYR   0.017   0.001   TYR A 337 
 ARG   0.013   0.001   ARG A 299 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 89
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.7999 (t0) cc_final: 0.7712 (t0)
REVERT: A  476 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8509 (tp30)
REVERT: A  526 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8060 (tp30)
REVERT: A  554 GLU cc_start: 0.7504 (tp30) cc_final: 0.7143 (tp30)
REVERT: A  594 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8380 (tm-30)
REVERT: A  957 ARG cc_start: 0.8192 (mpp80) cc_final: 0.7879 (mtt90)
REVERT: A  989 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.6728 (mm-40)
REVERT: A 1180 THR cc_start: 0.7612 (p) cc_final: 0.7346 (p)
REVERT: A 1186 GLU cc_start: 0.8068 (tp30) cc_final: 0.7652 (mp0)
REVERT: A 1254 GLU cc_start: 0.7868 (tt0) cc_final: 0.7553 (tt0)
  outliers start: 32
  outliers final: 24
  residues processed: 116
  average time/residue: 1.4415
  time to fit residues: 178.1125
Evaluate side-chains
  114 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 87
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  159 GLN
Chi-restraints excluded: chain A residue  184 ARG
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  404 ASP
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  534 GLU
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain A residue  809 SER
Chi-restraints excluded: chain A residue  810 LEU
Chi-restraints excluded: chain A residue  906 CYS
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  989 GLN
Chi-restraints excluded: chain A residue  991 ILE
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1095 VAL
Chi-restraints excluded: chain A residue 1101 VAL
Chi-restraints excluded: chain A residue 1233 ILE
Chi-restraints excluded: chain A residue 1295 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 96 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   chunk 101 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 170 GLN
A 312 GLN
A 492 GLN
A 530 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.106447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.092482 restraints weight = 13738.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.3056 rms_B_bonded: 1.17
r_work: 0.2987 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2904
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2904 r_free = 0.2904    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      384 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2903 r_free = 0.2903    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      387 |
|-----------------------------------------------------------------------------|
r_final: 0.2903
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9163  Z= 0.173
  Angle     :  0.531   7.310  12419  Z= 0.278
  Chirality :  0.041   0.186   1419
  Planarity :  0.003   0.032   1551
  Dihedral  :  6.525  84.040   1525
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 17.09 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.25), residues: 1123
  helix:  1.85 (0.19), residues: 762
  sheet:  0.17 (0.54), residues: 74
  loop : -1.23 (0.34), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 493 
 HIS   0.002   0.001   HIS A 428 
 PHE   0.022   0.001   PHE A 776 
 TYR   0.017   0.001   TYR A 337 
 ARG   0.009   0.000   ARG A1050 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 93
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.8008 (t0) cc_final: 0.7724 (t0)
REVERT: A  408 GLU cc_start: 0.6641 (mp0) cc_final: 0.6338 (tm-30)
REVERT: A  476 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8476 (tp30)
REVERT: A  526 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8101 (tp30)
REVERT: A  554 GLU cc_start: 0.7478 (tp30) cc_final: 0.7109 (tp30)
REVERT: A  583 ASP cc_start: 0.8906 (t0) cc_final: 0.8696 (t0)
REVERT: A  594 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8391 (tm-30)
REVERT: A  957 ARG cc_start: 0.8180 (mpp80) cc_final: 0.7861 (mtt90)
REVERT: A  989 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.6658 (mm-40)
REVERT: A 1180 THR cc_start: 0.7615 (p) cc_final: 0.7372 (p)
REVERT: A 1186 GLU cc_start: 0.8083 (tp30) cc_final: 0.7676 (mp0)
REVERT: A 1254 GLU cc_start: 0.7851 (tt0) cc_final: 0.7553 (tt0)
  outliers start: 29
  outliers final: 21
  residues processed: 117
  average time/residue: 1.3992
  time to fit residues: 174.0680
Evaluate side-chains
  111 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  404 ASP
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  534 GLU
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain A residue  809 SER
Chi-restraints excluded: chain A residue  810 LEU
Chi-restraints excluded: chain A residue  906 CYS
Chi-restraints excluded: chain A residue  920 ARG
Chi-restraints excluded: chain A residue  989 GLN
Chi-restraints excluded: chain A residue  991 ILE
Chi-restraints excluded: chain A residue 1013 HIS
Chi-restraints excluded: chain A residue 1055 LEU
Chi-restraints excluded: chain A residue 1095 VAL
Chi-restraints excluded: chain A residue 1101 VAL
Chi-restraints excluded: chain A residue 1233 ILE
Chi-restraints excluded: chain A residue 1295 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 96 optimal weight:    0.6980
   chunk 108 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 89 optimal weight:    6.9990
   chunk 58 optimal weight:   10.0000
   chunk 34 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 312 GLN
A 492 GLN
A 530 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.105250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.091271 restraints weight = 13683.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 1.16
r_work: 0.2995 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2886
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2886 r_free = 0.2886    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      387 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2886 r_free = 0.2886    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      386 |
|-----------------------------------------------------------------------------|
r_final: 0.2886
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9163  Z= 0.216
  Angle     :  0.561   7.272  12419  Z= 0.294
  Chirality :  0.042   0.198   1419
  Planarity :  0.004   0.048   1551
  Dihedral  :  6.659  81.893   1525
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 17.52 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.25), residues: 1123
  helix:  1.73 (0.18), residues: 764
  sheet:  0.09 (0.54), residues: 74
  loop : -1.25 (0.34), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 314 
 HIS   0.002   0.001   HIS A 428 
 PHE   0.023   0.001   PHE A 776 
 TYR   0.017   0.001   TYR A 337 
 ARG   0.014   0.001   ARG A 299 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6923.23 seconds
wall clock time: 122 minutes 55.96 seconds (7375.96 seconds total)