Starting phenix.real_space_refine
on Sat Aug 23 03:40:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pmj_17761/08_2025/8pmj_17761.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pmj_17761/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pmj_17761/08_2025/8pmj_17761.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pmj_17761/08_2025/8pmj_17761.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pmj_17761/08_2025/8pmj_17761.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pmj_17761/08_2025/8pmj_17761.map"
  }
  resolution = 2.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.86, per 1000 atoms: 0.21
  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: 0.70
  Conformation dependent library (CDL) restraints added in 307.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.24
  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: 1.14

  Time building geometry restraints manager: 0.89 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:             4.180
  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:          0.240
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.920
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.320
-------------------------------------------------------------------------------
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= 0.177
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (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
 ARG   0.012   0.000   ARG A1050 
 TYR   0.025   0.001   TYR A 337 
 PHE   0.029   0.001   PHE A 776 
 TRP   0.008   0.001   TRP A1071 
 HIS   0.004   0.001   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 9163)
  covalent geometry    : angle       0.64034 (12419)
  hydrogen bonds       : bond        0.18937 (  583)
  hydrogen bonds       : angle       5.37754 ( 1698)

*********************** 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  : 0.350 
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: 0.6028
  time to fit residues: 74.7816
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  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    0.0030
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    6.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    1.7996

-------------------------------------------------------------------------------
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 = 0.3389 r_free = 0.3389 target = 0.114558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.099804 restraints weight = 13016.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 1.29
r_work: 0.3100 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2983
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2983 r_free = 0.2983    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      161 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2868 r_free = 0.2868    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      264 |
|-----------------------------------------------------------------------------|
r_final: 0.2868
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.1095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9163  Z= 0.177
  Angle     :  0.591   8.901  12419  Z= 0.310
  Chirality :  0.043   0.153   1419
  Planarity :  0.004   0.043   1551
  Dihedral  :  7.507  68.927   1525
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 13.68 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.24), residues: 1123
  helix:  1.37 (0.18), residues: 759
  sheet: -0.06 (0.55), residues: 74
  loop : -1.33 (0.32), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1050 
 TYR   0.019   0.001   TYR A 337 
 PHE   0.028   0.002   PHE A 776 
 TRP   0.010   0.001   TRP A 314 
 HIS   0.003   0.001   HIS A 428 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 9163)
  covalent geometry    : angle       0.59083 (12419)
  hydrogen bonds       : bond        0.06952 (  583)
  hydrogen bonds       : angle       4.16283 ( 1698)

*********************** 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
  133 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 103
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  468 ILE cc_start: 0.8941 (mt) cc_final: 0.8696 (mt)
REVERT: A  476 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8473 (tp30)
REVERT: A  486 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7935 (mm)
REVERT: A  526 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8014 (tp30)
REVERT: A  554 GLU cc_start: 0.7403 (tp30) cc_final: 0.7029 (tp30)
REVERT: A  778 GLN cc_start: 0.7652 (tt0) cc_final: 0.7133 (mp10)
REVERT: A  779 ILE cc_start: 0.7429 (mm) cc_final: 0.6957 (mt)
REVERT: A 1252 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7535 (tp30)
  outliers start: 30
  outliers final: 15
  residues processed: 127
  average time/residue: 0.5215
  time to fit residues: 70.6139
Evaluate side-chains
  114 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
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  416 ILE
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  476 GLU
Chi-restraints excluded: chain A residue  486 ILE
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  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
Chi-restraints excluded: chain A residue 1252 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 105 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 74 optimal weight:    7.9990
   chunk 37 optimal weight:    0.1980
   chunk 20 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 56 optimal weight:    0.4980
   chunk 109 optimal weight:    5.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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
A1282 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.107909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.093291 restraints weight = 13682.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 1.21
r_work: 0.2991 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2904 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.2904
-------------------------------------------------------------------------------
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:      264 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      300 |
|-----------------------------------------------------------------------------|
r_final: 0.2896
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.1381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9163  Z= 0.127
  Angle     :  0.505   7.333  12419  Z= 0.266
  Chirality :  0.040   0.145   1419
  Planarity :  0.003   0.034   1551
  Dihedral  :  6.825  78.569   1525
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.96 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.25), residues: 1123
  helix:  1.75 (0.19), residues: 758
  sheet: -0.03 (0.55), residues: 74
  loop : -1.35 (0.32), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1050 
 TYR   0.019   0.001   TYR A 337 
 PHE   0.023   0.001   PHE A 776 
 TRP   0.007   0.001   TRP A 163 
 HIS   0.002   0.001   HIS A 615 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 9163)
  covalent geometry    : angle       0.50511 (12419)
  hydrogen bonds       : bond        0.05698 (  583)
  hydrogen bonds       : angle       3.89163 ( 1698)

*********************** 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
  128 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
REVERT: A  476 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8461 (tp30)
REVERT: A  526 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8030 (tp30)
REVERT: A  778 GLN cc_start: 0.7477 (tt0) cc_final: 0.6886 (mm-40)
REVERT: A  957 ARG cc_start: 0.8168 (mpp80) cc_final: 0.7913 (mtt90)
REVERT: A  989 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.6665 (mm-40)
REVERT: A 1180 THR cc_start: 0.7522 (p) cc_final: 0.7277 (p)
REVERT: A 1186 GLU cc_start: 0.8309 (mp0) cc_final: 0.8102 (tp30)
  outliers start: 23
  outliers final: 14
  residues processed: 123
  average time/residue: 0.5940
  time to fit residues: 77.2602
Evaluate side-chains
  112 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
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  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 1055 LEU
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 26 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 106 optimal weight:    4.9990
   chunk 42 optimal weight:    0.8980
   chunk 92 optimal weight:    2.9990
   chunk 99 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 78 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 70 optimal weight:    7.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 312 GLN
A 361 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 = 0.3258 r_free = 0.3258 target = 0.104379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.089821 restraints weight = 13862.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 1.18
r_work: 0.2962 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.2877 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2850
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2850 r_free = 0.2850    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      300 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      312 |
|-----------------------------------------------------------------------------|
r_final: 0.2847
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.1500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9163  Z= 0.196
  Angle     :  0.591   8.933  12419  Z= 0.309
  Chirality :  0.043   0.175   1419
  Planarity :  0.004   0.046   1551
  Dihedral  :  7.190  75.718   1525
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 14.53 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.24), residues: 1123
  helix:  1.48 (0.18), residues: 760
  sheet: -0.30 (0.52), residues: 74
  loop : -1.36 (0.32), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1050 
 TYR   0.013   0.002   TYR A 337 
 PHE   0.025   0.002   PHE A 776 
 TRP   0.009   0.001   TRP A 846 
 HIS   0.003   0.001   HIS A 428 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 9163)
  covalent geometry    : angle       0.59116 (12419)
  hydrogen bonds       : bond        0.06771 (  583)
  hydrogen bonds       : angle       4.01848 ( 1698)

*********************** 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
  140 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 104
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.7969 (t0) cc_final: 0.7689 (t0)
REVERT: A  243 LEU cc_start: 0.5017 (OUTLIER) cc_final: 0.4622 (pp)
REVERT: A  476 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8499 (tp30)
REVERT: A  526 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8115 (tp30)
REVERT: A  554 GLU cc_start: 0.7448 (tp30) cc_final: 0.7079 (tp30)
REVERT: A  778 GLN cc_start: 0.7517 (tt0) cc_final: 0.6931 (mm-40)
REVERT: A  989 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.6851 (mm-40)
  outliers start: 36
  outliers final: 20
  residues processed: 134
  average time/residue: 0.5859
  time to fit residues: 83.0497
Evaluate side-chains
  118 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
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  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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 112 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3273 r_free = 0.3273 target = 0.105692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.091182 restraints weight = 13680.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 1.18
r_work: 0.2968 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2881
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      312 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      333 |
|-----------------------------------------------------------------------------|
r_final: 0.2878
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9163  Z= 0.139
  Angle     :  0.526   7.908  12419  Z= 0.277
  Chirality :  0.041   0.160   1419
  Planarity :  0.003   0.032   1551
  Dihedral  :  6.870  80.988   1525
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 15.60 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.24), residues: 1123
  helix:  1.71 (0.19), residues: 759
  sheet: -0.16 (0.52), residues: 74
  loop : -1.28 (0.33), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A1050 
 TYR   0.017   0.001   TYR A 337 
 PHE   0.023   0.001   PHE A 776 
 TRP   0.007   0.001   TRP A 314 
 HIS   0.002   0.001   HIS A 428 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 9163)
  covalent geometry    : angle       0.52627 (12419)
  hydrogen bonds       : bond        0.05814 (  583)
  hydrogen bonds       : angle       3.89888 ( 1698)

*********************** 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
  129 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 100
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.7973 (t0) cc_final: 0.7695 (t0)
REVERT: A  243 LEU cc_start: 0.4899 (OUTLIER) cc_final: 0.4493 (pp)
REVERT: A  381 GLU cc_start: 0.8605 (tt0) cc_final: 0.8263 (tp30)
REVERT: A  476 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8515 (tp30)
REVERT: A  486 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7911 (mm)
REVERT: A  526 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8059 (tp30)
REVERT: A  554 GLU cc_start: 0.7466 (tp30) cc_final: 0.7105 (tp30)
REVERT: A  778 GLN cc_start: 0.7480 (tt0) cc_final: 0.6889 (mm-40)
REVERT: A  957 ARG cc_start: 0.8164 (mpp80) cc_final: 0.7851 (mtt90)
REVERT: A  989 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.6751 (mm-40)
  outliers start: 29
  outliers final: 17
  residues processed: 122
  average time/residue: 0.6126
  time to fit residues: 79.1429
Evaluate side-chains
  116 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
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  416 ILE
Chi-restraints excluded: chain A residue  431 SER
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  776 PHE
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 1013 HIS
Chi-restraints excluded: chain A residue 1055 LEU
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 27 optimal weight:    0.2980
   chunk 60 optimal weight:    8.9990
   chunk 29 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 84 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 95 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 = 0.3295 r_free = 0.3295 target = 0.107231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.092954 restraints weight = 13643.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 1.18
r_work: 0.2989 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.2906 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2916
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      333 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2914 r_free = 0.2914    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      367 |
|-----------------------------------------------------------------------------|
r_final: 0.2914
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.1715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9163  Z= 0.123
  Angle     :  0.500   6.836  12419  Z= 0.263
  Chirality :  0.040   0.171   1419
  Planarity :  0.003   0.039   1551
  Dihedral  :  6.522  84.604   1525
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 15.60 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.25), residues: 1123
  helix:  1.93 (0.19), residues: 758
  sheet: -0.01 (0.54), residues: 74
  loop : -1.25 (0.33), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 299 
 TYR   0.018   0.001   TYR A 337 
 PHE   0.022   0.001   PHE A 776 
 TRP   0.007   0.001   TRP A1071 
 HIS   0.002   0.001   HIS A 423 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 9163)
  covalent geometry    : angle       0.50000 (12419)
  hydrogen bonds       : bond        0.05295 (  583)
  hydrogen bonds       : angle       3.76958 ( 1698)

*********************** 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
  134 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 99
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.8031 (t0) cc_final: 0.7745 (t0)
REVERT: A  243 LEU cc_start: 0.4788 (OUTLIER) cc_final: 0.4414 (pp)
REVERT: A  476 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8496 (tp30)
REVERT: A  486 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7935 (mm)
REVERT: A  526 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8051 (tp30)
REVERT: A  957 ARG cc_start: 0.8165 (mpp80) cc_final: 0.7831 (mtt90)
REVERT: A  989 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.6657 (mm-40)
REVERT: A 1013 HIS cc_start: 0.6472 (OUTLIER) cc_final: 0.6271 (p-80)
REVERT: A 1180 THR cc_start: 0.7537 (p) cc_final: 0.7291 (p)
REVERT: A 1186 GLU cc_start: 0.8042 (tp30) cc_final: 0.7646 (mp0)
REVERT: A 1254 GLU cc_start: 0.7787 (tt0) cc_final: 0.7454 (tt0)
  outliers start: 35
  outliers final: 18
  residues processed: 125
  average time/residue: 0.6038
  time to fit residues: 80.0884
Evaluate side-chains
  113 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
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  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 1095 VAL
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 47 optimal weight:    4.9990
   chunk 87 optimal weight:    6.9990
   chunk 67 optimal weight:    2.9990
   chunk 95 optimal weight:    7.9990
   chunk 45 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.3244 r_free = 0.3244 target = 0.103607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.089438 restraints weight = 13872.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 1.16
r_work: 0.2938 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2850
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2850 r_free = 0.2850    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      367 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      363 |
|-----------------------------------------------------------------------------|
r_final: 0.2847
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9163  Z= 0.211
  Angle     :  0.615   8.373  12419  Z= 0.322
  Chirality :  0.044   0.150   1419
  Planarity :  0.004   0.047   1551
  Dihedral  :  7.176  77.367   1525
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 16.99 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.24), residues: 1123
  helix:  1.48 (0.18), residues: 763
  sheet: -0.33 (0.52), residues: 74
  loop : -1.24 (0.34), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1050 
 TYR   0.016   0.002   TYR A 337 
 PHE   0.023   0.002   PHE A 776 
 TRP   0.010   0.002   TRP A 846 
 HIS   0.003   0.001   HIS A 428 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 ( 9163)
  covalent geometry    : angle       0.61511 (12419)
  hydrogen bonds       : bond        0.06852 (  583)
  hydrogen bonds       : angle       3.99959 ( 1698)

*********************** 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
  129 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 96
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.8016 (t0) cc_final: 0.7730 (t0)
REVERT: A  243 LEU cc_start: 0.4721 (OUTLIER) cc_final: 0.4491 (pp)
REVERT: A  476 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8507 (tp30)
REVERT: A  526 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8108 (tp30)
REVERT: A  594 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8420 (tm-30)
REVERT: A  989 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.6916 (mm-40)
REVERT: A 1013 HIS cc_start: 0.6526 (OUTLIER) cc_final: 0.6314 (p-80)
REVERT: A 1186 GLU cc_start: 0.8056 (tp30) cc_final: 0.7642 (mp0)
REVERT: A 1254 GLU cc_start: 0.7886 (tt0) cc_final: 0.7619 (tt0)
  outliers start: 33
  outliers final: 20
  residues processed: 123
  average time/residue: 0.6168
  time to fit residues: 80.2657
Evaluate side-chains
  117 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 82 optimal weight:    9.9990
   chunk 40 optimal weight:    0.9990
   chunk 89 optimal weight:    5.9990
   chunk 64 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 99 optimal weight:    7.9990
   chunk 35 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 103 optimal weight:    3.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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 = 0.3260 r_free = 0.3260 target = 0.104651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.090629 restraints weight = 13910.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 1.16
r_work: 0.2990 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2905 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2896
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      363 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2895 r_free = 0.2895    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      369 |
|-----------------------------------------------------------------------------|
r_final: 0.2895
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.1738

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= 0.152
  Angle     :  0.551   7.720  12419  Z= 0.290
  Chirality :  0.042   0.169   1419
  Planarity :  0.004   0.044   1551
  Dihedral  :  6.937  80.822   1525
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 17.31 %
    Favored  : 79.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.24), residues: 1123
  helix:  1.65 (0.18), residues: 761
  sheet: -0.29 (0.52), residues: 74
  loop : -1.27 (0.33), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 299 
 TYR   0.016   0.001   TYR A 337 
 PHE   0.021   0.001   PHE A 776 
 TRP   0.008   0.001   TRP A 314 
 HIS   0.002   0.001   HIS A 428 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 9163)
  covalent geometry    : angle       0.55126 (12419)
  hydrogen bonds       : bond        0.06057 (  583)
  hydrogen bonds       : angle       3.90628 ( 1698)

*********************** 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
  121 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 92
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.7997 (t0) cc_final: 0.7711 (t0)
REVERT: A  243 LEU cc_start: 0.4749 (OUTLIER) cc_final: 0.4516 (pp)
REVERT: A  476 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8507 (tp30)
REVERT: A  526 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8077 (tp30)
REVERT: A  594 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8406 (tm-30)
REVERT: A  989 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.6803 (mm-40)
REVERT: A 1013 HIS cc_start: 0.6460 (OUTLIER) cc_final: 0.6254 (p-80)
REVERT: A 1180 THR cc_start: 0.7613 (p) cc_final: 0.7356 (p)
REVERT: A 1186 GLU cc_start: 0.8060 (tp30) cc_final: 0.7642 (mp0)
REVERT: A 1254 GLU cc_start: 0.7851 (tt0) cc_final: 0.7536 (tt0)
  outliers start: 29
  outliers final: 21
  residues processed: 117
  average time/residue: 0.5714
  time to fit residues: 70.9921
Evaluate side-chains
  116 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 90
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
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  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 74 optimal weight:    5.9990
   chunk 88 optimal weight:    5.9990
   chunk 28 optimal weight:    0.6980
   chunk 69 optimal weight:    6.9990
   chunk 110 optimal weight:    0.0570
   chunk 98 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 105 optimal weight:    3.9990
   chunk 58 optimal weight:    8.9990
   chunk 107 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   overall best weight:    2.3504

-------------------------------------------------------------------------------
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 = 0.3243 r_free = 0.3243 target = 0.103432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.089434 restraints weight = 13815.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 1.15
r_work: 0.2936 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2852 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2852
-------------------------------------------------------------------------------
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:      369 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2885 r_free = 0.2885    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      381 |
|-----------------------------------------------------------------------------|
r_final: 0.2885
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9163  Z= 0.198
  Angle     :  0.606   8.330  12419  Z= 0.318
  Chirality :  0.044   0.207   1419
  Planarity :  0.004   0.043   1551
  Dihedral  :  7.180  78.378   1525
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 16.77 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.24), residues: 1123
  helix:  1.45 (0.18), residues: 761
  sheet: -0.39 (0.51), residues: 74
  loop : -1.30 (0.33), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 299 
 TYR   0.016   0.002   TYR A 337 
 PHE   0.022   0.002   PHE A 776 
 TRP   0.009   0.001   TRP A 846 
 HIS   0.003   0.001   HIS A 428 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 9163)
  covalent geometry    : angle       0.60644 (12419)
  hydrogen bonds       : bond        0.06702 (  583)
  hydrogen bonds       : angle       4.00368 ( 1698)

*********************** 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
  130 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 93
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.8020 (t0) cc_final: 0.7739 (t0)
REVERT: A  476 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8516 (tp30)
REVERT: A  526 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8061 (tp30)
REVERT: A  594 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8410 (tm-30)
REVERT: A  957 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7723 (mpp80)
REVERT: A  989 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.6915 (mm-40)
REVERT: A 1013 HIS cc_start: 0.6481 (OUTLIER) cc_final: 0.6256 (p-80)
REVERT: A 1186 GLU cc_start: 0.8074 (tp30) cc_final: 0.7639 (mp0)
REVERT: A 1254 GLU cc_start: 0.7884 (tt0) cc_final: 0.7574 (tt0)
  outliers start: 37
  outliers final: 22
  residues processed: 123
  average time/residue: 0.5628
  time to fit residues: 73.5117
Evaluate side-chains
  119 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
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  404 ASP
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain A residue  431 SER
Chi-restraints excluded: chain A residue  435 VAL
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  957 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 6 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 40 optimal weight:    4.9990
   chunk 105 optimal weight:    3.9990
   chunk 88 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 62 optimal weight:    7.9990
   chunk 99 optimal weight:    6.9990
   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 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 = 0.3283 r_free = 0.3283 target = 0.106213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.092463 restraints weight = 13717.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 1.14
r_work: 0.2990 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2914
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2914 r_free = 0.2914    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      381 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2913 r_free = 0.2913    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      384 |
|-----------------------------------------------------------------------------|
r_final: 0.2913
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.1852

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= 0.129
  Angle     :  0.530   7.199  12419  Z= 0.277
  Chirality :  0.041   0.182   1419
  Planarity :  0.003   0.054   1551
  Dihedral  :  6.685  83.846   1525
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 17.74 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.25), residues: 1123
  helix:  1.83 (0.19), residues: 762
  sheet: -0.19 (0.53), residues: 74
  loop : -1.26 (0.34), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 299 
 TYR   0.016   0.001   TYR A 337 
 PHE   0.022   0.001   PHE A 776 
 TRP   0.008   0.001   TRP A 493 
 HIS   0.002   0.001   HIS A1142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 9163)
  covalent geometry    : angle       0.52985 (12419)
  hydrogen bonds       : bond        0.05460 (  583)
  hydrogen bonds       : angle       3.84443 ( 1698)

********************** 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
  123 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 95
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.7999 (t0) cc_final: 0.7728 (t0)
REVERT: A  443 MET cc_start: 0.8770 (mtm) cc_final: 0.8547 (ptt)
REVERT: A  476 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8521 (tp30)
REVERT: A  486 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7937 (mm)
REVERT: A  526 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8095 (tp30)
REVERT: A  957 ARG cc_start: 0.8153 (mpp80) cc_final: 0.7833 (mtt90)
REVERT: A  989 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.6702 (mm-40)
REVERT: A 1013 HIS cc_start: 0.6421 (OUTLIER) cc_final: 0.6206 (p-80)
REVERT: A 1180 THR cc_start: 0.7520 (p) cc_final: 0.7275 (p)
REVERT: A 1186 GLU cc_start: 0.8086 (tp30) cc_final: 0.7662 (mp0)
REVERT: A 1254 GLU cc_start: 0.7817 (tt0) cc_final: 0.7541 (tt0)
  outliers start: 28
  outliers final: 19
  residues processed: 118
  average time/residue: 0.5952
  time to fit residues: 74.5331
Evaluate side-chains
  115 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 91
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
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  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 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 15 optimal weight:    6.9990
   chunk 93 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 78 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 94 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 86 optimal weight:    4.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.104300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.090471 restraints weight = 13630.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 1.14
r_work: 0.2959 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2885
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2885 r_free = 0.2885    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      384 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2883 r_free = 0.2883    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      392 |
|-----------------------------------------------------------------------------|
r_final: 0.2883
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   9163  Z= 0.167
  Angle     :  0.583   9.819  12419  Z= 0.307
  Chirality :  0.042   0.145   1419
  Planarity :  0.004   0.041   1551
  Dihedral  :  6.853  81.467   1525
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 18.16 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.23 (0.25), residues: 1123
  helix:  1.69 (0.18), residues: 764
  sheet: -0.24 (0.53), residues: 74
  loop : -1.28 (0.34), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1050 
 TYR   0.017   0.001   TYR A 337 
 PHE   0.022   0.001   PHE A 776 
 TRP   0.007   0.001   TRP A 314 
 HIS   0.003   0.001   HIS A 428 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 9163)
  covalent geometry    : angle       0.58318 (12419)
  hydrogen bonds       : bond        0.06058 (  583)
  hydrogen bonds       : angle       3.89696 ( 1698)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2911.55 seconds
wall clock time: 50 minutes 15.18 seconds (3015.18 seconds total)