Starting phenix.real_space_refine
on Wed Mar  4 00:56:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8avy_15687/03_2026/8avy_15687.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8avy_15687/03_2026/8avy_15687.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8avy_15687/03_2026/8avy_15687.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8avy_15687/03_2026/8avy_15687.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8avy_15687/03_2026/8avy_15687.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8avy_15687/03_2026/8avy_15687.map"
  }
  resolution = 2.9
  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=   0.044
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      31      5.16       5
     C    6116      2.51       5
     N    1552      2.21       5
     O    1726      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9433
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1175, 9085
          Classifications: {'peptide': 1175}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 29, 'TRANS': 1145}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "A"
      Number of atoms: 348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 348
          Unusual residues: {' MG': 2, 'ATP': 2, 'Y01': 8}
          Classifications: {'undetermined': 12, 'water': 4}
          Link IDs: {None: 15}
  Time building chain proxies: 2.15, per 1000 atoms: 0.23
  Number of scatterers: 9433
  At special positions: 0
  Unit cell: (72.819, 87.048, 148.986, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      31     16.00
     P       6     15.00
     Mg      2     11.99
     O    1726      8.00
     N    1552      7.00
     C    6116      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: 0.86
  Conformation dependent library (CDL) restraints added in 406.3 milliseconds
  

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2156

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 4 sheets defined
      71.1% alpha, 7.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 62
    Processing helix  chain 'A' and resid 62 through 73
    Processing helix  chain 'A' and resid 74 through 85
    Processing helix  chain 'A' and resid 91 through 154
      removed outlier: 3.891A  pdb=" N   ARG A  97 " --> pdb=" O   GLU A  93 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ILE A 123 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   TRP A 132 " --> pdb=" O   GLN A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 162
    Processing helix  chain 'A' and resid 164 through 180
      removed outlier: 3.882A  pdb=" N   THR A 172 " --> pdb=" O   ASN A 168 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   VAL A 175 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 207
      removed outlier: 3.900A  pdb=" N   GLY A 187 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 256
      Proline residue:  A 219  - end of helix
    Processing helix  chain 'A' and resid 256 through 263
    Processing helix  chain 'A' and resid 265 through 319
      removed outlier: 3.545A  pdb=" N   ASN A 276 " --> pdb=" O   ARG A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 334
    Processing helix  chain 'A' and resid 335 through 367
      removed outlier: 4.486A  pdb=" N   PHE A 339 " --> pdb=" O   CYS A 335 " (cutoff:3.500A)
      Proline residue:  A 346  - end of helix
      removed outlier: 3.662A  pdb=" N   TYR A 359 " --> pdb=" O   ARG A 355 " (cutoff:3.500A)
      removed outlier: 5.016A  pdb=" N   GLU A 360 " --> pdb=" O   GLY A 356 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   VAL A 361 " --> pdb=" O   ALA A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 437
    Processing helix  chain 'A' and resid 458 through 465
    Processing helix  chain 'A' and resid 479 through 486
    Processing helix  chain 'A' and resid 492 through 503
    Processing helix  chain 'A' and resid 505 through 511
    Processing helix  chain 'A' and resid 514 through 518
    Processing helix  chain 'A' and resid 521 through 525
    Processing helix  chain 'A' and resid 528 through 543
      removed outlier: 4.028A  pdb=" N   ARG A 543 " --> pdb=" O   ARG A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 558 through 571
      removed outlier: 3.541A  pdb=" N   VAL A 564 " --> pdb=" O   GLU A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 576
      removed outlier: 3.638A  pdb=" N   GLY A 575 " --> pdb=" O   ALA A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 584 through 590
      removed outlier: 4.047A  pdb=" N   VAL A 588 " --> pdb=" O   ARG A 584 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ARG A 589 " --> pdb=" O   LEU A 585 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   ASN A 590 " --> pdb=" O   SER A 586 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 584 through 590'
    Processing helix  chain 'A' and resid 607 through 615
    Processing helix  chain 'A' and resid 616 through 623
    Processing helix  chain 'A' and resid 691 through 698
    Processing helix  chain 'A' and resid 699 through 702
      removed outlier: 4.914A  pdb=" N   THR A 702 " --> pdb=" O   LEU A 699 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 699 through 702'
    Processing helix  chain 'A' and resid 703 through 737
      removed outlier: 3.797A  pdb=" N   GLN A 721 " --> pdb=" O   ASN A 717 " (cutoff:3.500A)
      Proline residue:  A 722  - end of helix
      removed outlier: 4.237A  pdb=" N   SER A 725 " --> pdb=" O   GLN A 721 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL A 726 " --> pdb=" O   PRO A 722 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   VAL A 734 " --> pdb=" O   LYS A 730 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   ASN A 737 " --> pdb=" O   GLY A 733 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 741 through 743
      No H-bonds generated for 'chain 'A' and resid 741 through 743'
    Processing helix  chain 'A' and resid 744 through 795
      removed outlier: 3.675A  pdb=" N   PHE A 773 " --> pdb=" O   GLN A 769 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 796 through 801
      removed outlier: 3.516A  pdb=" N   PHE A 800 " --> pdb=" O   ASP A 796 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 805
    Processing helix  chain 'A' and resid 806 through 823
      removed outlier: 4.163A  pdb=" N   ALA A 818 " --> pdb=" O   LEU A 814 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ALA A 819 " --> pdb=" O   ALA A 815 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 826 through 850
    Processing helix  chain 'A' and resid 852 through 899
      removed outlier: 3.852A  pdb=" N   LEU A 856 " --> pdb=" O   GLN A 852 " (cutoff:3.500A)
      Proline residue:  A 862  - end of helix
      removed outlier: 3.625A  pdb=" N   ALA A 867 " --> pdb=" O   ILE A 863 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   LYS A 881 " --> pdb=" O   GLY A 877 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLU A 887 " --> pdb=" O   LYS A 883 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   GLY A 888 " --> pdb=" O   LYS A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 899 through 906
    Processing helix  chain 'A' and resid 908 through 920
    Processing helix  chain 'A' and resid 920 through 962
      removed outlier: 3.621A  pdb=" N   HIS A 932 " --> pdb=" O   MET A 928 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 966 through 989
      removed outlier: 3.573A  pdb=" N   PHE A 979 " --> pdb=" O   SER A 975 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 990 through 1010
      removed outlier: 3.866A  pdb=" N   LYS A 996 " --> pdb=" O   PRO A 992 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1071 through 1080
      removed outlier: 3.810A  pdb=" N   VAL A1076 " --> pdb=" O   LYS A1072 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1101 through 1107
    Processing helix  chain 'A' and resid 1122 through 1129
    Processing helix  chain 'A' and resid 1137 through 1148
    Processing helix  chain 'A' and resid 1150 through 1156
    Processing helix  chain 'A' and resid 1159 through 1163
    Processing helix  chain 'A' and resid 1166 through 1170
    Processing helix  chain 'A' and resid 1173 through 1187
    Processing helix  chain 'A' and resid 1203 through 1217
    Processing helix  chain 'A' and resid 1229 through 1233
      removed outlier: 3.554A  pdb=" N   THR A1232 " --> pdb=" O   ARG A1229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1252 through 1259
    Processing helix  chain 'A' and resid 1261 through 1267
      removed outlier: 3.565A  pdb=" N   VAL A1267 " --> pdb=" O   TYR A1263 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 413
      removed outlier: 6.859A  pdb=" N   LYS A 407 " --> pdb=" O   HIS A 394 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   HIS A 394 " --> pdb=" O   LYS A 407 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   LEU A 409 " --> pdb=" O   ASN A 392 " (cutoff:3.500A)
      removed outlier: 5.664A  pdb=" N   PHE A 390 " --> pdb=" O   SER A 448 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   SER A 448 " --> pdb=" O   PHE A 390 " (cutoff:3.500A)
      removed outlier: 5.534A  pdb=" N   ASN A 392 " --> pdb=" O   MET A 446 " (cutoff:3.500A)
      removed outlier: 4.853A  pdb=" N   MET A 446 " --> pdb=" O   ASN A 392 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 466 through 469
      removed outlier: 6.691A  pdb=" N   GLY A 467 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
      removed outlier: 7.864A  pdb=" N   ASP A 551 " --> pdb=" O   GLY A 467 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   VAL A 469 " --> pdb=" O   ASP A 551 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   LEU A 548 " --> pdb=" O   ILE A 579 " (cutoff:3.500A)
      removed outlier: 7.749A  pdb=" N   ILE A 581 " --> pdb=" O   LEU A 548 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   LEU A 550 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   VAL A 419 " --> pdb=" O   VAL A 580 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   THR A 418 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 7.510A  pdb=" N   ALA A 595 " --> pdb=" O   THR A 418 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   ALA A 420 " --> pdb=" O   ALA A 595 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   PHE A 597 " --> pdb=" O   ALA A 420 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   VAL A 422 " --> pdb=" O   PHE A 597 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   GLU A 604 " --> pdb=" O   GLY A 596 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1053 through 1056
      removed outlier: 5.626A  pdb=" N   PHE A1033 " --> pdb=" O   PHE A1091 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   PHE A1091 " --> pdb=" O   PHE A1033 " (cutoff:3.500A)
      removed outlier: 4.959A  pdb=" N   GLY A1035 " --> pdb=" O   SER A1089 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   SER A1089 " --> pdb=" O   GLY A1035 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1109 through 1112
      removed outlier: 6.233A  pdb=" N   GLY A1110 " --> pdb=" O   LEU A1194 " (cutoff:3.500A)
      removed outlier: 7.306A  pdb=" N   ASP A1196 " --> pdb=" O   GLY A1110 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   VAL A1112 " --> pdb=" O   ASP A1196 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   LEU A1193 " --> pdb=" O   ILE A1224 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   ILE A1226 " --> pdb=" O   LEU A1193 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   LEU A1195 " --> pdb=" O   ILE A1226 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   THR A1061 " --> pdb=" O   LEU A1238 " (cutoff:3.500A)
      removed outlier: 7.381A  pdb=" N   VAL A1240 " --> pdb=" O   THR A1061 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   ALA A1063 " --> pdb=" O   VAL A1240 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   ILE A1242 " --> pdb=" O   ALA A1063 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   VAL A1065 " --> pdb=" O   ILE A1242 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   GLN A1243 " --> pdb=" O   VAL A1247 " (cutoff:3.500A)
      removed outlier: 5.153A  pdb=" N   VAL A1247 " --> pdb=" O   GLN A1243 " (cutoff:3.500A)

    614 hydrogen bonds defined for protein.
    1791 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: 1.83

  Time building geometry restraints manager: 1.14 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1517
        1.30 -     1.42: 2378
        1.42 -     1.55: 5636
        1.55 -     1.68: 31
        1.68 -     1.81: 61
  Bond restraints: 9623
  Sorted by residual:
  bond pdb=" CA  ALA A  56 "
       pdb=" CB  ALA A  56 "
    ideal  model  delta    sigma   weight residual
    1.528  1.440  0.089 1.56e-02 4.11e+03 3.25e+01
  bond pdb=" C   TRP A 132 "
       pdb=" O   TRP A 132 "
    ideal  model  delta    sigma   weight residual
    1.236  1.167  0.069 1.29e-02 6.01e+03 2.90e+01
  bond pdb=" CA  ALA A 125 "
       pdb=" CB  ALA A 125 "
    ideal  model  delta    sigma   weight residual
    1.528  1.449  0.079 1.59e-02 3.96e+03 2.47e+01
  bond pdb=" CA  SER A 130 "
       pdb=" CB  SER A 130 "
    ideal  model  delta    sigma   weight residual
    1.529  1.454  0.075 1.55e-02 4.16e+03 2.33e+01
  bond pdb=" C   PHE A 131 "
       pdb=" O   PHE A 131 "
    ideal  model  delta    sigma   weight residual
    1.237  1.180  0.057 1.19e-02 7.06e+03 2.27e+01
  ... (remaining 9618 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.14: 12738
        2.14 -     4.29: 267
        4.29 -     6.43: 56
        6.43 -     8.58: 4
        8.58 -    10.72: 7
  Bond angle restraints: 13072
  Sorted by residual:
  angle pdb=" N   THR A  37 "
        pdb=" CA  THR A  37 "
        pdb=" C   THR A  37 "
      ideal   model   delta    sigma   weight residual
     111.40  100.68   10.72 1.22e+00 6.72e-01 7.73e+01
  angle pdb=" C   PHE A 131 "
        pdb=" CA  PHE A 131 "
        pdb=" CB  PHE A 131 "
      ideal   model   delta    sigma   weight residual
     110.85  121.06  -10.21 1.70e+00 3.46e-01 3.61e+01
  angle pdb=" C   THR A  54 "
        pdb=" CA  THR A  54 "
        pdb=" CB  THR A  54 "
      ideal   model   delta    sigma   weight residual
     110.85  120.04   -9.19 1.70e+00 3.46e-01 2.92e+01
  angle pdb=" C   PHE A 197 "
        pdb=" CA  PHE A 197 "
        pdb=" CB  PHE A 197 "
      ideal   model   delta    sigma   weight residual
     110.85  119.70   -8.85 1.70e+00 3.46e-01 2.71e+01
  angle pdb=" C   THR A  37 "
        pdb=" CA  THR A  37 "
        pdb=" CB  THR A  37 "
      ideal   model   delta    sigma   weight residual
     110.79  119.50   -8.71 1.68e+00 3.54e-01 2.69e+01
  ... (remaining 13067 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.46: 5843
       24.46 -    48.91: 234
       48.91 -    73.37: 40
       73.37 -    97.82: 20
       97.82 -   122.28: 5
  Dihedral angle restraints: 6142
    sinusoidal: 2777
      harmonic: 3365
  Sorted by residual:
  dihedral pdb=" C   THR A  54 "
           pdb=" N   THR A  54 "
           pdb=" CA  THR A  54 "
           pdb=" CB  THR A  54 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -135.00   13.00     0      2.50e+00 1.60e-01 2.70e+01
  dihedral pdb=" C   PHE A 190 "
           pdb=" N   PHE A 190 "
           pdb=" CA  PHE A 190 "
           pdb=" CB  PHE A 190 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.15   11.55     0      2.50e+00 1.60e-01 2.13e+01
  dihedral pdb=" C   PHE A 197 "
           pdb=" N   PHE A 197 "
           pdb=" CA  PHE A 197 "
           pdb=" CB  PHE A 197 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.22   10.62     0      2.50e+00 1.60e-01 1.80e+01
  ... (remaining 6139 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1394
       0.082 -    0.163: 102
       0.163 -    0.245: 8
       0.245 -    0.327: 4
       0.327 -    0.409: 5
  Chirality restraints: 1513
  Sorted by residual:
  chirality pdb=" CA  THR A  54 "
            pdb=" N   THR A  54 "
            pdb=" C   THR A  54 "
            pdb=" CB  THR A  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.12    0.41 2.00e-01 2.50e+01 4.18e+00
  chirality pdb=" CB  VAL A 124 "
            pdb=" CA  VAL A 124 "
            pdb=" CG1 VAL A 124 "
            pdb=" CG2 VAL A 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.23   -0.40 2.00e-01 2.50e+01 4.05e+00
  chirality pdb=" CBB Y01 A2009 "
            pdb=" CAC Y01 A2009 "
            pdb=" CAO Y01 A2009 "
            pdb=" CBE Y01 A2009 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.58    2.20    0.38 2.00e-01 2.50e+01 3.53e+00
  ... (remaining 1510 not shown)

  Planarity restraints: 1610
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A  34 "   -0.028 2.00e-02 2.50e+03   5.48e-02 3.00e+01
        pdb=" C   SER A  34 "    0.095 2.00e-02 2.50e+03
        pdb=" O   SER A  34 "   -0.035 2.00e-02 2.50e+03
        pdb=" N   VAL A  35 "   -0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' ATP A2001 "    0.046 2.00e-02 2.50e+03   2.08e-02 1.19e+01
        pdb=" C2  ATP A2001 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4  ATP A2001 "   -0.016 2.00e-02 2.50e+03
        pdb=" C5  ATP A2001 "   -0.011 2.00e-02 2.50e+03
        pdb=" C6  ATP A2001 "   -0.003 2.00e-02 2.50e+03
        pdb=" C8  ATP A2001 "    0.008 2.00e-02 2.50e+03
        pdb=" N1  ATP A2001 "    0.014 2.00e-02 2.50e+03
        pdb=" N3  ATP A2001 "   -0.010 2.00e-02 2.50e+03
        pdb=" N6  ATP A2001 "    0.025 2.00e-02 2.50e+03
        pdb=" N7  ATP A2001 "   -0.015 2.00e-02 2.50e+03
        pdb=" N9  ATP A2001 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A  37 "   -0.016 2.00e-02 2.50e+03   3.34e-02 1.11e+01
        pdb=" C   THR A  37 "    0.058 2.00e-02 2.50e+03
        pdb=" O   THR A  37 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   MET A  38 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1607 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 69
        2.59 -     3.17: 8034
        3.17 -     3.74: 15125
        3.74 -     4.32: 21496
        4.32 -     4.90: 34891
  Nonbonded interactions: 79615
  Sorted by model distance:
  nonbonded pdb=" O3G ATP A2003 "
            pdb="MG    MG A2004 "
     model   vdw
     2.008 2.170
  nonbonded pdb="MG    MG A2004 "
            pdb=" O   HOH A2101 "
     model   vdw
     2.009 2.170
  nonbonded pdb="MG    MG A2002 "
            pdb=" O   HOH A2102 "
     model   vdw
     2.059 2.170
  nonbonded pdb=" OG  SER A 430 "
            pdb="MG    MG A2002 "
     model   vdw
     2.072 2.170
  nonbonded pdb="MG    MG A2002 "
            pdb=" O   HOH A2103 "
     model   vdw
     2.077 2.170
  ... (remaining 79610 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.540
  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:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     10.140
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
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      :  0.005   0.089   9623  Z= 0.350
  Angle     :  0.777  10.724  13072  Z= 0.496
  Chirality :  0.052   0.409   1513
  Planarity :  0.004   0.055   1610
  Dihedral  : 14.562 122.279   3986
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  6.93 %
    Favored  : 92.33 %
  Cbeta Deviations :  0.37 %
  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 are not related in a simple way.
  whole:  1.35 (0.24), residues: 1171
  helix:  1.46 (0.19), residues: 790
  sheet:  0.76 (0.64), residues: 60
  loop : -0.38 (0.33), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 400 
 TYR   0.018   0.002   TYR A  49 
 PHE   0.027   0.002   PHE A 131 
 TRP   0.020   0.002   TRP A 228 
 HIS   0.007   0.001   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 ( 9623)
  covalent geometry    : angle       0.77736 (13072)
  hydrogen bonds       : bond        0.13999 (  614)
  hydrogen bonds       : angle       4.94265 ( 1791)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 161
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  424 ASN cc_start: 0.7805 (m110) cc_final: 0.7501 (m-40)
REVERT: A  848 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7994 (mp)
REVERT: A 1243 GLN cc_start: 0.7920 (tt0) cc_final: 0.7697 (tp40)
  outliers start: 7
  outliers final: 4
  residues processed: 167
  average time/residue: 0.5766
  time to fit residues: 103.0396
Evaluate side-chains
  118 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 113
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue 1112 VAL
Chi-restraints excluded: chain A residue 1267 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:   50.0000
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.2980
   chunk 100 optimal weight:    1.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 154 GLN
A 717 ASN
A1099 GLN
A1244 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.178212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.125606 restraints weight = 9590.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 1.74
r_work: 0.3029 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.1332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9623  Z= 0.175
  Angle     :  0.610  10.874  13072  Z= 0.301
  Chirality :  0.043   0.203   1513
  Planarity :  0.004   0.036   1610
  Dihedral  : 11.734  86.685   1904
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 12.39 %
    Favored  : 84.35 %
  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 are not related in a simple way.
  whole:  1.38 (0.24), residues: 1171
  helix:  1.47 (0.18), residues: 798
  sheet:  0.80 (0.63), residues: 60
  loop : -0.41 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1221 
 TYR   0.031   0.002   TYR A 306 
 PHE   0.024   0.002   PHE A 508 
 TRP   0.018   0.002   TRP A 228 
 HIS   0.004   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 9623)
  covalent geometry    : angle       0.61032 (13072)
  hydrogen bonds       : bond        0.05220 (  614)
  hydrogen bonds       : angle       4.07311 ( 1791)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 126
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ARG cc_start: 0.7674 (mtm-85) cc_final: 0.7390 (mtt90)
REVERT: A  168 ASN cc_start: 0.6966 (t0) cc_final: 0.6049 (m110)
REVERT: A  293 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7781 (tt)
REVERT: A  424 ASN cc_start: 0.8209 (m110) cc_final: 0.7631 (m-40)
REVERT: A  497 GLU cc_start: 0.6481 (mt-10) cc_final: 0.5924 (tt0)
REVERT: A  802 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7519 (t70)
REVERT: A  915 MET cc_start: 0.8708 (mtm) cc_final: 0.8383 (mtp)
REVERT: A 1102 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.7954 (p)
REVERT: A 1159 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6756 (t0)
REVERT: A 1223 VAL cc_start: 0.8083 (OUTLIER) cc_final: 0.7837 (t)
REVERT: A 1237 ASP cc_start: 0.7962 (m-30) cc_final: 0.7669 (m-30)
REVERT: A 1243 GLN cc_start: 0.7089 (tt0) cc_final: 0.6324 (tp40)
  outliers start: 31
  outliers final: 15
  residues processed: 142
  average time/residue: 0.5327
  time to fit residues: 81.3525
Evaluate side-chains
  133 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  377 SER
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  696 ILE
Chi-restraints excluded: chain A residue  802 ASP
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  939 SER
Chi-restraints excluded: chain A residue  948 SER
Chi-restraints excluded: chain A residue  977 ILE
Chi-restraints excluded: chain A residue 1102 VAL
Chi-restraints excluded: chain A residue 1112 VAL
Chi-restraints excluded: chain A residue 1159 ASP
Chi-restraints excluded: chain A residue 1223 VAL
Chi-restraints excluded: chain A residue 1232 THR
Chi-restraints excluded: chain A residue 1242 ILE
Chi-restraints excluded: chain A residue 1267 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 75 optimal weight:    9.9990
   chunk 85 optimal weight:    0.8980
   chunk 94 optimal weight:    3.9990
   chunk 93 optimal weight:    0.7980
   chunk 114 optimal weight:    0.4980
   chunk 0 optimal weight:    3.9990
   chunk 52 optimal weight:    7.9990
   chunk 98 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 437 GLN
A1244 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.180493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.127972 restraints weight = 9558.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 1.76
r_work: 0.3106 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.1599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9623  Z= 0.119
  Angle     :  0.515   9.036  13072  Z= 0.259
  Chirality :  0.040   0.208   1513
  Planarity :  0.003   0.036   1610
  Dihedral  : 10.547  89.855   1902
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 13.03 %
    Favored  : 84.24 %
  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 are not related in a simple way.
  whole:  1.69 (0.24), residues: 1171
  helix:  1.74 (0.18), residues: 798
  sheet:  0.83 (0.65), residues: 58
  loop : -0.38 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 144 
 TYR   0.030   0.001   TYR A 306 
 PHE   0.015   0.001   PHE A 508 
 TRP   0.018   0.001   TRP A 228 
 HIS   0.003   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 9623)
  covalent geometry    : angle       0.51517 (13072)
  hydrogen bonds       : bond        0.04534 (  614)
  hydrogen bonds       : angle       3.86615 ( 1791)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7516 (mtt90)
REVERT: A  168 ASN cc_start: 0.6944 (t0) cc_final: 0.6176 (m-40)
REVERT: A  293 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7908 (tt)
REVERT: A  377 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8636 (p)
REVERT: A  424 ASN cc_start: 0.8260 (m110) cc_final: 0.7677 (m-40)
REVERT: A  455 ARG cc_start: 0.7551 (mtt180) cc_final: 0.7237 (mtp180)
REVERT: A  497 GLU cc_start: 0.6588 (mt-10) cc_final: 0.6032 (tt0)
REVERT: A  508 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.7437 (p90)
REVERT: A  802 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7497 (t70)
REVERT: A  848 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7648 (mp)
REVERT: A  915 MET cc_start: 0.8768 (mtm) cc_final: 0.8463 (mtp)
REVERT: A 1026 MET cc_start: 0.8276 (ttm) cc_final: 0.7976 (ptp)
REVERT: A 1055 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7109 (pp20)
REVERT: A 1102 VAL cc_start: 0.8365 (t) cc_final: 0.8069 (p)
REVERT: A 1237 ASP cc_start: 0.7975 (m-30) cc_final: 0.7759 (m-30)
REVERT: A 1243 GLN cc_start: 0.7167 (tt0) cc_final: 0.6402 (tp40)
  outliers start: 26
  outliers final: 14
  residues processed: 132
  average time/residue: 0.5472
  time to fit residues: 77.8060
Evaluate side-chains
  128 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  306 TYR
Chi-restraints excluded: chain A residue  377 SER
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  696 ILE
Chi-restraints excluded: chain A residue  802 ASP
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  925 ARG
Chi-restraints excluded: chain A residue  939 SER
Chi-restraints excluded: chain A residue  953 PHE
Chi-restraints excluded: chain A residue  977 ILE
Chi-restraints excluded: chain A residue 1112 VAL
Chi-restraints excluded: chain A residue 1232 THR
Chi-restraints excluded: chain A residue 1267 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 58 optimal weight:    8.9990
   chunk 100 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 80 optimal weight:    0.7980
   chunk 57 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 116 optimal weight:   10.0000
   chunk 73 optimal weight:    3.9990
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
A  60 HIS
A 145 GLN
A 347 ASN
A1244 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.174611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.121108 restraints weight = 9748.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 1.77
r_work: 0.2976 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2817 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   9623  Z= 0.244
  Angle     :  0.614   8.591  13072  Z= 0.311
  Chirality :  0.044   0.204   1513
  Planarity :  0.004   0.042   1610
  Dihedral  : 10.358  83.443   1902
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 12.82 %
    Favored  : 83.40 %
  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 are not related in a simple way.
  whole:  1.23 (0.24), residues: 1171
  helix:  1.37 (0.18), residues: 797
  sheet:  0.76 (0.67), residues: 58
  loop : -0.49 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 908 
 TYR   0.036   0.002   TYR A 306 
 PHE   0.028   0.002   PHE A 508 
 TRP   0.017   0.002   TRP A 228 
 HIS   0.005   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00591 ( 9623)
  covalent geometry    : angle       0.61376 (13072)
  hydrogen bonds       : bond        0.05525 (  614)
  hydrogen bonds       : angle       4.04764 ( 1791)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 117
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ARG cc_start: 0.7792 (mtm-85) cc_final: 0.7494 (mtt90)
REVERT: A  168 ASN cc_start: 0.7167 (t0) cc_final: 0.6221 (m110)
REVERT: A  293 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8006 (tt)
REVERT: A  404 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8211 (mt0)
REVERT: A  424 ASN cc_start: 0.8127 (m110) cc_final: 0.7490 (m-40)
REVERT: A  455 ARG cc_start: 0.7676 (mtt180) cc_final: 0.7327 (mtp180)
REVERT: A  497 GLU cc_start: 0.6640 (mt-10) cc_final: 0.6112 (tt0)
REVERT: A  612 MET cc_start: 0.4464 (mmt) cc_final: 0.2893 (mpt)
REVERT: A  802 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7509 (t70)
REVERT: A  848 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7644 (mp)
REVERT: A  915 MET cc_start: 0.8815 (mtm) cc_final: 0.8470 (mtp)
REVERT: A  925 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.7266 (mtm-85)
REVERT: A 1026 MET cc_start: 0.8342 (ttm) cc_final: 0.8010 (ptp)
REVERT: A 1102 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8132 (p)
REVERT: A 1159 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.6986 (t0)
REVERT: A 1208 LYS cc_start: 0.6832 (ttpt) cc_final: 0.6485 (mtpp)
REVERT: A 1237 ASP cc_start: 0.7993 (m-30) cc_final: 0.7633 (m-30)
REVERT: A 1243 GLN cc_start: 0.7185 (tt0) cc_final: 0.6438 (tp40)
  outliers start: 36
  outliers final: 16
  residues processed: 141
  average time/residue: 0.5705
  time to fit residues: 86.1080
Evaluate side-chains
  134 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  340 SER
Chi-restraints excluded: chain A residue  377 SER
Chi-restraints excluded: chain A residue  404 GLN
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  508 PHE
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  696 ILE
Chi-restraints excluded: chain A residue  802 ASP
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  925 ARG
Chi-restraints excluded: chain A residue  948 SER
Chi-restraints excluded: chain A residue  953 PHE
Chi-restraints excluded: chain A residue  977 ILE
Chi-restraints excluded: chain A residue 1102 VAL
Chi-restraints excluded: chain A residue 1112 VAL
Chi-restraints excluded: chain A residue 1159 ASP
Chi-restraints excluded: chain A residue 1232 THR
Chi-restraints excluded: chain A residue 1267 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 6 optimal weight:   10.0000
   chunk 112 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 82 optimal weight:    0.7980
   chunk 106 optimal weight:    0.7980
   chunk 42 optimal weight:    0.6980
   chunk 114 optimal weight:    0.6980
   chunk 70 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A1244 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.178602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.125591 restraints weight = 9745.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 1.78
r_work: 0.3059 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2900 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9623  Z= 0.121
  Angle     :  0.508   7.987  13072  Z= 0.259
  Chirality :  0.040   0.200   1513
  Planarity :  0.003   0.037   1610
  Dihedral  :  9.987  87.830   1902
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 13.76 %
    Favored  : 82.88 %
  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 are not related in a simple way.
  whole:  1.52 (0.24), residues: 1171
  helix:  1.64 (0.18), residues: 799
  sheet:  0.75 (0.65), residues: 60
  loop : -0.50 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 144 
 TYR   0.031   0.001   TYR A 306 
 PHE   0.015   0.001   PHE A 508 
 TRP   0.017   0.001   TRP A 228 
 HIS   0.003   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9623)
  covalent geometry    : angle       0.50755 (13072)
  hydrogen bonds       : bond        0.04478 (  614)
  hydrogen bonds       : angle       3.82799 ( 1791)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 116
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ARG cc_start: 0.7676 (mtm-85) cc_final: 0.7394 (mtt90)
REVERT: A  168 ASN cc_start: 0.6979 (t0) cc_final: 0.6171 (m-40)
REVERT: A  293 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7846 (tt)
REVERT: A  377 SER cc_start: 0.8814 (OUTLIER) cc_final: 0.8585 (p)
REVERT: A  404 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8144 (mt0)
REVERT: A  414 LYS cc_start: 0.7080 (mtpt) cc_final: 0.6465 (mmpt)
REVERT: A  424 ASN cc_start: 0.8119 (m110) cc_final: 0.7490 (m-40)
REVERT: A  455 ARG cc_start: 0.7469 (mtt180) cc_final: 0.7147 (mtp180)
REVERT: A  497 GLU cc_start: 0.6475 (mt-10) cc_final: 0.5948 (tt0)
REVERT: A  802 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7411 (t70)
REVERT: A  848 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7579 (mp)
REVERT: A  925 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.7167 (mtm-85)
REVERT: A 1026 MET cc_start: 0.8297 (ttm) cc_final: 0.8008 (ptp)
REVERT: A 1055 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7163 (pp20)
REVERT: A 1102 VAL cc_start: 0.8297 (OUTLIER) cc_final: 0.8051 (p)
REVERT: A 1208 LYS cc_start: 0.6717 (ttpt) cc_final: 0.6342 (mtpp)
REVERT: A 1237 ASP cc_start: 0.7955 (m-30) cc_final: 0.7645 (m-30)
REVERT: A 1243 GLN cc_start: 0.7077 (tt0) cc_final: 0.6336 (tp40)
  outliers start: 32
  outliers final: 14
  residues processed: 137
  average time/residue: 0.5258
  time to fit residues: 77.4233
Evaluate side-chains
  134 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  377 SER
Chi-restraints excluded: chain A residue  404 GLN
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  696 ILE
Chi-restraints excluded: chain A residue  802 ASP
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  925 ARG
Chi-restraints excluded: chain A residue  939 SER
Chi-restraints excluded: chain A residue  953 PHE
Chi-restraints excluded: chain A residue  977 ILE
Chi-restraints excluded: chain A residue 1102 VAL
Chi-restraints excluded: chain A residue 1112 VAL
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1232 THR
Chi-restraints excluded: chain A residue 1242 ILE
Chi-restraints excluded: chain A residue 1267 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 108 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 96 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 102 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 103 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A1030 ASN
A1244 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.178387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.125291 restraints weight = 9653.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 1.77
r_work: 0.3020 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2860 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9623  Z= 0.130
  Angle     :  0.504   8.842  13072  Z= 0.256
  Chirality :  0.040   0.197   1513
  Planarity :  0.003   0.034   1610
  Dihedral  :  9.720  89.951   1900
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 13.45 %
    Favored  : 83.19 %
  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 are not related in a simple way.
  whole:  1.65 (0.24), residues: 1171
  helix:  1.74 (0.18), residues: 798
  sheet:  0.72 (0.66), residues: 60
  loop : -0.46 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 144 
 TYR   0.029   0.001   TYR A 306 
 PHE   0.018   0.001   PHE A 508 
 TRP   0.017   0.001   TRP A 228 
 HIS   0.003   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9623)
  covalent geometry    : angle       0.50431 (13072)
  hydrogen bonds       : bond        0.04432 (  614)
  hydrogen bonds       : angle       3.77274 ( 1791)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 115
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ARG cc_start: 0.7713 (mtm-85) cc_final: 0.7428 (mtt90)
REVERT: A  168 ASN cc_start: 0.6991 (t0) cc_final: 0.6163 (m-40)
REVERT: A  180 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7712 (mt-10)
REVERT: A  293 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7869 (tt)
REVERT: A  377 SER cc_start: 0.8813 (OUTLIER) cc_final: 0.8595 (p)
REVERT: A  404 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8128 (mt0)
REVERT: A  414 LYS cc_start: 0.7059 (mtpt) cc_final: 0.6452 (mmpt)
REVERT: A  424 ASN cc_start: 0.8116 (m110) cc_final: 0.7503 (m-40)
REVERT: A  455 ARG cc_start: 0.7476 (mtt180) cc_final: 0.7154 (mtp180)
REVERT: A  497 GLU cc_start: 0.6529 (mt-10) cc_final: 0.6007 (tt0)
REVERT: A  802 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7416 (t70)
REVERT: A  848 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7558 (mp)
REVERT: A  925 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7220 (mtm-85)
REVERT: A 1026 MET cc_start: 0.8293 (ttm) cc_final: 0.8010 (ptp)
REVERT: A 1055 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7157 (pp20)
REVERT: A 1102 VAL cc_start: 0.8327 (OUTLIER) cc_final: 0.8073 (p)
REVERT: A 1208 LYS cc_start: 0.6657 (ttpt) cc_final: 0.6277 (mtpp)
REVERT: A 1237 ASP cc_start: 0.7939 (m-30) cc_final: 0.7632 (m-30)
REVERT: A 1243 GLN cc_start: 0.7062 (tt0) cc_final: 0.6353 (tp40)
  outliers start: 32
  outliers final: 14
  residues processed: 136
  average time/residue: 0.5322
  time to fit residues: 77.8298
Evaluate side-chains
  132 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  306 TYR
Chi-restraints excluded: chain A residue  340 SER
Chi-restraints excluded: chain A residue  377 SER
Chi-restraints excluded: chain A residue  404 GLN
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  696 ILE
Chi-restraints excluded: chain A residue  802 ASP
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  925 ARG
Chi-restraints excluded: chain A residue  953 PHE
Chi-restraints excluded: chain A residue  977 ILE
Chi-restraints excluded: chain A residue 1102 VAL
Chi-restraints excluded: chain A residue 1112 VAL
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1232 THR
Chi-restraints excluded: chain A residue 1267 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 99 optimal weight:    0.5980
   chunk 75 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
A1244 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.174639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.120090 restraints weight = 9750.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 1.81
r_work: 0.3040 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2885 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9623  Z= 0.127
  Angle     :  0.503   9.450  13072  Z= 0.255
  Chirality :  0.040   0.195   1513
  Planarity :  0.003   0.037   1610
  Dihedral  :  9.621  88.485   1900
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 15.02 %
    Favored  : 82.25 %
  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 are not related in a simple way.
  whole:  1.72 (0.24), residues: 1171
  helix:  1.81 (0.18), residues: 798
  sheet:  0.60 (0.66), residues: 60
  loop : -0.44 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 144 
 TYR   0.030   0.001   TYR A 306 
 PHE   0.018   0.001   PHE A 508 
 TRP   0.016   0.001   TRP A 228 
 HIS   0.003   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 9623)
  covalent geometry    : angle       0.50276 (13072)
  hydrogen bonds       : bond        0.04370 (  614)
  hydrogen bonds       : angle       3.74584 ( 1791)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 113
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.7406 (mtt90)
REVERT: A  168 ASN cc_start: 0.6886 (t0) cc_final: 0.6071 (m-40)
REVERT: A  180 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7675 (mt-10)
REVERT: A  293 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7863 (tt)
REVERT: A  377 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8626 (p)
REVERT: A  404 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8121 (mt0)
REVERT: A  414 LYS cc_start: 0.7089 (mtpt) cc_final: 0.6504 (mmpt)
REVERT: A  424 ASN cc_start: 0.8124 (m110) cc_final: 0.7473 (m-40)
REVERT: A  455 ARG cc_start: 0.7401 (mtt180) cc_final: 0.7052 (mtp180)
REVERT: A  497 GLU cc_start: 0.6519 (mt-10) cc_final: 0.5999 (tt0)
REVERT: A  802 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7400 (t70)
REVERT: A  848 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7557 (mp)
REVERT: A  915 MET cc_start: 0.8658 (mtm) cc_final: 0.8391 (mtp)
REVERT: A  925 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7251 (mtm-85)
REVERT: A 1026 MET cc_start: 0.8347 (ttm) cc_final: 0.8026 (ptp)
REVERT: A 1055 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7150 (pp20)
REVERT: A 1102 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.8084 (p)
REVERT: A 1115 GLU cc_start: 0.7134 (mp0) cc_final: 0.6756 (mt-10)
REVERT: A 1208 LYS cc_start: 0.6623 (ttpt) cc_final: 0.6244 (mtpp)
REVERT: A 1237 ASP cc_start: 0.7952 (m-30) cc_final: 0.7646 (m-30)
REVERT: A 1243 GLN cc_start: 0.7028 (tt0) cc_final: 0.6340 (tp40)
  outliers start: 26
  outliers final: 16
  residues processed: 131
  average time/residue: 0.5192
  time to fit residues: 73.1349
Evaluate side-chains
  133 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  306 TYR
Chi-restraints excluded: chain A residue  377 SER
Chi-restraints excluded: chain A residue  404 GLN
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  696 ILE
Chi-restraints excluded: chain A residue  760 ILE
Chi-restraints excluded: chain A residue  802 ASP
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  884 LYS
Chi-restraints excluded: chain A residue  925 ARG
Chi-restraints excluded: chain A residue  939 SER
Chi-restraints excluded: chain A residue  953 PHE
Chi-restraints excluded: chain A residue  977 ILE
Chi-restraints excluded: chain A residue 1102 VAL
Chi-restraints excluded: chain A residue 1112 VAL
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1232 THR
Chi-restraints excluded: chain A residue 1242 ILE
Chi-restraints excluded: chain A residue 1267 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 104 optimal weight:    0.5980
   chunk 52 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 57 optimal weight:    8.9990
   chunk 11 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A1099 GLN
A1244 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.174122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.119369 restraints weight = 9734.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 1.81
r_work: 0.3032 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9623  Z= 0.140
  Angle     :  0.512   9.839  13072  Z= 0.260
  Chirality :  0.040   0.195   1513
  Planarity :  0.003   0.037   1610
  Dihedral  :  9.589  88.471   1899
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 14.50 %
    Favored  : 82.04 %
  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 are not related in a simple way.
  whole:  1.71 (0.24), residues: 1171
  helix:  1.80 (0.18), residues: 798
  sheet:  0.58 (0.66), residues: 60
  loop : -0.45 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 908 
 TYR   0.031   0.001   TYR A 306 
 PHE   0.021   0.001   PHE A 508 
 TRP   0.016   0.001   TRP A 228 
 HIS   0.003   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9623)
  covalent geometry    : angle       0.51215 (13072)
  hydrogen bonds       : bond        0.04458 (  614)
  hydrogen bonds       : angle       3.75982 ( 1791)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 112
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7414 (mtt90)
REVERT: A  168 ASN cc_start: 0.6896 (t0) cc_final: 0.6070 (m-40)
REVERT: A  180 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7700 (mt-10)
REVERT: A  293 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7869 (tt)
REVERT: A  377 SER cc_start: 0.8844 (OUTLIER) cc_final: 0.8625 (p)
REVERT: A  404 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8127 (mt0)
REVERT: A  414 LYS cc_start: 0.7049 (mtpt) cc_final: 0.6470 (mmpt)
REVERT: A  424 ASN cc_start: 0.8123 (m110) cc_final: 0.7475 (m-40)
REVERT: A  455 ARG cc_start: 0.7399 (mtt180) cc_final: 0.7053 (mtp180)
REVERT: A  497 GLU cc_start: 0.6538 (mt-10) cc_final: 0.6018 (tt0)
REVERT: A  802 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7412 (t70)
REVERT: A  848 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7564 (mp)
REVERT: A  915 MET cc_start: 0.8663 (mtm) cc_final: 0.8395 (mtp)
REVERT: A  925 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7266 (mtm-85)
REVERT: A 1026 MET cc_start: 0.8340 (ttm) cc_final: 0.8020 (ptp)
REVERT: A 1055 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7110 (pp20)
REVERT: A 1102 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8089 (p)
REVERT: A 1208 LYS cc_start: 0.6638 (ttpt) cc_final: 0.6260 (mtpp)
REVERT: A 1237 ASP cc_start: 0.7921 (m-30) cc_final: 0.7606 (m-30)
REVERT: A 1243 GLN cc_start: 0.7031 (tt0) cc_final: 0.6341 (tp40)
  outliers start: 33
  outliers final: 19
  residues processed: 136
  average time/residue: 0.5520
  time to fit residues: 80.5178
Evaluate side-chains
  137 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 110
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  306 TYR
Chi-restraints excluded: chain A residue  340 SER
Chi-restraints excluded: chain A residue  377 SER
Chi-restraints excluded: chain A residue  404 GLN
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  696 ILE
Chi-restraints excluded: chain A residue  755 PHE
Chi-restraints excluded: chain A residue  802 ASP
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  882 ASP
Chi-restraints excluded: chain A residue  925 ARG
Chi-restraints excluded: chain A residue  939 SER
Chi-restraints excluded: chain A residue  953 PHE
Chi-restraints excluded: chain A residue  977 ILE
Chi-restraints excluded: chain A residue 1102 VAL
Chi-restraints excluded: chain A residue 1112 VAL
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1232 THR
Chi-restraints excluded: chain A residue 1242 ILE
Chi-restraints excluded: chain A residue 1267 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 103 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 14 optimal weight:    0.4980
   chunk 90 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9990
   chunk 80 optimal weight:    0.6980
   chunk 76 optimal weight:    0.0000
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.5784

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

Flipped N/Q/H residues before XYZ refinement:
A 608 HIS
A1244 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.176997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.123043 restraints weight = 9695.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 1.81
r_work: 0.3074 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9623  Z= 0.111
  Angle     :  0.487  10.078  13072  Z= 0.247
  Chirality :  0.039   0.193   1513
  Planarity :  0.003   0.038   1610
  Dihedral  :  9.281  84.061   1899
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 15.65 %
    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 are not related in a simple way.
  whole:  1.88 (0.24), residues: 1171
  helix:  1.95 (0.18), residues: 798
  sheet:  0.51 (0.65), residues: 60
  loop : -0.40 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 144 
 TYR   0.027   0.001   TYR A 306 
 PHE   0.024   0.001   PHE A 934 
 TRP   0.017   0.001   TRP A 228 
 HIS   0.003   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 9623)
  covalent geometry    : angle       0.48750 (13072)
  hydrogen bonds       : bond        0.04104 (  614)
  hydrogen bonds       : angle       3.66922 ( 1791)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 113
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ARG cc_start: 0.7783 (mtm-85) cc_final: 0.7561 (mtt90)
REVERT: A  168 ASN cc_start: 0.6907 (t0) cc_final: 0.6140 (m-40)
REVERT: A  180 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7644 (mt-10)
REVERT: A  293 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7848 (tt)
REVERT: A  377 SER cc_start: 0.8813 (OUTLIER) cc_final: 0.8604 (p)
REVERT: A  404 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8110 (mt0)
REVERT: A  414 LYS cc_start: 0.7040 (mtpt) cc_final: 0.6477 (mmpt)
REVERT: A  424 ASN cc_start: 0.8104 (m110) cc_final: 0.7461 (m-40)
REVERT: A  455 ARG cc_start: 0.7407 (mtt180) cc_final: 0.7059 (mtp180)
REVERT: A  562 GLU cc_start: 0.6882 (tm-30) cc_final: 0.6479 (tt0)
REVERT: A  802 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7460 (t70)
REVERT: A  848 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7549 (mp)
REVERT: A 1026 MET cc_start: 0.8340 (ttm) cc_final: 0.8044 (ptp)
REVERT: A 1055 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7107 (pp20)
REVERT: A 1102 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8095 (p)
REVERT: A 1208 LYS cc_start: 0.6626 (ttpt) cc_final: 0.5975 (mtpp)
REVERT: A 1237 ASP cc_start: 0.7925 (m-30) cc_final: 0.7646 (m-30)
REVERT: A 1243 GLN cc_start: 0.7092 (tt0) cc_final: 0.6395 (tp40)
  outliers start: 26
  outliers final: 16
  residues processed: 132
  average time/residue: 0.5849
  time to fit residues: 82.5960
Evaluate side-chains
  128 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  306 TYR
Chi-restraints excluded: chain A residue  340 SER
Chi-restraints excluded: chain A residue  377 SER
Chi-restraints excluded: chain A residue  404 GLN
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  696 ILE
Chi-restraints excluded: chain A residue  802 ASP
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  939 SER
Chi-restraints excluded: chain A residue  953 PHE
Chi-restraints excluded: chain A residue  977 ILE
Chi-restraints excluded: chain A residue 1102 VAL
Chi-restraints excluded: chain A residue 1112 VAL
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1232 THR
Chi-restraints excluded: chain A residue 1267 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 114 optimal weight:    5.9990
   chunk 107 optimal weight:    0.7980
   chunk 81 optimal weight:    0.2980
   chunk 26 optimal weight:    2.9990
   chunk 108 optimal weight:    2.9990
   chunk 102 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A1244 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.174681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.120047 restraints weight = 9718.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 1.81
r_work: 0.3054 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2902 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9623  Z= 0.132
  Angle     :  0.507  10.224  13072  Z= 0.257
  Chirality :  0.040   0.194   1513
  Planarity :  0.003   0.038   1610
  Dihedral  :  9.306  84.003   1899
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 15.55 %
    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 are not related in a simple way.
  whole:  1.81 (0.24), residues: 1171
  helix:  1.90 (0.18), residues: 798
  sheet:  0.40 (0.64), residues: 60
  loop : -0.44 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 144 
 TYR   0.029   0.001   TYR A 306 
 PHE   0.028   0.001   PHE A 934 
 TRP   0.016   0.001   TRP A 228 
 HIS   0.003   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9623)
  covalent geometry    : angle       0.50671 (13072)
  hydrogen bonds       : bond        0.04335 (  614)
  hydrogen bonds       : angle       3.71494 ( 1791)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 ASN cc_start: 0.6878 (t0) cc_final: 0.6074 (m-40)
REVERT: A  180 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7691 (mt-10)
REVERT: A  293 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7874 (tt)
REVERT: A  377 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8641 (p)
REVERT: A  404 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8098 (mt0)
REVERT: A  414 LYS cc_start: 0.7030 (mtpt) cc_final: 0.6473 (mmpt)
REVERT: A  424 ASN cc_start: 0.8091 (m110) cc_final: 0.7455 (m-40)
REVERT: A  455 ARG cc_start: 0.7409 (mtt180) cc_final: 0.7166 (mtp180)
REVERT: A  497 GLU cc_start: 0.6609 (mt-10) cc_final: 0.6081 (tt0)
REVERT: A  802 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7413 (t70)
REVERT: A  848 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7549 (mp)
REVERT: A  915 MET cc_start: 0.8638 (mtm) cc_final: 0.8394 (mtp)
REVERT: A 1026 MET cc_start: 0.8338 (ttm) cc_final: 0.8027 (ptp)
REVERT: A 1055 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7120 (pp20)
REVERT: A 1102 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8086 (p)
REVERT: A 1208 LYS cc_start: 0.6526 (ttpt) cc_final: 0.6123 (mtpp)
REVERT: A 1237 ASP cc_start: 0.7920 (m-30) cc_final: 0.7636 (m-30)
REVERT: A 1243 GLN cc_start: 0.7090 (tt0) cc_final: 0.6389 (tp40)
  outliers start: 27
  outliers final: 18
  residues processed: 131
  average time/residue: 0.5680
  time to fit residues: 79.6912
Evaluate side-chains
  133 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 108
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  306 TYR
Chi-restraints excluded: chain A residue  340 SER
Chi-restraints excluded: chain A residue  377 SER
Chi-restraints excluded: chain A residue  404 GLN
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  696 ILE
Chi-restraints excluded: chain A residue  802 ASP
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  882 ASP
Chi-restraints excluded: chain A residue  939 SER
Chi-restraints excluded: chain A residue  953 PHE
Chi-restraints excluded: chain A residue  977 ILE
Chi-restraints excluded: chain A residue 1102 VAL
Chi-restraints excluded: chain A residue 1112 VAL
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1232 THR
Chi-restraints excluded: chain A residue 1242 ILE
Chi-restraints excluded: chain A residue 1267 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 100 optimal weight:    0.3980
   chunk 78 optimal weight:    4.9990
   chunk 81 optimal weight:    0.1980
   chunk 99 optimal weight:    0.9980
   chunk 63 optimal weight:    5.9990
   chunk 74 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 115 optimal weight:    8.9990
   chunk 114 optimal weight:    0.9980
   chunk 98 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A1244 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.177290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.123329 restraints weight = 9638.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 1.81
r_work: 0.3082 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9623  Z= 0.112
  Angle     :  0.489  10.194  13072  Z= 0.248
  Chirality :  0.039   0.193   1513
  Planarity :  0.003   0.037   1610
  Dihedral  :  9.077  80.038   1899
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 15.44 %
    Favored  : 81.72 %
  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 are not related in a simple way.
  whole:  1.93 (0.24), residues: 1171
  helix:  2.01 (0.18), residues: 798
  sheet:  0.37 (0.64), residues: 60
  loop : -0.41 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 144 
 TYR   0.027   0.001   TYR A 306 
 PHE   0.030   0.001   PHE A 934 
 TRP   0.018   0.001   TRP A 228 
 HIS   0.003   0.001   HIS A 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 9623)
  covalent geometry    : angle       0.48872 (13072)
  hydrogen bonds       : bond        0.04083 (  614)
  hydrogen bonds       : angle       3.65341 ( 1791)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3433.00 seconds
wall clock time: 59 minutes 4.95 seconds (3544.95 seconds total)