Starting phenix.real_space_refine
on Sun Jun  8 11:50:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ctc_45903/06_2025/9ctc_45903.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ctc_45903/06_2025/9ctc_45903.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ctc_45903/06_2025/9ctc_45903.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ctc_45903/06_2025/9ctc_45903.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ctc_45903/06_2025/9ctc_45903.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ctc_45903/06_2025/9ctc_45903.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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       3      5.49       5
     S      37      5.16       5
     C    6255      2.51       5
     N    1553      2.21       5
     O    1673      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 9525
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1170, 9104
          Classifications: {'peptide': 1170}
          Link IDs: {'PTRANS': 29, 'TRANS': 1140}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 421
          Unusual residues: {'ATP': 1, 'UPL': 22, 'ZQU': 2}
          Classifications: {'undetermined': 25}
          Link IDs: {None: 24}
          Unresolved non-hydrogen bonds: 436
          Unresolved non-hydrogen angles: 457
          Unresolved non-hydrogen dihedrals: 478
          Unresolved non-hydrogen chiralities: 21
  Time building chain proxies: 5.97, per 1000 atoms: 0.63
  Number of scatterers: 9525
  At special positions: 0
  Unit cell: (106.572, 119.52, 117.528, 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      37     16.00
     P       3     15.00
     F       4      9.00
     O    1673      8.00
     N    1553      7.00
     C    6255      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.55
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 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:
      51 helices and 5 sheets defined
      67.6% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 40
      removed outlier: 3.777A  pdb=" N   PHE A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 62
    Processing helix  chain 'A' and resid 64 through 90
      removed outlier: 4.436A  pdb=" N   LEU A  70 " --> pdb=" O   PRO A  66 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLY A  73 " --> pdb=" O   MET A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 158
      removed outlier: 3.882A  pdb=" N   ARG A 113 " --> pdb=" O   GLU A 109 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TYR A 114 " --> pdb=" O   ASP A 110 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   TYR A 130 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   HIS A 145 " --> pdb=" O   GLY A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 166
      removed outlier: 3.540A  pdb=" N   VAL A 165 " --> pdb=" O   GLY A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 186
      removed outlier: 3.536A  pdb=" N   THR A 176 " --> pdb=" O   ASN A 172 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   VAL A 179 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   SER A 180 " --> pdb=" O   THR A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 211
      removed outlier: 4.464A  pdb=" N   GLY A 191 " --> pdb=" O   GLY A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 221
      removed outlier: 3.686A  pdb=" N   THR A 215 " --> pdb=" O   GLY A 211 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   VAL A 217 " --> pdb=" O   LYS A 213 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE A 218 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ILE A 221 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 238
    Processing helix  chain 'A' and resid 247 through 260
      removed outlier: 3.651A  pdb=" N   VAL A 253 " --> pdb=" O   LYS A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 268
    Processing helix  chain 'A' and resid 269 through 324
      removed outlier: 4.507A  pdb=" N   GLU A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ALA A 284 " --> pdb=" O   ASN A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 345
    Processing helix  chain 'A' and resid 348 through 370
      removed outlier: 3.556A  pdb=" N   ILE A 352 " --> pdb=" O   ALA A 348 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   GLU A 364 " --> pdb=" O   GLY A 360 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ILE A 365 " --> pdb=" O   ALA A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 405
      removed outlier: 3.923A  pdb=" N   LYS A 405 " --> pdb=" O   PRO A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 441
      removed outlier: 4.093A  pdb=" N   GLN A 441 " --> pdb=" O   VAL A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 469
    Processing helix  chain 'A' and resid 483 through 492
      removed outlier: 3.866A  pdb=" N   GLY A 491 " --> pdb=" O   ASN A 487 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   ARG A 492 " --> pdb=" O   ILE A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 507
    Processing helix  chain 'A' and resid 511 through 516
    Processing helix  chain 'A' and resid 518 through 522
    Processing helix  chain 'A' and resid 532 through 547
      removed outlier: 3.618A  pdb=" N   ARG A 547 " --> pdb=" O   ARG A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 577
    Processing helix  chain 'A' and resid 590 through 594
      removed outlier: 3.536A  pdb=" N   ARG A 593 " --> pdb=" O   SER A 590 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ASN A 594 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 590 through 594'
    Processing helix  chain 'A' and resid 611 through 619
    Processing helix  chain 'A' and resid 620 through 630
    Processing helix  chain 'A' and resid 696 through 704
      removed outlier: 3.569A  pdb=" N   LEU A 703 " --> pdb=" O   ARG A 699 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   ASN A 704 " --> pdb=" O   ILE A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 707 through 723
    Processing helix  chain 'A' and resid 724 through 741
      removed outlier: 4.038A  pdb=" N   PHE A 739 " --> pdb=" O   ILE A 735 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 744 through 799
    Processing helix  chain 'A' and resid 800 through 806
      removed outlier: 3.912A  pdb=" N   PHE A 804 " --> pdb=" O   ASP A 800 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 810 through 825
      removed outlier: 4.668A  pdb=" N   ALA A 822 " --> pdb=" O   LEU A 818 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   ALA A 823 " --> pdb=" O   ALA A 819 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 826 through 828
      No H-bonds generated for 'chain 'A' and resid 826 through 828'
    Processing helix  chain 'A' and resid 829 through 854
      removed outlier: 4.632A  pdb=" N   THR A 845 " --> pdb=" O   ALA A 841 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 862
    Processing helix  chain 'A' and resid 864 through 880
    Processing helix  chain 'A' and resid 890 through 902
    Processing helix  chain 'A' and resid 903 through 910
    Processing helix  chain 'A' and resid 913 through 966
      removed outlier: 4.287A  pdb=" N   VAL A 926 " --> pdb=" O   GLN A 922 " (cutoff:3.500A)
      Proline residue:  A 927  - end of helix
      removed outlier: 3.755A  pdb=" N   HIS A 936 " --> pdb=" O   LEU A 932 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   MET A 949 " --> pdb=" O   THR A 945 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   TYR A 950 " --> pdb=" O   GLN A 946 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   TYR A 953 " --> pdb=" O   MET A 949 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   ALA A 954 " --> pdb=" O   TYR A 950 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 982
    Processing helix  chain 'A' and resid 982 through 992
    Processing helix  chain 'A' and resid 997 through 1013
      removed outlier: 3.590A  pdb=" N   ALA A1001 " --> pdb=" O   ASP A 997 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   HIS A1007 " --> pdb=" O   ILE A1003 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1074 through 1084
      removed outlier: 4.307A  pdb=" N   THR A1078 " --> pdb=" O   CYS A1074 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLU A1084 " --> pdb=" O   VAL A1080 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1105 through 1112
    Processing helix  chain 'A' and resid 1126 through 1132
    Processing helix  chain 'A' and resid 1141 through 1152
    Processing helix  chain 'A' and resid 1178 through 1191
    Processing helix  chain 'A' and resid 1209 through 1223
      removed outlier: 3.889A  pdb=" N   VAL A1213 " --> pdb=" O   GLU A1209 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   GLU A1223 " --> pdb=" O   ASP A1219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1232 through 1236
      removed outlier: 3.736A  pdb=" N   THR A1236 " --> pdb=" O   ARG A1233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1257 through 1263
    Processing helix  chain 'A' and resid 1265 through 1270
    Processing sheet with id=AA1, first strand: chain 'A' and resid 413 through 415
      removed outlier: 3.595A  pdb=" N   LEU A 413 " --> pdb=" O   VAL A 397 " (cutoff:3.500A)
      removed outlier: 7.862A  pdb=" N   LEU A 415 " --> pdb=" O   ARG A 395 " (cutoff:3.500A)
      removed outlier: 5.745A  pdb=" N   ARG A 395 " --> pdb=" O   LEU A 415 " (cutoff:3.500A)
      removed outlier: 5.291A  pdb=" N   PHE A 394 " --> pdb=" O   SER A 452 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   SER A 452 " --> pdb=" O   PHE A 394 " (cutoff:3.500A)
      removed outlier: 5.415A  pdb=" N   ASN A 396 " --> pdb=" O   MET A 450 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   MET A 450 " --> pdb=" O   ASN A 396 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 470 through 473
      removed outlier: 3.533A  pdb=" N   GLY A 471 " --> pdb=" O   ILE A 551 " (cutoff:3.500A)
      removed outlier: 8.032A  pdb=" N   LEU A 552 " --> pdb=" O   ILE A 583 " (cutoff:3.500A)
      removed outlier: 8.646A  pdb=" N   ILE A 585 " --> pdb=" O   LEU A 552 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   LEU A 554 " --> pdb=" O   ILE A 585 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   VAL A 423 " --> pdb=" O   VAL A 584 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1056 through 1059
      removed outlier: 5.141A  pdb=" N   LEU A1056 " --> pdb=" O   GLU A1039 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   THR A1036 " --> pdb=" O   LEU A1095 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   VAL A1040 " --> pdb=" O   ALA A1091 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ALA A1091 " --> pdb=" O   VAL A1040 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1228 through 1229
      removed outlier: 6.938A  pdb=" N   LEU A1066 " --> pdb=" O   VAL A1229 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   ILE A1243 " --> pdb=" O   HIS A1254 " (cutoff:3.500A)
      removed outlier: 5.329A  pdb=" N   HIS A1254 " --> pdb=" O   ILE A1243 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   VAL A1245 " --> pdb=" O   LYS A1252 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1114 through 1116

    567 hydrogen bonds defined for protein.
    1677 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.22

  Time building geometry restraints manager: 2.93 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2944
        1.34 -     1.46: 2014
        1.46 -     1.58: 4656
        1.58 -     1.69: 5
        1.69 -     1.81: 67
  Bond restraints: 9686
  Sorted by residual:
  bond pdb=" C01 ZQU A1303 "
       pdb=" C02 ZQU A1303 "
    ideal  model  delta    sigma   weight residual
    1.538  1.502  0.036 2.00e-02 2.50e+03 3.17e+00
  bond pdb=" C01 ZQU A1302 "
       pdb=" C02 ZQU A1302 "
    ideal  model  delta    sigma   weight residual
    1.538  1.503  0.035 2.00e-02 2.50e+03 3.06e+00
  bond pdb=" C02 ZQU A1302 "
       pdb=" C03 ZQU A1302 "
    ideal  model  delta    sigma   weight residual
    1.480  1.509 -0.029 2.00e-02 2.50e+03 2.12e+00
  bond pdb=" C02 ZQU A1303 "
       pdb=" C03 ZQU A1303 "
    ideal  model  delta    sigma   weight residual
    1.480  1.509 -0.029 2.00e-02 2.50e+03 2.08e+00
  bond pdb=" C01 ZQU A1302 "
       pdb=" C03 ZQU A1302 "
    ideal  model  delta    sigma   weight residual
    1.479  1.506 -0.027 2.00e-02 2.50e+03 1.87e+00
  ... (remaining 9681 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.18: 12649
        1.18 -     2.36: 263
        2.36 -     3.53: 53
        3.53 -     4.71: 13
        4.71 -     5.89: 6
  Bond angle restraints: 12984
  Sorted by residual:
  angle pdb=" C   HIS A 587 "
        pdb=" N   ARG A 588 "
        pdb=" CA  ARG A 588 "
      ideal   model   delta    sigma   weight residual
     121.54  126.89   -5.35 1.91e+00 2.74e-01 7.85e+00
  angle pdb=" C   LYS A 888 "
        pdb=" N   GLU A 889 "
        pdb=" CA  GLU A 889 "
      ideal   model   delta    sigma   weight residual
     121.54  126.38   -4.84 1.91e+00 2.74e-01 6.42e+00
  angle pdb=" C   LEU A 561 "
        pdb=" N   ASP A 562 "
        pdb=" CA  ASP A 562 "
      ideal   model   delta    sigma   weight residual
     121.54  125.60   -4.06 1.91e+00 2.74e-01 4.52e+00
  angle pdb=" C   GLY A1038 "
        pdb=" N   GLU A1039 "
        pdb=" CA  GLU A1039 "
      ideal   model   delta    sigma   weight residual
     121.54  125.45   -3.91 1.91e+00 2.74e-01 4.20e+00
  angle pdb=" C   ALA A 841 "
        pdb=" N   ASN A 842 "
        pdb=" CA  ASN A 842 "
      ideal   model   delta    sigma   weight residual
     122.60  119.22    3.38 1.88e+00 2.83e-01 3.24e+00
  ... (remaining 12979 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.49: 5651
       24.49 -    48.98: 217
       48.98 -    73.47: 15
       73.47 -    97.97: 8
       97.97 -   122.46: 1
  Dihedral angle restraints: 5892
    sinusoidal: 2534
      harmonic: 3358
  Sorted by residual:
  dihedral pdb=" N01 ZQU A1303 "
           pdb=" C11 ZQU A1303 "
           pdb=" C15 ZQU A1303 "
           pdb=" N02 ZQU A1303 "
      ideal   model   delta sinusoidal    sigma   weight residual
      58.39  -64.07  122.46     1      3.00e+01 1.11e-03 1.64e+01
  dihedral pdb=" C11 ZQU A1303 "
           pdb=" C15 ZQU A1303 "
           pdb=" N02 ZQU A1303 "
           pdb=" C16 ZQU A1303 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.26   34.92  -91.18     1      3.00e+01 1.11e-03 1.09e+01
  dihedral pdb=" C11 ZQU A1303 "
           pdb=" C15 ZQU A1303 "
           pdb=" N02 ZQU A1303 "
           pdb=" C21 ZQU A1303 "
      ideal   model   delta sinusoidal    sigma   weight residual
     179.21  -89.78  -91.01     1      3.00e+01 1.11e-03 1.09e+01
  ... (remaining 5889 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 948
       0.029 -    0.058: 346
       0.058 -    0.087: 108
       0.087 -    0.116: 49
       0.116 -    0.145: 9
  Chirality restraints: 1460
  Sorted by residual:
  chirality pdb=" CA  ILE A 461 "
            pdb=" N   ILE A 461 "
            pdb=" C   ILE A 461 "
            pdb=" CB  ILE A 461 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.28e-01
  chirality pdb=" CA  TRP A 708 "
            pdb=" N   TRP A 708 "
            pdb=" C   TRP A 708 "
            pdb=" CB  TRP A 708 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.89e-01
  chirality pdb=" CA  ILE A 692 "
            pdb=" N   ILE A 692 "
            pdb=" C   ILE A 692 "
            pdb=" CB  ILE A 692 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.66e-01
  ... (remaining 1457 not shown)

  Planarity restraints: 1590
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 840 "    0.008 2.00e-02 2.50e+03   1.58e-02 2.51e+00
        pdb=" C   ILE A 840 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   ILE A 840 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ALA A 841 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C02 ZQU A1302 "   -0.000 2.00e-02 2.50e+03   1.00e-02 2.01e+00
        pdb=" C05 ZQU A1302 "   -0.011 2.00e-02 2.50e+03
        pdb=" C06 ZQU A1302 "   -0.007 2.00e-02 2.50e+03
        pdb=" C08 ZQU A1302 "    0.024 2.00e-02 2.50e+03
        pdb=" C10 ZQU A1302 "    0.003 2.00e-02 2.50e+03
        pdb=" C14 ZQU A1302 "   -0.008 2.00e-02 2.50e+03
        pdb=" C18 ZQU A1302 "   -0.001 2.00e-02 2.50e+03
        pdb=" C20 ZQU A1302 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 817 "    0.007 2.00e-02 2.50e+03   1.41e-02 2.00e+00
        pdb=" C   ARG A 817 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   ARG A 817 "    0.009 2.00e-02 2.50e+03
        pdb=" N   LEU A 818 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1587 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1941
        2.78 -     3.31: 9392
        3.31 -     3.84: 14963
        3.84 -     4.37: 17319
        4.37 -     4.90: 30564
  Nonbonded interactions: 74179
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 393 "
            pdb=" NZ  LYS A 416 "
     model   vdw
     2.252 3.120
  nonbonded pdb=" NE2 GLN A1215 "
            pdb=" O   SER A1235 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" ND2 ASN A1153 "
            pdb=" OE2 GLU A1216 "
     model   vdw
     2.331 3.120
  nonbonded pdb=" O   PHE A 239 "
            pdb=" OG1 THR A 240 "
     model   vdw
     2.340 3.040
  nonbonded pdb=" O   TYR A 130 "
            pdb=" OG  SER A 134 "
     model   vdw
     2.357 3.040
  ... (remaining 74174 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 group one per residue
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:             1.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.340
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
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      :  0.002   0.036   9686  Z= 0.123
  Angle     :  0.455   5.890  12984  Z= 0.242
  Chirality :  0.037   0.145   1460
  Planarity :  0.003   0.029   1590
  Dihedral  : 12.321 122.456   3736
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.25), residues: 1164
  helix:  1.46 (0.19), residues: 762
  sheet: -0.24 (0.85), residues: 32
  loop : -1.70 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 708 
 HIS   0.003   0.001   HIS A 966 
 PHE   0.012   0.001   PHE A 200 
 TYR   0.010   0.001   TYR A 310 
 ARG   0.003   0.000   ARG A 588 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16601 (  567)
  hydrogen bonds       : angle       5.14305 ( 1677)
  covalent geometry    : bond        0.00233 ( 9686)
  covalent geometry    : angle       0.45501 (12984)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.8953 (mmt) cc_final: 0.8745 (mmt)
REVERT: A  255 GLU cc_start: 0.8494 (tp30) cc_final: 0.8249 (tp30)
REVERT: A  408 LYS cc_start: 0.8532 (ptmt) cc_final: 0.8023 (ttmt)
REVERT: A  450 MET cc_start: 0.6582 (ptp) cc_final: 0.6074 (tmm)
REVERT: A  457 ASP cc_start: 0.7778 (p0) cc_final: 0.7412 (t0)
REVERT: A  468 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7810 (tm-30)
REVERT: A  949 MET cc_start: 0.8499 (mtt) cc_final: 0.8220 (mtt)
REVERT: A 1064 GLN cc_start: 0.7259 (tt0) cc_final: 0.6822 (tp-100)
REVERT: A 1100 GLU cc_start: 0.6236 (pt0) cc_final: 0.5728 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.2666
  time to fit residues: 67.4430
Evaluate side-chains
  114 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 88 optimal weight:    1.9990
   chunk 49 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 47 optimal weight:    9.9990
   chunk 91 optimal weight:    3.9990
   chunk 35 optimal weight:   10.0000
   chunk 55 optimal weight:    0.1980
   chunk 68 optimal weight:    1.9990
   chunk 106 optimal weight:    9.9990
   overall best weight:    1.8388

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

Flipped N/Q/H residues before XYZ refinement:
A 914 GLN
A1136 ASN
A1195 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.180247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.125716 restraints weight = 12760.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.123755 restraints weight = 18505.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.125706 restraints weight = 16366.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9686  Z= 0.207
  Angle     :  0.620   8.435  12984  Z= 0.321
  Chirality :  0.042   0.151   1460
  Planarity :  0.004   0.031   1590
  Dihedral  :  8.728  85.770   1615
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 10.53 %
    Favored  : 87.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.25), residues: 1164
  helix:  1.34 (0.19), residues: 772
  sheet:  0.03 (0.83), residues: 33
  loop : -1.81 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 803 
 HIS   0.004   0.001   HIS A 966 
 PHE   0.024   0.002   PHE A 335 
 TYR   0.020   0.002   TYR A 310 
 ARG   0.006   0.001   ARG A 538 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06151 (  567)
  hydrogen bonds       : angle       4.40133 ( 1677)
  covalent geometry    : bond        0.00485 ( 9686)
  covalent geometry    : angle       0.62009 (12984)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 1.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.8918 (mmt) cc_final: 0.8681 (mmt)
REVERT: A  408 LYS cc_start: 0.8485 (ptmt) cc_final: 0.8056 (ttmt)
REVERT: A  413 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7350 (tt)
REVERT: A  450 MET cc_start: 0.6380 (ptp) cc_final: 0.5923 (tmm)
REVERT: A  468 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7678 (tm-30)
REVERT: A  490 TYR cc_start: 0.6818 (t80) cc_final: 0.6098 (t80)
REVERT: A  916 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.8097 (m-80)
REVERT: A  949 MET cc_start: 0.8499 (mtt) cc_final: 0.8285 (mtp)
  outliers start: 22
  outliers final: 12
  residues processed: 138
  average time/residue: 0.2082
  time to fit residues: 41.0498
Evaluate side-chains
  120 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   89 MET
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  436 THR
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  831 SER
Chi-restraints excluded: chain A residue  916 PHE
Chi-restraints excluded: chain A residue 1074 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 3 optimal weight:    0.0770
   chunk 89 optimal weight:    0.0670
   chunk 60 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 83 optimal weight:    4.9990
   chunk 54 optimal weight:    8.9990
   chunk 63 optimal weight:    0.0870
   chunk 66 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.4254

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

Flipped N/Q/H residues before XYZ refinement:
A 629 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.176401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.120258 restraints weight = 13241.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.117299 restraints weight = 13030.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.118706 restraints weight = 11335.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9686  Z= 0.122
  Angle     :  0.524   9.075  12984  Z= 0.272
  Chirality :  0.039   0.142   1460
  Planarity :  0.003   0.052   1590
  Dihedral  :  8.018  84.685   1615
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 12.38 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.25), residues: 1164
  helix:  1.65 (0.19), residues: 766
  sheet:  0.35 (0.83), residues: 33
  loop : -1.75 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1108 
 HIS   0.010   0.001   HIS A 612 
 PHE   0.013   0.001   PHE A1157 
 TYR   0.011   0.001   TYR A 310 
 ARG   0.003   0.000   ARG A 538 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05165 (  567)
  hydrogen bonds       : angle       3.98900 ( 1677)
  covalent geometry    : bond        0.00242 ( 9686)
  covalent geometry    : angle       0.52448 (12984)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 LYS cc_start: 0.8539 (ptmt) cc_final: 0.7873 (ttmt)
REVERT: A  413 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7161 (tt)
REVERT: A  450 MET cc_start: 0.6265 (ptp) cc_final: 0.5722 (tmm)
REVERT: A  468 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7814 (tm-30)
REVERT: A  490 TYR cc_start: 0.6912 (t80) cc_final: 0.6165 (t80)
REVERT: A  799 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8284 (mp10)
REVERT: A  904 PHE cc_start: 0.7437 (t80) cc_final: 0.7210 (t80)
REVERT: A  916 PHE cc_start: 0.8283 (m-80) cc_final: 0.7940 (m-80)
REVERT: A 1064 GLN cc_start: 0.6527 (tp-100) cc_final: 0.6021 (tp40)
REVERT: A 1101 ILE cc_start: 0.8142 (pt) cc_final: 0.7441 (pt)
REVERT: A 1201 GLU cc_start: 0.6622 (mm-30) cc_final: 0.6405 (mm-30)
  outliers start: 13
  outliers final: 5
  residues processed: 126
  average time/residue: 0.2024
  time to fit residues: 37.1584
Evaluate side-chains
  115 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 108
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  700 ILE
Chi-restraints excluded: chain A residue  799 GLN
Chi-restraints excluded: chain A residue  831 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 60 optimal weight:    0.0980
   chunk 41 optimal weight:   10.0000
   chunk 114 optimal weight:    7.9990
   chunk 110 optimal weight:   30.0000
   chunk 3 optimal weight:    0.0270
   chunk 52 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   overall best weight:    0.7640

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

Flipped N/Q/H residues before XYZ refinement:
A 456 GLN
A 799 GLN
A1257 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.176172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.120488 restraints weight = 13097.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.119236 restraints weight = 14515.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.119917 restraints weight = 12286.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9686  Z= 0.124
  Angle     :  0.512   7.837  12984  Z= 0.265
  Chirality :  0.039   0.145   1460
  Planarity :  0.003   0.030   1590
  Dihedral  :  7.813  82.829   1615
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 12.90 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.25), residues: 1164
  helix:  1.70 (0.19), residues: 765
  sheet:  0.53 (0.84), residues: 32
  loop : -1.79 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1108 
 HIS   0.007   0.001   HIS A 612 
 PHE   0.015   0.001   PHE A 465 
 TYR   0.014   0.001   TYR A 310 
 ARG   0.005   0.000   ARG A1250 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04935 (  567)
  hydrogen bonds       : angle       3.84407 ( 1677)
  covalent geometry    : bond        0.00262 ( 9686)
  covalent geometry    : angle       0.51190 (12984)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 LYS cc_start: 0.8528 (ptmt) cc_final: 0.7912 (ttmt)
REVERT: A  450 MET cc_start: 0.6161 (ptp) cc_final: 0.5661 (tmm)
REVERT: A  468 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7714 (tp30)
REVERT: A  490 TYR cc_start: 0.6977 (t80) cc_final: 0.6216 (t80)
REVERT: A  799 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8124 (mp10)
REVERT: A  879 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8439 (mp)
REVERT: A  904 PHE cc_start: 0.7651 (t80) cc_final: 0.7425 (t80)
REVERT: A  916 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7911 (m-80)
REVERT: A 1064 GLN cc_start: 0.6411 (tp-100) cc_final: 0.5949 (tp40)
  outliers start: 18
  outliers final: 9
  residues processed: 128
  average time/residue: 0.2023
  time to fit residues: 37.6124
Evaluate side-chains
  118 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  436 THR
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  799 GLN
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  831 SER
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  916 PHE
Chi-restraints excluded: chain A residue  949 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 74 optimal weight:    0.7980
   chunk 83 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 88 optimal weight:    1.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 799 GLN
A1130 ASN
A1257 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.172127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.117377 restraints weight = 13135.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.116368 restraints weight = 15110.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.117076 restraints weight = 15408.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9686  Z= 0.144
  Angle     :  0.525   7.604  12984  Z= 0.272
  Chirality :  0.039   0.145   1460
  Planarity :  0.003   0.034   1590
  Dihedral  :  7.871  81.433   1615
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 13.42 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.25), residues: 1164
  helix:  1.64 (0.19), residues: 766
  sheet:  0.42 (0.81), residues: 32
  loop : -1.79 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1108 
 HIS   0.012   0.001   HIS A 612 
 PHE   0.017   0.001   PHE A1157 
 TYR   0.015   0.001   TYR A 310 
 ARG   0.006   0.000   ARG A 905 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04990 (  567)
  hydrogen bonds       : angle       3.88179 ( 1677)
  covalent geometry    : bond        0.00325 ( 9686)
  covalent geometry    : angle       0.52454 (12984)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 1.008 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 LYS cc_start: 0.8556 (ptmt) cc_final: 0.7901 (ttmt)
REVERT: A  450 MET cc_start: 0.6150 (ptp) cc_final: 0.5584 (tmm)
REVERT: A  468 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7781 (tp30)
REVERT: A  490 TYR cc_start: 0.7207 (t80) cc_final: 0.6569 (t80)
REVERT: A  796 MET cc_start: 0.8766 (mtt) cc_final: 0.8445 (mtt)
REVERT: A  799 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8446 (mp10)
REVERT: A  879 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8360 (mp)
REVERT: A  914 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.7120 (mm110)
REVERT: A  916 PHE cc_start: 0.8308 (m-80) cc_final: 0.8057 (m-80)
REVERT: A 1083 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8453 (tp)
  outliers start: 20
  outliers final: 11
  residues processed: 125
  average time/residue: 0.1930
  time to fit residues: 35.5769
Evaluate side-chains
  120 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  436 THR
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  799 GLN
Chi-restraints excluded: chain A residue  831 SER
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  914 GLN
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1167 THR
Chi-restraints excluded: chain A residue 1226 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 53 optimal weight:    8.9990
   chunk 6 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   chunk 88 optimal weight:    0.4980
   chunk 89 optimal weight:    3.9990
   chunk 64 optimal weight:    0.0770
   chunk 12 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 97 optimal weight:    7.9990
   overall best weight:    0.7740

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

Flipped N/Q/H residues before XYZ refinement:
A 456 GLN
A 799 GLN
** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1257 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.178783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.125483 restraints weight = 12989.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.123273 restraints weight = 20383.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.124987 restraints weight = 17854.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.2982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9686  Z= 0.123
  Angle     :  0.532  12.120  12984  Z= 0.268
  Chirality :  0.039   0.144   1460
  Planarity :  0.003   0.037   1590
  Dihedral  :  7.674  81.266   1615
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 13.93 %
    Favored  : 84.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.25), residues: 1164
  helix:  1.75 (0.19), residues: 765
  sheet:  0.28 (0.81), residues: 32
  loop : -1.78 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1108 
 HIS   0.012   0.001   HIS A 612 
 PHE   0.017   0.001   PHE A1157 
 TYR   0.013   0.001   TYR A 310 
 ARG   0.005   0.000   ARG A 905 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04751 (  567)
  hydrogen bonds       : angle       3.82968 ( 1677)
  covalent geometry    : bond        0.00265 ( 9686)
  covalent geometry    : angle       0.53216 (12984)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 LYS cc_start: 0.8569 (ptmt) cc_final: 0.7960 (ttmt)
REVERT: A  450 MET cc_start: 0.6067 (ptp) cc_final: 0.5735 (tmm)
REVERT: A  468 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7697 (tp30)
REVERT: A  490 TYR cc_start: 0.7062 (t80) cc_final: 0.6409 (t80)
REVERT: A  891 GLU cc_start: 0.7907 (pp20) cc_final: 0.7428 (pp20)
REVERT: A  916 PHE cc_start: 0.8224 (m-80) cc_final: 0.7974 (m-80)
REVERT: A 1083 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8347 (tp)
REVERT: A 1119 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7448 (mm-30)
  outliers start: 19
  outliers final: 13
  residues processed: 127
  average time/residue: 0.1902
  time to fit residues: 35.8636
Evaluate side-chains
  118 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  436 THR
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  831 SER
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1167 THR
Chi-restraints excluded: chain A residue 1226 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 115 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   chunk 103 optimal weight:    2.9990
   chunk 99 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9980
   chunk 78 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1257 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.178387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.123725 restraints weight = 13282.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.122839 restraints weight = 18657.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.123548 restraints weight = 16966.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.3169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9686  Z= 0.180
  Angle     :  0.576   9.137  12984  Z= 0.294
  Chirality :  0.041   0.149   1460
  Planarity :  0.003   0.039   1590
  Dihedral  :  8.226  79.442   1615
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 14.14 %
    Favored  : 83.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.25), residues: 1164
  helix:  1.57 (0.19), residues: 768
  sheet:  0.16 (0.84), residues: 32
  loop : -1.76 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A1108 
 HIS   0.009   0.001   HIS A 612 
 PHE   0.020   0.002   PHE A 465 
 TYR   0.017   0.001   TYR A 310 
 ARG   0.005   0.000   ARG A 489 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05312 (  567)
  hydrogen bonds       : angle       4.02766 ( 1677)
  covalent geometry    : bond        0.00421 ( 9686)
  covalent geometry    : angle       0.57612 (12984)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 LYS cc_start: 0.8552 (ptmt) cc_final: 0.7927 (ttmt)
REVERT: A  450 MET cc_start: 0.6098 (ptp) cc_final: 0.5610 (tpp)
REVERT: A  468 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7772 (tp30)
REVERT: A  490 TYR cc_start: 0.7076 (t80) cc_final: 0.6590 (t80)
REVERT: A  879 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8452 (mp)
REVERT: A  891 GLU cc_start: 0.7941 (pp20) cc_final: 0.7482 (pp20)
REVERT: A  916 PHE cc_start: 0.8269 (m-80) cc_final: 0.8008 (m-80)
REVERT: A 1201 GLU cc_start: 0.6958 (mm-30) cc_final: 0.6701 (mm-30)
  outliers start: 19
  outliers final: 12
  residues processed: 121
  average time/residue: 0.2169
  time to fit residues: 38.3324
Evaluate side-chains
  118 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  436 THR
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  831 SER
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue 1167 THR
Chi-restraints excluded: chain A residue 1226 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 116 optimal weight:    0.9990
   chunk 82 optimal weight:    0.7980
   chunk 102 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 50 optimal weight:    8.9990
   chunk 91 optimal weight:    0.9980
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 456 GLN
** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1257 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.180856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.128852 restraints weight = 13344.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.126824 restraints weight = 22602.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.128057 restraints weight = 20846.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.3267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9686  Z= 0.123
  Angle     :  0.548  13.728  12984  Z= 0.276
  Chirality :  0.040   0.169   1460
  Planarity :  0.003   0.040   1590
  Dihedral  :  7.828  80.123   1615
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 15.69 %
    Favored  : 82.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.25), residues: 1164
  helix:  1.71 (0.19), residues: 765
  sheet: -0.01 (0.81), residues: 33
  loop : -1.70 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1108 
 HIS   0.009   0.001   HIS A 612 
 PHE   0.012   0.001   PHE A 200 
 TYR   0.012   0.001   TYR A 310 
 ARG   0.004   0.000   ARG A 905 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04761 (  567)
  hydrogen bonds       : angle       3.82099 ( 1677)
  covalent geometry    : bond        0.00267 ( 9686)
  covalent geometry    : angle       0.54798 (12984)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 LYS cc_start: 0.8543 (ptmt) cc_final: 0.7952 (ttmt)
REVERT: A  450 MET cc_start: 0.6035 (ptp) cc_final: 0.5802 (tmm)
REVERT: A  490 TYR cc_start: 0.6942 (t80) cc_final: 0.6332 (t80)
REVERT: A  879 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8470 (mp)
REVERT: A  891 GLU cc_start: 0.7883 (pp20) cc_final: 0.7445 (pp20)
REVERT: A 1084 GLU cc_start: 0.8043 (tp30) cc_final: 0.7812 (tp30)
REVERT: A 1201 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6556 (mm-30)
  outliers start: 13
  outliers final: 11
  residues processed: 122
  average time/residue: 0.2215
  time to fit residues: 40.5729
Evaluate side-chains
  121 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  436 THR
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  831 SER
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue 1167 THR
Chi-restraints excluded: chain A residue 1226 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 99 optimal weight:    8.9990
   chunk 109 optimal weight:    0.4980
   chunk 18 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 112 optimal weight:    7.9990
   chunk 10 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1257 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.180408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.129146 restraints weight = 13004.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.126801 restraints weight = 20433.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.128488 restraints weight = 18770.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.3420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9686  Z= 0.128
  Angle     :  0.549  13.475  12984  Z= 0.278
  Chirality :  0.040   0.176   1460
  Planarity :  0.003   0.039   1590
  Dihedral  :  7.687  79.404   1615
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 15.69 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.25), residues: 1164
  helix:  1.72 (0.19), residues: 766
  sheet: -0.15 (0.83), residues: 33
  loop : -1.74 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1108 
 HIS   0.009   0.001   HIS A 612 
 PHE   0.019   0.001   PHE A 916 
 TYR   0.014   0.001   TYR A 310 
 ARG   0.004   0.000   ARG A 905 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04656 (  567)
  hydrogen bonds       : angle       3.82286 ( 1677)
  covalent geometry    : bond        0.00281 ( 9686)
  covalent geometry    : angle       0.54916 (12984)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 1.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 LYS cc_start: 0.8521 (ptmt) cc_final: 0.7935 (ttmt)
REVERT: A  879 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8468 (mp)
REVERT: A  891 GLU cc_start: 0.7901 (pp20) cc_final: 0.7437 (pp20)
REVERT: A 1043 ASN cc_start: 0.8105 (t0) cc_final: 0.7881 (t0)
REVERT: A 1084 GLU cc_start: 0.8007 (tp30) cc_final: 0.7751 (tp30)
REVERT: A 1201 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6559 (mm-30)
  outliers start: 14
  outliers final: 11
  residues processed: 124
  average time/residue: 0.2256
  time to fit residues: 41.7836
Evaluate side-chains
  122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  436 THR
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  831 SER
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue 1167 THR
Chi-restraints excluded: chain A residue 1226 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 74 optimal weight:    0.5980
   chunk 98 optimal weight:    6.9990
   chunk 12 optimal weight:    7.9990
   chunk 73 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 69 optimal weight:    0.6980
   chunk 52 optimal weight:    9.9990
   chunk 6 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 53 optimal weight:    6.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 456 GLN
** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1257 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.181376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.129673 restraints weight = 13354.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.125828 restraints weight = 21554.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.128184 restraints weight = 21343.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.3489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9686  Z= 0.128
  Angle     :  0.557  13.676  12984  Z= 0.282
  Chirality :  0.040   0.190   1460
  Planarity :  0.003   0.039   1590
  Dihedral  :  7.624  78.796   1615
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 15.69 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.25), residues: 1164
  helix:  1.73 (0.19), residues: 766
  sheet: -0.21 (0.84), residues: 33
  loop : -1.76 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1108 
 HIS   0.010   0.001   HIS A 612 
 PHE   0.019   0.001   PHE A1157 
 TYR   0.014   0.001   TYR A 310 
 ARG   0.004   0.000   ARG A 905 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04635 (  567)
  hydrogen bonds       : angle       3.81854 ( 1677)
  covalent geometry    : bond        0.00283 ( 9686)
  covalent geometry    : angle       0.55691 (12984)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 LYS cc_start: 0.8530 (ptmt) cc_final: 0.7926 (ttmt)
REVERT: A  799 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7979 (mp10)
REVERT: A  879 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8267 (mp)
REVERT: A  891 GLU cc_start: 0.7915 (pp20) cc_final: 0.7461 (pp20)
REVERT: A 1084 GLU cc_start: 0.8031 (tp30) cc_final: 0.7743 (tp30)
REVERT: A 1201 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6468 (mm-30)
  outliers start: 16
  outliers final: 11
  residues processed: 122
  average time/residue: 0.1849
  time to fit residues: 33.8296
Evaluate side-chains
  118 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  436 THR
Chi-restraints excluded: chain A residue  551 ILE
Chi-restraints excluded: chain A residue  799 GLN
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  831 SER
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue 1167 THR
Chi-restraints excluded: chain A residue 1226 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 66 optimal weight:    0.5980
   chunk 41 optimal weight:    7.9990
   chunk 100 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 89 optimal weight:    0.4980
   chunk 113 optimal weight:    5.9990
   chunk 80 optimal weight:    0.7980
   chunk 86 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 95 optimal weight:    7.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1257 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.180725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.127770 restraints weight = 13283.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.126937 restraints weight = 21248.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.128081 restraints weight = 21284.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.3573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9686  Z= 0.137
  Angle     :  0.565  13.252  12984  Z= 0.286
  Chirality :  0.040   0.188   1460
  Planarity :  0.003   0.040   1590
  Dihedral  :  7.704  78.018   1615
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 16.10 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.25), residues: 1164
  helix:  1.66 (0.19), residues: 767
  sheet: -0.20 (0.85), residues: 33
  loop : -1.81 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1108 
 HIS   0.009   0.001   HIS A 612 
 PHE   0.019   0.001   PHE A1157 
 TYR   0.014   0.001   TYR A 310 
 ARG   0.004   0.000   ARG A 905 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04723 (  567)
  hydrogen bonds       : angle       3.85177 ( 1677)
  covalent geometry    : bond        0.00310 ( 9686)
  covalent geometry    : angle       0.56549 (12984)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3070.19 seconds
wall clock time: 55 minutes 16.59 seconds (3316.59 seconds total)