Starting phenix.real_space_refine
on Wed Sep 17 15:55:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ctc_45903/09_2025/9ctc_45903.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ctc_45903/09_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_45903/09_2025/9ctc_45903.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ctc_45903/09_2025/9ctc_45903.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ctc_45903/09_2025/9ctc_45903.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ctc_45903/09_2025/9ctc_45903.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.35, per 1000 atoms: 0.25
  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: 0.89
  Conformation dependent library (CDL) restraints added in 355.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.29
  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: 1.50

  Time building geometry restraints manager: 1.17 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:             1.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.020
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.650
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (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
 ARG   0.003   0.000   ARG A 588 
 TYR   0.010   0.001   TYR A 310 
 PHE   0.012   0.001   PHE A 200 
 TRP   0.005   0.001   TRP A 708 
 HIS   0.003   0.001   HIS A 966 

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

*********************** 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  : 0.338 
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: 0.8747 (mmt)
REVERT: A  255 GLU cc_start: 0.8494 (tp30) cc_final: 0.8250 (tp30)
REVERT: A  408 LYS cc_start: 0.8532 (ptmt) cc_final: 0.8022 (ttmt)
REVERT: A  450 MET cc_start: 0.6582 (ptp) cc_final: 0.6075 (tmm)
REVERT: A  457 ASP cc_start: 0.7778 (p0) cc_final: 0.7411 (t0)
REVERT: A  468 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7809 (tm-30)
REVERT: A  949 MET cc_start: 0.8499 (mtt) cc_final: 0.8221 (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: 0.5751 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.1175
  time to fit residues: 29.7421
Evaluate side-chains
  113 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    9.9990
   chunk 113 optimal weight:    0.2980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:    4.9990
   overall best weight:    2.4586

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

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS
A 914 GLN
A1136 ASN
A1195 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.178302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.123820 restraints weight = 12971.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.121919 restraints weight = 17175.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.123116 restraints weight = 16592.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.123293 restraints weight = 9219.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.124204 restraints weight = 8005.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   9686  Z= 0.264
  Angle     :  0.680   8.704  12984  Z= 0.350
  Chirality :  0.044   0.155   1460
  Planarity :  0.004   0.034   1590
  Dihedral  :  9.209  85.556   1615
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 11.56 %
    Favored  : 86.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.25), residues: 1164
  helix:  1.19 (0.19), residues: 772
  sheet: -0.03 (0.83), residues: 33
  loop : -1.86 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1147 
 TYR   0.022   0.002   TYR A 310 
 PHE   0.027   0.002   PHE A 335 
 TRP   0.016   0.002   TRP A 803 
 HIS   0.004   0.001   HIS A 966 

Details of bonding type rmsd
  covalent geometry    : bond        0.00631 ( 9686)
  covalent geometry    : angle       0.67971 (12984)
  hydrogen bonds       : bond        0.06475 (  567)
  hydrogen bonds       : angle       4.59509 ( 1677)

*********************** 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
  143 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 LYS cc_start: 0.8507 (ptmt) cc_final: 0.8056 (ttmt)
REVERT: A  413 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7372 (tt)
REVERT: A  450 MET cc_start: 0.6333 (ptp) cc_final: 0.5836 (tmm)
REVERT: A  468 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7591 (tm-30)
REVERT: A  490 TYR cc_start: 0.6942 (t80) cc_final: 0.6206 (t80)
REVERT: A  916 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.8069 (m-80)
REVERT: A  949 MET cc_start: 0.8577 (mtt) cc_final: 0.8364 (mtp)
REVERT: A 1101 ILE cc_start: 0.8708 (tp) cc_final: 0.8204 (pt)
  outliers start: 20
  outliers final: 10
  residues processed: 136
  average time/residue: 0.0926
  time to fit residues: 18.1393
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  : 0.316 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 56 optimal weight:    0.0000
   chunk 106 optimal weight:   10.0000
   chunk 58 optimal weight:   20.0000
   chunk 17 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 34 optimal weight:    9.9990
   chunk 104 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 89 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.6584

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

Flipped N/Q/H residues before XYZ refinement:
A 629 GLN
A 799 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.175049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.119553 restraints weight = 13108.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.117696 restraints weight = 13495.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.118460 restraints weight = 14276.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.119087 restraints weight = 7958.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.121602 restraints weight = 6614.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9686  Z= 0.128
  Angle     :  0.533   9.010  12984  Z= 0.278
  Chirality :  0.040   0.156   1460
  Planarity :  0.004   0.062   1590
  Dihedral  :  8.272  84.316   1615
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 13.42 %
    Favored  : 85.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.25), residues: 1164
  helix:  1.61 (0.19), residues: 765
  sheet:  0.31 (0.82), residues: 33
  loop : -1.86 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 538 
 TYR   0.012   0.001   TYR A 310 
 PHE   0.013   0.001   PHE A 200 
 TRP   0.012   0.001   TRP A1108 
 HIS   0.010   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 9686)
  covalent geometry    : angle       0.53336 (12984)
  hydrogen bonds       : bond        0.05259 (  567)
  hydrogen bonds       : angle       4.04276 ( 1677)

*********************** 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: 12
    poor density    : 119
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 LYS cc_start: 0.8545 (ptmt) cc_final: 0.7871 (ttmt)
REVERT: A  413 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7187 (tt)
REVERT: A  450 MET cc_start: 0.6190 (ptp) cc_final: 0.5845 (tmm)
REVERT: A  468 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7714 (tm-30)
REVERT: A  490 TYR cc_start: 0.6967 (t80) cc_final: 0.6263 (t80)
REVERT: A  799 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8029 (mp10)
REVERT: A  904 PHE cc_start: 0.7573 (t80) cc_final: 0.7257 (t80)
REVERT: A  916 PHE cc_start: 0.8267 (m-80) cc_final: 0.7933 (m-80)
REVERT: A 1064 GLN cc_start: 0.6553 (tp-100) cc_final: 0.6037 (tp40)
  outliers start: 12
  outliers final: 5
  residues processed: 126
  average time/residue: 0.0814
  time to fit residues: 15.2417
Evaluate side-chains
  113 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
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  417 VAL
Chi-restraints excluded: chain A residue  551 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 49 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 55 optimal weight:    0.4980
   chunk 12 optimal weight:    5.9990
   chunk 108 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 113 optimal weight:    0.7980
   chunk 71 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 41 optimal weight:    5.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4110 r_free = 0.4110 target = 0.175497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.119705 restraints weight = 13254.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.117513 restraints weight = 14823.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.118400 restraints weight = 15010.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.119109 restraints weight = 8046.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.121406 restraints weight = 6728.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9686  Z= 0.127
  Angle     :  0.516   7.451  12984  Z= 0.268
  Chirality :  0.039   0.149   1460
  Planarity :  0.003   0.032   1590
  Dihedral  :  8.002  82.588   1615
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 14.04 %
    Favored  : 84.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.25), residues: 1164
  helix:  1.64 (0.19), residues: 766
  sheet:  0.37 (0.80), residues: 32
  loop : -1.82 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1250 
 TYR   0.014   0.001   TYR A 310 
 PHE   0.015   0.001   PHE A 465 
 TRP   0.010   0.001   TRP A1108 
 HIS   0.008   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 9686)
  covalent geometry    : angle       0.51589 (12984)
  hydrogen bonds       : bond        0.04980 (  567)
  hydrogen bonds       : angle       3.92762 ( 1677)

*********************** 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
  137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  450 MET cc_start: 0.6164 (ptp) cc_final: 0.5605 (tmm)
REVERT: A  468 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7641 (tp30)
REVERT: A  490 TYR cc_start: 0.7052 (t80) cc_final: 0.6362 (t80)
REVERT: A  879 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8420 (mp)
REVERT: A  891 GLU cc_start: 0.7868 (pp20) cc_final: 0.7470 (pp20)
REVERT: A  904 PHE cc_start: 0.7742 (t80) cc_final: 0.7445 (t80)
REVERT: A  916 PHE cc_start: 0.8298 (m-80) cc_final: 0.8014 (m-80)
REVERT: A 1064 GLN cc_start: 0.6430 (tp-100) cc_final: 0.5986 (tp40)
  outliers start: 16
  outliers final: 7
  residues processed: 132
  average time/residue: 0.0882
  time to fit residues: 17.0975
Evaluate side-chains
  110 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 102
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
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  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  879 LEU
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 63 optimal weight:    0.0970
   chunk 106 optimal weight:    2.9990
   chunk 116 optimal weight:   20.0000
   chunk 73 optimal weight:    0.5980
   chunk 100 optimal weight:    1.9990
   chunk 56 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   chunk 58 optimal weight:   30.0000
   chunk 60 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   overall best weight:    1.3382

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.179857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.126644 restraints weight = 13243.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.124024 restraints weight = 22662.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.125860 restraints weight = 21673.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.126385 restraints weight = 11428.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.127247 restraints weight = 9749.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.2969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9686  Z= 0.163
  Angle     :  0.550   7.881  12984  Z= 0.285
  Chirality :  0.040   0.147   1460
  Planarity :  0.003   0.041   1590
  Dihedral  :  8.242  80.772   1615
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 14.34 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.25), residues: 1164
  helix:  1.50 (0.19), residues: 769
  sheet:  0.37 (0.79), residues: 32
  loop : -1.84 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 464 
 TYR   0.016   0.001   TYR A 310 
 PHE   0.015   0.001   PHE A 200 
 TRP   0.011   0.001   TRP A1108 
 HIS   0.010   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 9686)
  covalent geometry    : angle       0.54995 (12984)
  hydrogen bonds       : bond        0.05213 (  567)
  hydrogen bonds       : angle       3.97268 ( 1677)

*********************** 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
  126 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  450 MET cc_start: 0.6102 (ptp) cc_final: 0.5789 (tmm)
REVERT: A  490 TYR cc_start: 0.6990 (t80) cc_final: 0.6292 (t80)
REVERT: A  799 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8123 (mp10)
REVERT: A  879 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8388 (mp)
REVERT: A  891 GLU cc_start: 0.7866 (pp20) cc_final: 0.7465 (pp20)
REVERT: A  916 PHE cc_start: 0.8238 (m-80) cc_final: 0.8021 (m-80)
  outliers start: 18
  outliers final: 12
  residues processed: 123
  average time/residue: 0.0817
  time to fit residues: 15.3071
Evaluate side-chains
  115 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
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  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 1226 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 91 optimal weight:    0.2980
   chunk 84 optimal weight:    2.9990
   chunk 76 optimal weight:    0.4980
   chunk 17 optimal weight:    0.7980
   chunk 54 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9980
   chunk 86 optimal weight:    0.5980
   chunk 100 optimal weight:    0.7980
   chunk 52 optimal weight:    5.9990
   chunk 37 optimal weight:    9.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A1064 GLN
A1257 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.181491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.129372 restraints weight = 13277.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.127457 restraints weight = 20914.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.128957 restraints weight = 17316.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.128989 restraints weight = 10763.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.129602 restraints weight = 9851.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9686  Z= 0.120
  Angle     :  0.542  13.904  12984  Z= 0.275
  Chirality :  0.039   0.157   1460
  Planarity :  0.003   0.041   1590
  Dihedral  :  7.815  81.257   1615
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 14.55 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.25), residues: 1164
  helix:  1.60 (0.19), residues: 766
  sheet:  0.14 (0.74), residues: 33
  loop : -1.86 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1250 
 TYR   0.012   0.001   TYR A 310 
 PHE   0.015   0.001   PHE A 465 
 TRP   0.012   0.001   TRP A1108 
 HIS   0.013   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 9686)
  covalent geometry    : angle       0.54151 (12984)
  hydrogen bonds       : bond        0.04757 (  567)
  hydrogen bonds       : angle       3.83166 ( 1677)

*********************** 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: 18
    poor density    : 114
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  450 MET cc_start: 0.5989 (ptp) cc_final: 0.5753 (tmm)
REVERT: A  468 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7476 (tp30)
REVERT: A  490 TYR cc_start: 0.6907 (t80) cc_final: 0.6291 (t80)
REVERT: A  799 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7993 (mp10)
REVERT: A  879 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8503 (mp)
REVERT: A  891 GLU cc_start: 0.7821 (pp20) cc_final: 0.7416 (pp20)
REVERT: A  916 PHE cc_start: 0.8113 (m-80) cc_final: 0.7892 (m-80)
  outliers start: 18
  outliers final: 10
  residues processed: 128
  average time/residue: 0.0756
  time to fit residues: 14.6697
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  : 0.350 
-------------------------------------------------------------------------------
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 1226 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 110 optimal weight:   10.0000
   chunk 99 optimal weight:    6.9990
   chunk 40 optimal weight:    0.2980
   chunk 48 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 53 optimal weight:   10.0000
   chunk 70 optimal weight:    0.9990
   chunk 94 optimal weight:    0.5980
   chunk 39 optimal weight:    6.9990
   chunk 83 optimal weight:    4.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
A 456 GLN
A1064 GLN
A1257 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.181090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.124889 restraints weight = 13276.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.122372 restraints weight = 16970.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.123538 restraints weight = 13092.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.126342 restraints weight = 8509.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.126203 restraints weight = 6548.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.3287

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= 0.119
  Angle     :  0.529   8.997  12984  Z= 0.269
  Chirality :  0.040   0.167   1460
  Planarity :  0.003   0.036   1590
  Dihedral  :  7.609  80.450   1615
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 15.27 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.25), residues: 1164
  helix:  1.67 (0.19), residues: 767
  sheet: -0.00 (0.76), residues: 33
  loop : -1.87 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 464 
 TYR   0.014   0.001   TYR A 310 
 PHE   0.032   0.001   PHE A 904 
 TRP   0.016   0.001   TRP A1108 
 HIS   0.008   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9686)
  covalent geometry    : angle       0.52863 (12984)
  hydrogen bonds       : bond        0.04635 (  567)
  hydrogen bonds       : angle       3.80625 ( 1677)

*********************** 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
  130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  450 MET cc_start: 0.6043 (ptp) cc_final: 0.5588 (tmm)
REVERT: A  468 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7555 (tp30)
REVERT: A  490 TYR cc_start: 0.7017 (t80) cc_final: 0.6355 (t80)
REVERT: A  799 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8077 (mp10)
REVERT: A  879 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8417 (mp)
REVERT: A  891 GLU cc_start: 0.7911 (pp20) cc_final: 0.7463 (pp20)
REVERT: A 1084 GLU cc_start: 0.8339 (tp30) cc_final: 0.8085 (tp30)
  outliers start: 18
  outliers final: 12
  residues processed: 126
  average time/residue: 0.0818
  time to fit residues: 15.4656
Evaluate side-chains
  122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 ASN
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 43 optimal weight:    0.1980
   chunk 115 optimal weight:   40.0000
   chunk 103 optimal weight:    8.9990
   chunk 13 optimal weight:    4.9990
   chunk 52 optimal weight:    7.9990
   chunk 63 optimal weight:    0.0980
   chunk 40 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A1064 GLN
A1257 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.179967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.127628 restraints weight = 12919.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.125185 restraints weight = 20132.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.127142 restraints weight = 18185.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.127094 restraints weight = 10349.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.128188 restraints weight = 9069.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.3403

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= 0.141
  Angle     :  0.568  13.846  12984  Z= 0.282
  Chirality :  0.041   0.213   1460
  Planarity :  0.003   0.037   1590
  Dihedral  :  7.716  79.534   1615
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 15.79 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.25), residues: 1164
  helix:  1.67 (0.19), residues: 765
  sheet: -0.02 (0.81), residues: 33
  loop : -1.86 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 464 
 TYR   0.016   0.001   TYR A 310 
 PHE   0.028   0.002   PHE A 916 
 TRP   0.019   0.001   TRP A1108 
 HIS   0.009   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 9686)
  covalent geometry    : angle       0.56765 (12984)
  hydrogen bonds       : bond        0.04744 (  567)
  hydrogen bonds       : angle       3.88536 ( 1677)

*********************** 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
  117 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  450 MET cc_start: 0.5988 (ptp) cc_final: 0.5752 (tmm)
REVERT: A  468 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7503 (tp30)
REVERT: A  796 MET cc_start: 0.8420 (mtt) cc_final: 0.7943 (mtt)
REVERT: A  799 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7954 (mp10)
REVERT: A  879 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8449 (mp)
REVERT: A  891 GLU cc_start: 0.7842 (pp20) cc_final: 0.7443 (pp20)
REVERT: A 1084 GLU cc_start: 0.7980 (tp30) cc_final: 0.7635 (tp30)
REVERT: A 1201 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6535 (mm-30)
  outliers start: 14
  outliers final: 11
  residues processed: 114
  average time/residue: 0.0777
  time to fit residues: 13.6034
Evaluate side-chains
  113 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
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  810 THR
Chi-restraints excluded: chain A residue  831 SER
Chi-restraints excluded: chain A residue  879 LEU
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 74 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   chunk 92 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 106 optimal weight:    8.9990
   chunk 68 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 4 optimal weight:    0.4980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 456 GLN
A1064 GLN
A1257 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.180968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.128014 restraints weight = 13298.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.125386 restraints weight = 19753.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.127148 restraints weight = 19502.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.127570 restraints weight = 10849.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.128283 restraints weight = 9518.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.3488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9686  Z= 0.125
  Angle     :  0.554  11.998  12984  Z= 0.278
  Chirality :  0.040   0.190   1460
  Planarity :  0.003   0.037   1590
  Dihedral  :  7.603  79.215   1615
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 15.38 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.25), residues: 1164
  helix:  1.71 (0.19), residues: 765
  sheet: -0.07 (0.82), residues: 33
  loop : -1.85 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 464 
 TYR   0.014   0.001   TYR A 310 
 PHE   0.022   0.001   PHE A 904 
 TRP   0.018   0.001   TRP A1108 
 HIS   0.008   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 9686)
  covalent geometry    : angle       0.55392 (12984)
  hydrogen bonds       : bond        0.04591 (  567)
  hydrogen bonds       : angle       3.83991 ( 1677)

*********************** 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
  124 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 PHE cc_start: 0.7232 (p90) cc_final: 0.7021 (p90)
REVERT: A  450 MET cc_start: 0.5990 (ptp) cc_final: 0.5741 (tmm)
REVERT: A  468 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7582 (tp30)
REVERT: A  799 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7955 (mp10)
REVERT: A  879 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8400 (mp)
REVERT: A  891 GLU cc_start: 0.7890 (pp20) cc_final: 0.7476 (pp20)
REVERT: A 1201 GLU cc_start: 0.6963 (mm-30) cc_final: 0.6589 (mm-30)
  outliers start: 16
  outliers final: 12
  residues processed: 121
  average time/residue: 0.0839
  time to fit residues: 15.4174
Evaluate side-chains
  116 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 ASN
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 106 optimal weight:    7.9990
   chunk 50 optimal weight:    0.0770
   chunk 57 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9990
   chunk 98 optimal weight:    5.9990
   chunk 85 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 87 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.7142

-------------------------------------------------------------------------------
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 = 0.4190 r_free = 0.4190 target = 0.181741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.128997 restraints weight = 13193.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.126504 restraints weight = 21434.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.128207 restraints weight = 19817.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.128458 restraints weight = 11345.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.129086 restraints weight = 10038.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.3595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9686  Z= 0.124
  Angle     :  0.550   8.418  12984  Z= 0.279
  Chirality :  0.040   0.185   1460
  Planarity :  0.003   0.037   1590
  Dihedral  :  7.524  78.652   1615
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 15.58 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.25), residues: 1164
  helix:  1.74 (0.19), residues: 765
  sheet: -0.11 (0.82), residues: 33
  loop : -1.82 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 464 
 TYR   0.014   0.001   TYR A 310 
 PHE   0.031   0.001   PHE A 938 
 TRP   0.022   0.001   TRP A1108 
 HIS   0.010   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 9686)
  covalent geometry    : angle       0.55041 (12984)
  hydrogen bonds       : bond        0.04561 (  567)
  hydrogen bonds       : angle       3.83622 ( 1677)

********************** 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
  119 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 PHE cc_start: 0.7246 (p90) cc_final: 0.7031 (p90)
REVERT: A  450 MET cc_start: 0.5980 (ptp) cc_final: 0.5747 (tmm)
REVERT: A  796 MET cc_start: 0.8373 (mtt) cc_final: 0.7872 (mtt)
REVERT: A  799 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7941 (mp10)
REVERT: A  879 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8471 (mp)
REVERT: A  891 GLU cc_start: 0.7903 (pp20) cc_final: 0.7490 (pp20)
REVERT: A 1201 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6569 (mm-30)
  outliers start: 14
  outliers final: 11
  residues processed: 116
  average time/residue: 0.0792
  time to fit residues: 13.8537
Evaluate side-chains
  115 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 ASN
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 1226 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 97 optimal weight:   10.0000
   chunk 61 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 40 optimal weight:    0.3980
   chunk 81 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   chunk 100 optimal weight:    0.0060
   overall best weight:    0.5796

-------------------------------------------------------------------------------
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 = 0.4201 r_free = 0.4201 target = 0.181848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.130095 restraints weight = 12826.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.127460 restraints weight = 18495.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.129051 restraints weight = 17624.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.129252 restraints weight = 10655.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.129756 restraints weight = 9439.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.3669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   9686  Z= 0.119
  Angle     :  0.560  14.440  12984  Z= 0.283
  Chirality :  0.040   0.184   1460
  Planarity :  0.003   0.037   1590
  Dihedral  :  7.347  78.313   1615
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 15.79 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.25), residues: 1164
  helix:  1.77 (0.19), residues: 765
  sheet: -0.16 (0.81), residues: 33
  loop : -1.81 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 464 
 TYR   0.013   0.001   TYR A 310 
 PHE   0.030   0.001   PHE A 938 
 TRP   0.019   0.001   TRP A1108 
 HIS   0.012   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 9686)
  covalent geometry    : angle       0.56012 (12984)
  hydrogen bonds       : bond        0.04461 (  567)
  hydrogen bonds       : angle       3.80651 ( 1677)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1528.33 seconds
wall clock time: 27 minutes 10.57 seconds (1630.57 seconds total)