Starting phenix.real_space_refine
on Wed Mar  4 00:47:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d49_27178/03_2026/8d49_27178.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d49_27178/03_2026/8d49_27178.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d49_27178/03_2026/8d49_27178.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d49_27178/03_2026/8d49_27178.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d49_27178/03_2026/8d49_27178.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d49_27178/03_2026/8d49_27178.cif"
  }
  resolution = 3.2
  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=   0.018
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: 5
    Type Number    sf(0)   Gaussians
     P      25      5.49       5
     S      24      5.16       5
     C    5812      2.51       5
     N    1568      2.21       5
     O    1852      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 87 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9281
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8748
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1072, 8748
          Classifications: {'peptide': 1072}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 27, 'TRANS': 1044}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 533
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 533
          Classifications: {'RNA': 26}
          Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 5, 'rna3p_pyr': 14}
          Link IDs: {'rna2p': 6, 'rna3p': 19}
          Chain breaks: 1
  Time building chain proxies: 1.95, per 1000 atoms: 0.21
  Number of scatterers: 9281
  At special positions: 0
  Unit cell: (86.48, 96.82, 125.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      24     16.00
     P      25     15.00
     O    1852      8.00
     N    1568      7.00
     C    5812      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: 0.76
  Conformation dependent library (CDL) restraints added in 439.4 milliseconds
  

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2046

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 10 sheets defined
      55.8% alpha, 11.8% beta
      4 base pairs and 16 stacking pairs defined.
    Time for finding SS restraints: 1.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 49
      removed outlier: 3.703A  pdb=" N   SER A  47 " --> pdb=" O   GLU A  43 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   SER A  48 " --> pdb=" O   ASN A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 79
    Processing helix  chain 'A' and resid 92 through 102
    Processing helix  chain 'A' and resid 117 through 119
      No H-bonds generated for 'chain 'A' and resid 117 through 119'
    Processing helix  chain 'A' and resid 128 through 163
      removed outlier: 3.601A  pdb=" N   ILE A 132 " --> pdb=" O   LEU A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 197
      removed outlier: 4.066A  pdb=" N   ILE A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
      Proline residue:  A 193  - end of helix
    Processing helix  chain 'A' and resid 201 through 205
      removed outlier: 4.619A  pdb=" N   SER A 205 " --> pdb=" O   PRO A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 220
      removed outlier: 3.961A  pdb=" N   ILE A 216 " --> pdb=" O   GLU A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 239
    Processing helix  chain 'A' and resid 263 through 274
    Processing helix  chain 'A' and resid 275 through 284
      removed outlier: 3.530A  pdb=" N   LEU A 279 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 297
    Processing helix  chain 'A' and resid 299 through 305
    Processing helix  chain 'A' and resid 310 through 319
    Processing helix  chain 'A' and resid 324 through 340
      removed outlier: 4.386A  pdb=" N   HIS A 329 " --> pdb=" O   PHE A 325 " (cutoff:3.500A)
      removed outlier: 5.175A  pdb=" N   GLN A 330 " --> pdb=" O   LEU A 326 " (cutoff:3.500A)
      Proline residue:  A 338  - end of helix
    Processing helix  chain 'A' and resid 342 through 352
      removed outlier: 3.910A  pdb=" N   VAL A 349 " --> pdb=" O   ALA A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 366
    Processing helix  chain 'A' and resid 376 through 392
      removed outlier: 3.698A  pdb=" N   LEU A 392 " --> pdb=" O   LEU A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 412
      removed outlier: 4.276A  pdb=" N   CYS A 403 " --> pdb=" O   PRO A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 417
    Processing helix  chain 'A' and resid 418 through 438
      removed outlier: 3.674A  pdb=" N   VAL A 436 " --> pdb=" O   LYS A 432 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LEU A 437 " --> pdb=" O   ASN A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 443
      removed outlier: 4.134A  pdb=" N   LEU A 443 " --> pdb=" O   LYS A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 461
      removed outlier: 3.766A  pdb=" N   PHE A 450 " --> pdb=" O   ASN A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 481
    Processing helix  chain 'A' and resid 488 through 503
    Processing helix  chain 'A' and resid 504 through 506
      No H-bonds generated for 'chain 'A' and resid 504 through 506'
    Processing helix  chain 'A' and resid 531 through 559
      removed outlier: 3.762A  pdb=" N   GLN A 539 " --> pdb=" O   ASN A 535 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   PHE A 548 " --> pdb=" O   TYR A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 597
    Processing helix  chain 'A' and resid 716 through 727
    Processing helix  chain 'A' and resid 747 through 757
      removed outlier: 3.719A  pdb=" N   PHE A 757 " --> pdb=" O   TRP A 753 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 808 through 818
    Processing helix  chain 'A' and resid 818 through 839
      removed outlier: 3.825A  pdb=" N   GLN A 822 " --> pdb=" O   ASP A 818 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   ASP A 839 " --> pdb=" O   HIS A 835 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 882 through 886
      removed outlier: 3.727A  pdb=" N   SER A 886 " --> pdb=" O   ARG A 883 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 920 through 922
      No H-bonds generated for 'chain 'A' and resid 920 through 922'
    Processing helix  chain 'A' and resid 939 through 961
      removed outlier: 3.535A  pdb=" N   THR A 960 " --> pdb=" O   HIS A 956 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 961 through 967
    Processing helix  chain 'A' and resid 968 through 970
      No H-bonds generated for 'chain 'A' and resid 968 through 970'
    Processing helix  chain 'A' and resid 974 through 986
      removed outlier: 3.829A  pdb=" N   GLY A 984 " --> pdb=" O   LYS A 980 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   LEU A 985 " --> pdb=" O   ARG A 981 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 999 through 1016
      removed outlier: 3.811A  pdb=" N   ASP A1009 " --> pdb=" O   GLU A1005 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1019 through 1028
      removed outlier: 3.969A  pdb=" N   ILE A1026 " --> pdb=" O   GLU A1022 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1030 through 1034
      removed outlier: 4.376A  pdb=" N   ASN A1034 " --> pdb=" O   ALA A1031 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1035 through 1054
      removed outlier: 3.924A  pdb=" N   ALA A1041 " --> pdb=" O   GLN A1037 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ASN A1042 " --> pdb=" O   GLY A1038 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1065 through 1070
    Processing helix  chain 'A' and resid 1090 through 1096
    Processing helix  chain 'A' and resid 1102 through 1119
      removed outlier: 3.778A  pdb=" N   LYS A1119 " --> pdb=" O   LYS A1115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1139 through 1144
    Processing helix  chain 'A' and resid 1213 through 1232
      removed outlier: 4.256A  pdb=" N   ALA A1217 " --> pdb=" O   ASP A1213 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LYS A1232 " --> pdb=" O   LEU A1228 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 14
    Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18
      removed outlier: 6.617A  pdb=" N   LYS A 248 " --> pdb=" O   HIS A 566 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   GLY A 568 " --> pdb=" O   LYS A 248 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   THR A 250 " --> pdb=" O   GLY A 568 " (cutoff:3.500A)
      removed outlier: 8.121A  pdb=" N   ILE A 570 " --> pdb=" O   THR A 250 " (cutoff:3.500A)
      removed outlier: 16.277A  pdb=" N   HIS A 566 " --> pdb=" O   SER A 613 " (cutoff:3.500A)
      removed outlier: 13.920A  pdb=" N   SER A 613 " --> pdb=" O   HIS A 566 " (cutoff:3.500A)
      removed outlier: 9.122A  pdb=" N   GLY A 568 " --> pdb=" O   VAL A 611 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   VAL A 611 " --> pdb=" O   GLY A 568 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 17 through 18
      removed outlier: 6.617A  pdb=" N   LYS A 248 " --> pdb=" O   HIS A 566 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   GLY A 568 " --> pdb=" O   LYS A 248 " (cutoff:3.500A)
      removed outlier: 6.002A  pdb=" N   THR A 250 " --> pdb=" O   GLY A 568 " (cutoff:3.500A)
      removed outlier: 8.121A  pdb=" N   ILE A 570 " --> pdb=" O   THR A 250 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 115
    Processing sheet with id=AA5, first strand: chain 'A' and resid 122 through 123
    Processing sheet with id=AA6, first strand: chain 'A' and resid 866 through 867
      removed outlier: 4.462A  pdb=" N   VAL A 859 " --> pdb=" O   LEU A 867 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 866 through 867
      removed outlier: 4.462A  pdb=" N   VAL A 859 " --> pdb=" O   LEU A 867 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   GLU A1063 " --> pdb=" O   ILE A 847 " (cutoff:3.500A)
      removed outlier: 8.516A  pdb=" N   HIS A1159 " --> pdb=" O   ALA A1058 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   ILE A1060 " --> pdb=" O   HIS A1159 " (cutoff:3.500A)
      removed outlier: 7.466A  pdb=" N   ILE A1161 " --> pdb=" O   ILE A1060 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   LEU A1062 " --> pdb=" O   ILE A1161 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 891 through 896
      removed outlier: 5.702A  pdb=" N   GLN A 892 " --> pdb=" O   LYS A 874 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   LYS A 874 " --> pdb=" O   GLN A 892 " (cutoff:3.500A)
      removed outlier: 8.797A  pdb=" N   GLU A 871 " --> pdb=" O   LYS A 914 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   LEU A 916 " --> pdb=" O   GLU A 871 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 877 through 878
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1120 through 1121

    467 hydrogen bonds defined for protein.
    1326 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      9 hydrogen bonds
      18 hydrogen bond angles
      0 basepair planarities
      4 basepair parallelities
      16 stacking parallelities
  Total time for adding SS restraints: 1.83

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1531
        1.31 -     1.44: 2613
        1.44 -     1.56: 5277
        1.56 -     1.68: 49
        1.68 -     1.81: 35
  Bond restraints: 9505
  Sorted by residual:
  bond pdb=" C   THR A 244 "
       pdb=" O   THR A 244 "
    ideal  model  delta    sigma   weight residual
    1.242  1.203  0.039 9.70e-03 1.06e+04 1.63e+01
  bond pdb=" C   TYR A 579 "
       pdb=" O   TYR A 579 "
    ideal  model  delta    sigma   weight residual
    1.234  1.187  0.047 1.28e-02 6.10e+03 1.35e+01
  bond pdb=" N   VAL A 593 "
       pdb=" CA  VAL A 593 "
    ideal  model  delta    sigma   weight residual
    1.461  1.500 -0.039 1.17e-02 7.31e+03 1.12e+01
  bond pdb=" C   PRO A 245 "
       pdb=" O   PRO A 245 "
    ideal  model  delta    sigma   weight residual
    1.235  1.197  0.038 1.30e-02 5.92e+03 8.64e+00
  bond pdb=" CA  GLY A 242 "
       pdb=" C   GLY A 242 "
    ideal  model  delta    sigma   weight residual
    1.512  1.488  0.024 8.70e-03 1.32e+04 7.66e+00
  ... (remaining 9500 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.75: 12720
        2.75 -     5.50: 169
        5.50 -     8.25: 13
        8.25 -    11.00: 3
       11.00 -    13.74: 2
  Bond angle restraints: 12907
  Sorted by residual:
  angle pdb=" C   THR A 244 "
        pdb=" CA  THR A 244 "
        pdb=" CB  THR A 244 "
      ideal   model   delta    sigma   weight residual
     111.01  100.12   10.89 1.38e+00 5.25e-01 6.22e+01
  angle pdb=" C   ASP A 601 "
        pdb=" CA  ASP A 601 "
        pdb=" CB  ASP A 601 "
      ideal   model   delta    sigma   weight residual
     114.40  105.14    9.26 1.25e+00 6.40e-01 5.49e+01
  angle pdb=" C   ASN A 240 "
        pdb=" CA  ASN A 240 "
        pdb=" CB  ASN A 240 "
      ideal   model   delta    sigma   weight residual
     112.44  100.27   12.17 1.72e+00 3.38e-01 5.01e+01
  angle pdb=" N   PRO A 245 "
        pdb=" CA  PRO A 245 "
        pdb=" CB  PRO A 245 "
      ideal   model   delta    sigma   weight residual
     103.25   96.75    6.50 1.05e+00 9.07e-01 3.83e+01
  angle pdb=" C   GLY A 241 "
        pdb=" N   GLY A 242 "
        pdb=" CA  GLY A 242 "
      ideal   model   delta    sigma   weight residual
     121.65  117.70    3.95 6.80e-01 2.16e+00 3.38e+01
  ... (remaining 12902 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.56: 5577
       30.56 -    61.12: 219
       61.12 -    91.67: 30
       91.67 -   122.23: 1
      122.23 -   152.79: 2
  Dihedral angle restraints: 5829
    sinusoidal: 2664
      harmonic: 3165
  Sorted by residual:
  dihedral pdb=" O4'   U B  14 "
           pdb=" C1'   U B  14 "
           pdb=" N1    U B  14 "
           pdb=" C2    U B  14 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   47.21  152.79     1      1.50e+01 4.44e-03 8.06e+01
  dihedral pdb=" O4'   C B  22 "
           pdb=" C1'   C B  22 "
           pdb=" N1    C B  22 "
           pdb=" C2    C B  22 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00    6.39 -134.39     1      1.70e+01 3.46e-03 5.65e+01
  dihedral pdb=" CA  PHE A 325 "
           pdb=" C   PHE A 325 "
           pdb=" N   LEU A 326 "
           pdb=" CA  LEU A 326 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.63  -30.37     0      5.00e+00 4.00e-02 3.69e+01
  ... (remaining 5826 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1138
       0.059 -    0.119: 257
       0.119 -    0.178: 26
       0.178 -    0.237: 9
       0.237 -    0.296: 3
  Chirality restraints: 1433
  Sorted by residual:
  chirality pdb=" CA  LYS A 874 "
            pdb=" N   LYS A 874 "
            pdb=" C   LYS A 874 "
            pdb=" CB  LYS A 874 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.19e+00
  chirality pdb=" CA  THR A 244 "
            pdb=" N   THR A 244 "
            pdb=" C   THR A 244 "
            pdb=" CB  THR A 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.78   -0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" P     U B  33 "
            pdb=" OP1   U B  33 "
            pdb=" OP2   U B  33 "
            pdb=" O5'   U B  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.65   -0.24 2.00e-01 2.50e+01 1.48e+00
  ... (remaining 1430 not shown)

  Planarity restraints: 1570
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 337 "   -0.084 5.00e-02 4.00e+02   1.25e-01 2.50e+01
        pdb=" N   PRO A 338 "    0.216 5.00e-02 4.00e+02
        pdb=" CA  PRO A 338 "   -0.064 5.00e-02 4.00e+02
        pdb=" CD  PRO A 338 "   -0.068 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 325 "   -0.026 2.00e-02 2.50e+03   1.84e-02 5.93e+00
        pdb=" CG  PHE A 325 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 325 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 325 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 325 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 325 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 325 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 596 "    0.010 2.00e-02 2.50e+03   2.09e-02 4.38e+00
        pdb=" C   ILE A 596 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   ILE A 596 "    0.013 2.00e-02 2.50e+03
        pdb=" N   LEU A 597 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1567 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 133
        2.66 -     3.22: 8728
        3.22 -     3.78: 13891
        3.78 -     4.34: 19659
        4.34 -     4.90: 32565
  Nonbonded interactions: 74976
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 135 "
            pdb=" OE2 GLU A 189 "
     model   vdw
     2.098 3.040
  nonbonded pdb=" OH  TYR A 393 "
            pdb=" OD1 ASP A 426 "
     model   vdw
     2.128 3.040
  nonbonded pdb=" CD1 ILE A  51 "
            pdb=" CG2 THR A 775 "
     model   vdw
     2.201 3.880
  nonbonded pdb=" O   ILE A 986 "
            pdb=" OH  TYR A 995 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OE2 GLU A 841 "
            pdb=" NH1 ARG A 863 "
     model   vdw
     2.225 3.120
  ... (remaining 74971 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.290
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
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      :  0.009   0.061   9505  Z= 0.388
  Angle     :  0.842  13.744  12907  Z= 0.502
  Chirality :  0.052   0.296   1433
  Planarity :  0.005   0.125   1570
  Dihedral  : 16.096 152.791   3783
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.05 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  0.83 %
    Favored  : 98.03 %
  Cbeta Deviations :  0.29 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.25), residues: 1062
  helix:  0.32 (0.21), residues: 545
  sheet: -1.42 (0.43), residues: 136
  loop : -1.12 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 883 
 TYR   0.029   0.002   TYR A 579 
 PHE   0.040   0.003   PHE A 325 
 TRP   0.019   0.002   TRP A  78 
 HIS   0.007   0.002   HIS A 798 

Details of bonding type rmsd
  covalent geometry    : bond        0.00872 ( 9505)
  covalent geometry    : angle       0.84194 (12907)
  hydrogen bonds       : bond        0.14121 (  465)
  hydrogen bonds       : angle       5.93566 ( 1344)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 37
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 11
  outliers final: 1
  residues processed: 47
  average time/residue: 0.1405
  time to fit residues: 8.7445
Evaluate side-chains
  27 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 175 ASN
A 812 GLN
A1141 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.080531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.061928 restraints weight = 24682.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 3.09
r_work: 0.2903 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.1134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9505  Z= 0.163
  Angle     :  0.550  12.527  12907  Z= 0.292
  Chirality :  0.040   0.179   1433
  Planarity :  0.004   0.080   1570
  Dihedral  : 12.871 151.581   1554
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  5.71 %
    Favored  : 94.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.26), residues: 1062
  helix:  1.08 (0.22), residues: 556
  sheet: -1.49 (0.42), residues: 140
  loop : -0.89 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 896 
 TYR   0.009   0.001   TYR A 579 
 PHE   0.033   0.001   PHE A 325 
 TRP   0.010   0.001   TRP A 480 
 HIS   0.003   0.001   HIS A 798 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 9505)
  covalent geometry    : angle       0.55003 (12907)
  hydrogen bonds       : bond        0.04818 (  465)
  hydrogen bonds       : angle       4.50965 ( 1344)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 31
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 33
  average time/residue: 0.1000
  time to fit residues: 4.9740
Evaluate side-chains
  23 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 21
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  871 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 90 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 75 optimal weight:    5.9990
   chunk 95 optimal weight:    0.2980
   chunk 77 optimal weight:    0.9980
   chunk 44 optimal weight:    7.9990
   chunk 9 optimal weight:    0.5980
   chunk 26 optimal weight:    3.9990
   chunk 100 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A1118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.079429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.060654 restraints weight = 24715.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 3.15
r_work: 0.2898 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.1625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9505  Z= 0.156
  Angle     :  0.493  11.922  12907  Z= 0.259
  Chirality :  0.038   0.156   1433
  Planarity :  0.004   0.062   1570
  Dihedral  : 12.749 148.276   1554
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  6.74 %
    Favored  : 92.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.26), residues: 1062
  helix:  1.58 (0.22), residues: 556
  sheet: -1.38 (0.42), residues: 140
  loop : -0.74 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 896 
 TYR   0.011   0.001   TYR A 490 
 PHE   0.025   0.001   PHE A 325 
 TRP   0.015   0.001   TRP A 480 
 HIS   0.003   0.001   HIS A 798 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 9505)
  covalent geometry    : angle       0.49342 (12907)
  hydrogen bonds       : bond        0.04095 (  465)
  hydrogen bonds       : angle       4.09696 ( 1344)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 23
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: A  386 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7423 (mp0)
  outliers start: 8
  outliers final: 2
  residues processed: 31
  average time/residue: 0.1051
  time to fit residues: 4.9074
Evaluate side-chains
  24 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  386 GLU
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  906 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 57 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9990
   chunk 93 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A1118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.078777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.060060 restraints weight = 24931.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 3.17
r_work: 0.2885 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9505  Z= 0.187
  Angle     :  0.502  12.384  12907  Z= 0.262
  Chirality :  0.039   0.162   1433
  Planarity :  0.003   0.054   1570
  Dihedral  : 12.672 148.602   1553
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  8.20 %
    Favored  : 91.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.27), residues: 1062
  helix:  1.72 (0.22), residues: 557
  sheet: -1.17 (0.43), residues: 140
  loop : -0.72 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 896 
 TYR   0.011   0.001   TYR A 544 
 PHE   0.039   0.001   PHE A 325 
 TRP   0.012   0.001   TRP A 480 
 HIS   0.004   0.001   HIS A 798 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 9505)
  covalent geometry    : angle       0.50235 (12907)
  hydrogen bonds       : bond        0.04095 (  465)
  hydrogen bonds       : angle       4.06298 ( 1344)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
REVERT: A  386 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7373 (mp0)
  outliers start: 5
  outliers final: 2
  residues processed: 27
  average time/residue: 0.0891
  time to fit residues: 3.9530
Evaluate side-chains
  23 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 20
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  386 GLU
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain A residue  906 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 99 optimal weight:    0.0980
   chunk 46 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.8186

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

Flipped N/Q/H residues before XYZ refinement:
A1118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.080501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.061867 restraints weight = 24734.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 3.19
r_work: 0.2908 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9505  Z= 0.120
  Angle     :  0.459  10.899  12907  Z= 0.239
  Chirality :  0.037   0.154   1433
  Planarity :  0.003   0.049   1570
  Dihedral  : 12.617 147.818   1553
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  9.13 %
    Favored  : 90.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.27), residues: 1062
  helix:  1.90 (0.22), residues: 557
  sheet: -1.13 (0.45), residues: 137
  loop : -0.59 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 896 
 TYR   0.009   0.001   TYR A 544 
 PHE   0.026   0.001   PHE A 325 
 TRP   0.011   0.001   TRP A 480 
 HIS   0.002   0.000   HIS A 798 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9505)
  covalent geometry    : angle       0.45927 (12907)
  hydrogen bonds       : bond        0.03720 (  465)
  hydrogen bonds       : angle       3.85597 ( 1344)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 27
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 GLU cc_start: 0.9060 (tt0) cc_final: 0.8789 (pp20)
REVERT: A  386 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7318 (mp0)
  outliers start: 5
  outliers final: 2
  residues processed: 31
  average time/residue: 0.0904
  time to fit residues: 4.5046
Evaluate side-chains
  28 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  386 GLU
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue 1220 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0980
   chunk 65 optimal weight:    0.2980
   chunk 84 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 68 optimal weight:    6.9990
   chunk 51 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
A1118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.080936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.062617 restraints weight = 24750.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 3.16
r_work: 0.2932 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.2200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9505  Z= 0.101
  Angle     :  0.442   9.411  12907  Z= 0.230
  Chirality :  0.037   0.149   1433
  Planarity :  0.003   0.046   1570
  Dihedral  : 12.537 147.391   1553
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  9.13 %
    Favored  : 90.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.27), residues: 1062
  helix:  2.05 (0.22), residues: 558
  sheet: -1.03 (0.45), residues: 137
  loop : -0.54 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 896 
 TYR   0.009   0.001   TYR A 579 
 PHE   0.017   0.001   PHE A 180 
 TRP   0.010   0.001   TRP A 480 
 HIS   0.002   0.000   HIS A 798 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 9505)
  covalent geometry    : angle       0.44166 (12907)
  hydrogen bonds       : bond        0.03456 (  465)
  hydrogen bonds       : angle       3.71005 ( 1344)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 GLU cc_start: 0.9034 (tt0) cc_final: 0.8777 (pp20)
  outliers start: 6
  outliers final: 5
  residues processed: 35
  average time/residue: 0.0950
  time to fit residues: 4.9704
Evaluate side-chains
  28 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 23
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 PHE
Chi-restraints excluded: chain A residue  386 GLU
Chi-restraints excluded: chain A residue  580 LEU
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  906 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 106 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 98 optimal weight:    0.8980
   chunk 70 optimal weight:    4.9990
   chunk 80 optimal weight:    5.9990
   chunk 86 optimal weight:    0.0470
   chunk 96 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    2.5884

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

Flipped N/Q/H residues before XYZ refinement:
A 887 HIS
A1118 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.075474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.055793 restraints weight = 24902.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 3.45
r_work: 0.2722 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.039   9505  Z= 0.299
  Angle     :  0.604  15.033  12907  Z= 0.310
  Chirality :  0.042   0.170   1433
  Planarity :  0.004   0.043   1570
  Dihedral  : 12.572 148.786   1553
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  9.54 %
    Favored  : 89.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.27), residues: 1062
  helix:  1.88 (0.22), residues: 557
  sheet: -1.25 (0.43), residues: 147
  loop : -0.66 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 883 
 TYR   0.015   0.001   TYR A 544 
 PHE   0.029   0.002   PHE A 325 
 TRP   0.014   0.002   TRP A  78 
 HIS   0.005   0.001   HIS A 798 

Details of bonding type rmsd
  covalent geometry    : bond        0.00687 ( 9505)
  covalent geometry    : angle       0.60438 (12907)
  hydrogen bonds       : bond        0.04373 (  465)
  hydrogen bonds       : angle       4.12333 ( 1344)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 22
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 GLU cc_start: 0.8991 (tt0) cc_final: 0.8679 (pp20)
  outliers start: 10
  outliers final: 6
  residues processed: 31
  average time/residue: 0.0623
  time to fit residues: 3.2143
Evaluate side-chains
  26 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 20
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  325 PHE
Chi-restraints excluded: chain A residue  386 GLU
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain A residue  906 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 45 optimal weight:    7.9990
   chunk 69 optimal weight:    7.9990
   chunk 100 optimal weight:    0.6980
   chunk 84 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.077635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.058228 restraints weight = 24463.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.2922 rms_B_bonded: 3.51
r_work: 0.2753 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9505  Z= 0.115
  Angle     :  0.471  10.735  12907  Z= 0.246
  Chirality :  0.038   0.152   1433
  Planarity :  0.003   0.042   1570
  Dihedral  : 12.499 147.231   1553
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 10.06 %
    Favored  : 89.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.27), residues: 1062
  helix:  2.05 (0.22), residues: 558
  sheet: -1.13 (0.45), residues: 137
  loop : -0.57 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 883 
 TYR   0.011   0.001   TYR A 579 
 PHE   0.018   0.001   PHE A 325 
 TRP   0.009   0.001   TRP A 480 
 HIS   0.003   0.000   HIS A 798 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 9505)
  covalent geometry    : angle       0.47136 (12907)
  hydrogen bonds       : bond        0.03622 (  465)
  hydrogen bonds       : angle       3.78111 ( 1344)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 21
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 GLU cc_start: 0.8819 (tt0) cc_final: 0.8441 (pp20)
  outliers start: 6
  outliers final: 6
  residues processed: 26
  average time/residue: 0.0791
  time to fit residues: 3.5302
Evaluate side-chains
  27 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 21
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  325 PHE
Chi-restraints excluded: chain A residue  386 GLU
Chi-restraints excluded: chain A residue  768 GLU
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  906 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 106 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A1118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.077589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.058241 restraints weight = 24397.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.2924 rms_B_bonded: 3.49
r_work: 0.2756 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9505  Z= 0.127
  Angle     :  0.461  10.576  12907  Z= 0.240
  Chirality :  0.038   0.154   1433
  Planarity :  0.003   0.041   1570
  Dihedral  : 12.402 147.183   1553
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 10.17 %
    Favored  : 89.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.27), residues: 1062
  helix:  2.13 (0.22), residues: 557
  sheet: -1.18 (0.43), residues: 147
  loop : -0.52 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1016 
 TYR   0.009   0.001   TYR A 544 
 PHE   0.017   0.001   PHE A 180 
 TRP   0.009   0.001   TRP A 480 
 HIS   0.002   0.000   HIS A 798 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9505)
  covalent geometry    : angle       0.46090 (12907)
  hydrogen bonds       : bond        0.03566 (  465)
  hydrogen bonds       : angle       3.72778 ( 1344)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 GLU cc_start: 0.8815 (tt0) cc_final: 0.8434 (pp20)
  outliers start: 6
  outliers final: 5
  residues processed: 28
  average time/residue: 0.0728
  time to fit residues: 3.4578
Evaluate side-chains
  26 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 21
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  325 PHE
Chi-restraints excluded: chain A residue  386 GLU
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  906 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 104 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 49 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
A1118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.076615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.057141 restraints weight = 24402.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.2923 rms_B_bonded: 3.47
r_work: 0.2757 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.2451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9505  Z= 0.127
  Angle     :  0.455  10.012  12907  Z= 0.238
  Chirality :  0.037   0.153   1433
  Planarity :  0.003   0.042   1570
  Dihedral  : 12.325 147.236   1553
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 10.27 %
    Favored  : 89.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.27), residues: 1062
  helix:  2.18 (0.22), residues: 558
  sheet: -1.15 (0.43), residues: 147
  loop : -0.50 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1016 
 TYR   0.009   0.001   TYR A 544 
 PHE   0.017   0.001   PHE A 180 
 TRP   0.008   0.001   TRP A  78 
 HIS   0.003   0.000   HIS A 798 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9505)
  covalent geometry    : angle       0.45488 (12907)
  hydrogen bonds       : bond        0.03505 (  465)
  hydrogen bonds       : angle       3.69087 ( 1344)

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

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

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2124 Ramachandran restraints generated.
    1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 25
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 GLU cc_start: 0.8827 (tt0) cc_final: 0.8477 (pp20)
  outliers start: 6
  outliers final: 6
  residues processed: 29
  average time/residue: 0.1018
  time to fit residues: 4.4349
Evaluate side-chains
  27 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 21
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  325 PHE
Chi-restraints excluded: chain A residue  386 GLU
Chi-restraints excluded: chain A residue  768 GLU
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  906 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 79 optimal weight:    0.0670
   chunk 64 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   chunk 72 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    1.8124

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

Flipped N/Q/H residues before XYZ refinement:
A1118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.075988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.056657 restraints weight = 24590.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.2931 rms_B_bonded: 3.32
r_work: 0.2764 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   9505  Z= 0.210
  Angle     :  0.520  12.138  12907  Z= 0.270
  Chirality :  0.039   0.163   1433
  Planarity :  0.003   0.042   1570
  Dihedral  : 12.327 148.041   1553
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 10.27 %
    Favored  : 89.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.27), residues: 1062
  helix:  2.10 (0.22), residues: 557
  sheet: -1.23 (0.43), residues: 147
  loop : -0.56 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1016 
 TYR   0.012   0.001   TYR A 544 
 PHE   0.021   0.001   PHE A 325 
 TRP   0.012   0.001   TRP A  78 
 HIS   0.003   0.001   HIS A 798 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 ( 9505)
  covalent geometry    : angle       0.52002 (12907)
  hydrogen bonds       : bond        0.03940 (  465)
  hydrogen bonds       : angle       3.87199 ( 1344)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1748.89 seconds
wall clock time: 30 minutes 53.30 seconds (1853.30 seconds total)