Starting phenix.real_space_refine
on Wed Feb  4 03:46:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lq4_63292/02_2026/9lq4_63292.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lq4_63292/02_2026/9lq4_63292.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lq4_63292/02_2026/9lq4_63292.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lq4_63292/02_2026/9lq4_63292.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lq4_63292/02_2026/9lq4_63292.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lq4_63292/02_2026/9lq4_63292.cif"
  }
  resolution = 4.12
  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=   0.002 sd=   0.029
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: 4
    Type Number    sf(0)   Gaussians
     S      58      5.16       5
     C    5433      2.51       5
     N    1467      2.21       5
     O    1536      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8494
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6748
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 850, 6748
          Classifications: {'peptide': 850}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 820}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 33
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "F"
      Number of atoms: 895
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 895
          Classifications: {'peptide': 106}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 97}
    Chain: "G"
      Number of atoms: 851
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 851
          Classifications: {'peptide': 105}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 8, 'TRANS': 96}
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 29
  Time building chain proxies: 1.72, per 1000 atoms: 0.20
  Number of scatterers: 8494
  At special positions: 0
  Unit cell: (91.3, 122.1, 129.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      58     16.00
     O    1536      8.00
     N    1467      7.00
     C    5433      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: 0.69
  Conformation dependent library (CDL) restraints added in 348.8 milliseconds
  

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2020

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 8 sheets defined
      45.1% alpha, 16.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 146 through 156
      removed outlier: 3.776A  pdb=" N   ARG A 153 " --> pdb=" O   ASP A 149 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   ARG A 156 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 197
      removed outlier: 3.754A  pdb=" N   LEU A 187 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 216
      removed outlier: 3.510A  pdb=" N   SER A 216 " --> pdb=" O   CYS A 212 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 212 through 216'
    Processing helix  chain 'A' and resid 223 through 229
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 4.066A  pdb=" N   ASP A 236 " --> pdb=" O   GLU A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 243
    Processing helix  chain 'A' and resid 244 through 246
      No H-bonds generated for 'chain 'A' and resid 244 through 246'
    Processing helix  chain 'A' and resid 278 through 288
    Processing helix  chain 'A' and resid 302 through 304
      No H-bonds generated for 'chain 'A' and resid 302 through 304'
    Processing helix  chain 'A' and resid 305 through 313
      removed outlier: 4.537A  pdb=" N   LEU A 309 " --> pdb=" O   ALA A 305 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   GLN A 310 " --> pdb=" O   LEU A 306 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LEU A 311 " --> pdb=" O   ARG A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 338
    Processing helix  chain 'A' and resid 339 through 352
    Processing helix  chain 'A' and resid 353 through 359
      removed outlier: 3.534A  pdb=" N   LEU A 359 " --> pdb=" O   ALA A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 379
      removed outlier: 3.556A  pdb=" N   CYS A 366 " --> pdb=" O   ALA A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 388
    Processing helix  chain 'A' and resid 389 through 400
      removed outlier: 3.513A  pdb=" N   LEU A 393 " --> pdb=" O   THR A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 426
    Processing helix  chain 'A' and resid 432 through 438
    Processing helix  chain 'A' and resid 443 through 451
      removed outlier: 4.341A  pdb=" N   LEU A 447 " --> pdb=" O   SER A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 482
    Processing helix  chain 'A' and resid 487 through 491
      removed outlier: 3.502A  pdb=" N   ASP A 491 " --> pdb=" O   GLU A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 504
    Processing helix  chain 'A' and resid 505 through 512
    Processing helix  chain 'A' and resid 515 through 525
    Processing helix  chain 'A' and resid 527 through 539
      removed outlier: 3.990A  pdb=" N   ALA A 531 " --> pdb=" O   ASN A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 553
      removed outlier: 3.805A  pdb=" N   LEU A 551 " --> pdb=" O   LYS A 547 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   CYS A 553 " --> pdb=" O   GLU A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 557
    Processing helix  chain 'A' and resid 564 through 579
    Processing helix  chain 'A' and resid 580 through 589
      removed outlier: 3.512A  pdb=" N   ALA A 584 " --> pdb=" O   GLU A 580 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   VAL A 586 " --> pdb=" O   GLU A 582 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   VAL A 587 " --> pdb=" O   LEU A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 612
      removed outlier: 3.561A  pdb=" N   VAL A 604 " --> pdb=" O   ASN A 600 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   LYS A 612 " --> pdb=" O   SER A 608 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 668
      removed outlier: 3.563A  pdb=" N   SER A 660 " --> pdb=" O   GLN A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 668 through 674
      removed outlier: 4.536A  pdb=" N   SER A 672 " --> pdb=" O   CYS A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 700
    Processing helix  chain 'A' and resid 717 through 727
      removed outlier: 4.552A  pdb=" N   ARG A 721 " --> pdb=" O   ASP A 717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 758
      removed outlier: 4.390A  pdb=" N   LEU A 756 " --> pdb=" O   LEU A 752 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 774 through 786
      removed outlier: 3.724A  pdb=" N   LYS A 786 " --> pdb=" O   PHE A 782 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 803 through 814
    Processing helix  chain 'A' and resid 834 through 845
    Processing helix  chain 'A' and resid 859 through 871
    Processing helix  chain 'A' and resid 888 through 900
    Processing helix  chain 'A' and resid 918 through 928
    Processing helix  chain 'A' and resid 944 through 946
      No H-bonds generated for 'chain 'A' and resid 944 through 946'
    Processing helix  chain 'A' and resid 947 through 958
      removed outlier: 3.782A  pdb=" N   LEU A 951 " --> pdb=" O   TYR A 947 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 973 through 984
    Processing helix  chain 'A' and resid 1001 through 1015
    Processing helix  chain 'F' and resid 63 through 68
    Processing helix  chain 'G' and resid 63 through 68
    Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 211
      removed outlier: 6.566A  pdb=" N   THR A 173 " --> pdb=" O   ILE A 317 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   VAL A 319 " --> pdb=" O   THR A 173 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   VAL A 175 " --> pdb=" O   VAL A 319 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 221 through 222
    Processing sheet with id=AA3, first strand: chain 'A' and resid 430 through 431
    Processing sheet with id=AA4, first strand: chain 'A' and resid 620 through 622
      removed outlier: 3.762A  pdb=" N   LYS A 683 " --> pdb=" O   LEU A 622 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   VAL A 714 " --> pdb=" O   GLN A 684 " (cutoff:3.500A)
      removed outlier: 7.485A  pdb=" N   PHE A 686 " --> pdb=" O   VAL A 714 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ASN A 713 " --> pdb=" O   ALA A 739 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 742 through 743
      removed outlier: 7.184A  pdb=" N   ILE A 742 " --> pdb=" O   CYS A 772 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 909 through 911
      removed outlier: 3.593A  pdb=" N   TRP A 939 " --> pdb=" O   LEU A 910 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   GLY A 967 " --> pdb=" O   LEU A 938 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   LEU A 993 " --> pdb=" O   ASP A1021 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 19 through 22
      removed outlier: 5.913A  pdb=" N   ALA F  20 " --> pdb=" O   LEU F  27 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   LEU F  27 " --> pdb=" O   ALA F  20 " (cutoff:3.500A)
      removed outlier: 12.871A  pdb=" N   LEU F  35 " --> pdb=" O   ASP G  43 " (cutoff:3.500A)
      removed outlier: 10.308A  pdb=" N   ASP G  43 " --> pdb=" O   LEU F  35 " (cutoff:3.500A)
      removed outlier: 5.496A  pdb=" N   LEU F  37 " --> pdb=" O   ILE G  41 " (cutoff:3.500A)
      removed outlier: 5.078A  pdb=" N   LEU G  37 " --> pdb=" O   ILE F  41 " (cutoff:3.500A)
      removed outlier: 9.950A  pdb=" N   ASP F  43 " --> pdb=" O   LEU G  35 " (cutoff:3.500A)
      removed outlier: 10.963A  pdb=" N   LEU G  35 " --> pdb=" O   ASP F  43 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'G' and resid 33 through 43
    current: chain 'F' and resid 103 through 110
      removed outlier: 3.863A  pdb=" N   TYR F  96 " --> pdb=" O   LEU F 107 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   GLU F 109 " --> pdb=" O   LEU F  94 " (cutoff:3.500A)
      removed outlier: 5.844A  pdb=" N   LEU F  94 " --> pdb=" O   GLU F 109 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 19 through 22
      removed outlier: 5.913A  pdb=" N   ALA F  20 " --> pdb=" O   LEU F  27 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   LEU F  27 " --> pdb=" O   ALA F  20 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 33 through 43
    current: chain 'G' and resid 103 through 110
      removed outlier: 4.387A  pdb=" N   TYR G  96 " --> pdb=" O   LEU G 107 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   GLU G 109 " --> pdb=" O   LEU G  94 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   LEU G  94 " --> pdb=" O   GLU G 109 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   VAL G  25 " --> pdb=" O   TRP G  21 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'G' and resid 33 through 43
    current: chain 'F' and resid 103 through 110
      removed outlier: 3.863A  pdb=" N   TYR F  96 " --> pdb=" O   LEU F 107 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   GLU F 109 " --> pdb=" O   LEU F  94 " (cutoff:3.500A)
      removed outlier: 5.844A  pdb=" N   LEU F  94 " --> pdb=" O   GLU F 109 " (cutoff:3.500A)

    351 hydrogen bonds defined for protein.
    1005 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: 1.48

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2773
        1.34 -     1.46: 1692
        1.46 -     1.58: 4127
        1.58 -     1.69: 0
        1.69 -     1.81: 80
  Bond restraints: 8672
  Sorted by residual:
  bond pdb=" C   ASP F  13 "
       pdb=" N   HIS F  14 "
    ideal  model  delta    sigma   weight residual
    1.329  1.350 -0.021 1.35e-02 5.49e+03 2.49e+00
  bond pdb=" CB  GLU A 327 "
       pdb=" CG  GLU A 327 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.93e-01
  bond pdb=" N   GLY F  82 "
       pdb=" CA  GLY F  82 "
    ideal  model  delta    sigma   weight residual
    1.449  1.461 -0.012 1.45e-02 4.76e+03 7.15e-01
  bond pdb=" CB  ARG G  53 "
       pdb=" CG  ARG G  53 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 6.92e-01
  bond pdb=" CA  SER A 595 "
       pdb=" CB  SER A 595 "
    ideal  model  delta    sigma   weight residual
    1.535  1.518  0.017 2.02e-02 2.45e+03 6.82e-01
  ... (remaining 8667 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.02: 10989
        1.02 -     2.04: 592
        2.04 -     3.06: 102
        3.06 -     4.08: 49
        4.08 -     5.10: 4
  Bond angle restraints: 11736
  Sorted by residual:
  angle pdb=" N   ASP F  81 "
        pdb=" CA  ASP F  81 "
        pdb=" CB  ASP F  81 "
      ideal   model   delta    sigma   weight residual
     114.17  110.27    3.90 1.14e+00 7.69e-01 1.17e+01
  angle pdb=" N   ASN A 145 "
        pdb=" CA  ASN A 145 "
        pdb=" CB  ASN A 145 "
      ideal   model   delta    sigma   weight residual
     114.17  110.87    3.30 1.14e+00 7.69e-01 8.36e+00
  angle pdb=" CA  GLU A 327 "
        pdb=" CB  GLU A 327 "
        pdb=" CG  GLU A 327 "
      ideal   model   delta    sigma   weight residual
     114.10  119.10   -5.00 2.00e+00 2.50e-01 6.25e+00
  angle pdb=" N   SER F  89 "
        pdb=" CA  SER F  89 "
        pdb=" CB  SER F  89 "
      ideal   model   delta    sigma   weight residual
     114.27  110.20    4.07 1.64e+00 3.72e-01 6.17e+00
  angle pdb=" N   LYS A 847 "
        pdb=" CA  LYS A 847 "
        pdb=" C   LYS A 847 "
      ideal   model   delta    sigma   weight residual
     114.56  111.57    2.99 1.27e+00 6.20e-01 5.55e+00
  ... (remaining 11731 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 4665
       17.85 -    35.69: 475
       35.69 -    53.54: 101
       53.54 -    71.39: 16
       71.39 -    89.23: 7
  Dihedral angle restraints: 5264
    sinusoidal: 2165
      harmonic: 3099
  Sorted by residual:
  dihedral pdb=" CB  GLU F 109 "
           pdb=" CG  GLU F 109 "
           pdb=" CD  GLU F 109 "
           pdb=" OE1 GLU F 109 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.23  -89.23     1      3.00e+01 1.11e-03 1.05e+01
  dihedral pdb=" CA  ASP A 339 "
           pdb=" CB  ASP A 339 "
           pdb=" CG  ASP A 339 "
           pdb=" OD1 ASP A 339 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.82   54.82     1      2.00e+01 2.50e-03 1.02e+01
  dihedral pdb=" CG  ARG F  48 "
           pdb=" CD  ARG F  48 "
           pdb=" NE  ARG F  48 "
           pdb=" CZ  ARG F  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -133.38   43.38     2      1.50e+01 4.44e-03 1.01e+01
  ... (remaining 5261 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 985
       0.036 -    0.073: 261
       0.073 -    0.109: 63
       0.109 -    0.146: 22
       0.146 -    0.182: 1
  Chirality restraints: 1332
  Sorted by residual:
  chirality pdb=" CA  ILE A 158 "
            pdb=" N   ILE A 158 "
            pdb=" C   ILE A 158 "
            pdb=" CB  ILE A 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.18 2.00e-01 2.50e+01 8.28e-01
  chirality pdb=" CA  ILE A 711 "
            pdb=" N   ILE A 711 "
            pdb=" C   ILE A 711 "
            pdb=" CB  ILE A 711 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.73e-01
  chirality pdb=" CA  VAL A 682 "
            pdb=" N   VAL A 682 "
            pdb=" C   VAL A 682 "
            pdb=" CB  VAL A 682 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.26e-01
  ... (remaining 1329 not shown)

  Planarity restraints: 1486
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 803 "    0.011 2.00e-02 2.50e+03   2.23e-02 4.96e+00
        pdb=" C   ASP A 803 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   ASP A 803 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLU A 804 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP F  81 "   -0.009 2.00e-02 2.50e+03   1.85e-02 3.41e+00
        pdb=" C   ASP F  81 "    0.032 2.00e-02 2.50e+03
        pdb=" O   ASP F  81 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   GLY F  82 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU G  35 "    0.018 5.00e-02 4.00e+02   2.71e-02 1.18e+00
        pdb=" N   PRO G  36 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO G  36 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO G  36 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1483 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 134
        2.67 -     3.23: 7995
        3.23 -     3.78: 11784
        3.78 -     4.34: 15903
        4.34 -     4.90: 26703
  Nonbonded interactions: 62519
  Sorted by model distance:
  nonbonded pdb=" O   LYS G  30 "
            pdb=" NZ  LYS G  30 "
     model   vdw
     2.112 3.120
  nonbonded pdb=" N   GLU G   9 "
            pdb=" OE1 GLU G   9 "
     model   vdw
     2.131 3.120
  nonbonded pdb=" O   ASP F  81 "
            pdb=" OD1 ASP F  81 "
     model   vdw
     2.150 3.040
  nonbonded pdb=" O   ASP F  88 "
            pdb=" OG  SER F  89 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" NH2 ARG A 746 "
            pdb=" O   MET F  62 "
     model   vdw
     2.240 3.120
  ... (remaining 62514 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
Found NCS groups:
ncs_group {
  reference = (chain 'F' and (resid 9 through 16 or (resid 17 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 18 through 21 or (resid 22 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 23 through 43 or (resid 44 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 45 through 57 or (re \ 
sid 58 and (name N or name CA or name C or name O or name CB )) or resid 59 thro \ 
ugh 78 or (resid 79 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 80 or (resid 81 and (name N or name CA or name C or name O or name CB )) o \ 
r resid 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 84 through 113))
  selection = chain 'G'
}

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:             1.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     9.380
  Find NCS groups from input model:        0.050
  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:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5547
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8672  Z= 0.177
  Angle     :  0.569   5.096  11736  Z= 0.314
  Chirality :  0.037   0.182   1332
  Planarity :  0.003   0.027   1486
  Dihedral  : 15.030  89.232   3244
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.23 %
    Favored  : 86.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.33 (0.27), residues: 1049
  helix:  1.56 (0.27), residues: 411
  sheet: -1.09 (0.34), residues: 217
  loop : -0.26 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 917 
 TYR   0.012   0.001   TYR F  79 
 PHE   0.009   0.001   PHE A 781 
 TRP   0.009   0.001   TRP F  34 
 HIS   0.008   0.001   HIS G  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 8672)
  covalent geometry    : angle       0.56877 (11736)
  hydrogen bonds       : bond        0.17456 (  338)
  hydrogen bonds       : angle       7.10821 ( 1005)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  359 LEU cc_start: 0.7892 (mp) cc_final: 0.6509 (mp)
REVERT: A  587 VAL cc_start: 0.4380 (t) cc_final: 0.2687 (m)
REVERT: A  671 PHE cc_start: 0.6958 (m-80) cc_final: 0.6757 (m-10)
REVERT: A  710 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6590 (mp0)
REVERT: A  788 ASN cc_start: 0.7748 (t0) cc_final: 0.7217 (m-40)
REVERT: A  813 MET cc_start: 0.7629 (ttm) cc_final: 0.7364 (ttm)
REVERT: F   16 ASP cc_start: 0.7365 (m-30) cc_final: 0.7055 (t0)
REVERT: F   28 ASP cc_start: 0.7536 (p0) cc_final: 0.7248 (p0)
REVERT: F   92 TRP cc_start: 0.6740 (m100) cc_final: 0.5974 (m100)
REVERT: G   46 GLN cc_start: 0.4187 (mm-40) cc_final: 0.3944 (mm-40)
REVERT: G   52 ARG cc_start: 0.6644 (ttm170) cc_final: 0.6386 (mtt-85)
  outliers start: 0
  outliers final: 0
  residues processed: 233
  average time/residue: 0.1173
  time to fit residues: 35.5633
Evaluate side-chains
  159 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.2980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.0270
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
A 155 GLN
A 310 GLN
A 517 GLN
A 606 HIS
A 856 ASN
F  97 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4594 r_free = 0.4594 target = 0.189576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.153217 restraints weight = 17586.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.156482 restraints weight = 11470.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.158712 restraints weight = 8360.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 67)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.160378 restraints weight = 6661.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.161245 restraints weight = 5627.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.4218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6112
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8672  Z= 0.138
  Angle     :  0.652   9.956  11736  Z= 0.326
  Chirality :  0.042   0.185   1332
  Planarity :  0.004   0.047   1486
  Dihedral  :  4.078  20.540   1141
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.74 %
    Favored  : 96.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.46 (0.26), residues: 1049
  helix:  1.44 (0.26), residues: 423
  sheet: -0.69 (0.39), residues: 183
  loop : -0.26 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 490 
 TYR   0.015   0.001   TYR A 480 
 PHE   0.025   0.001   PHE A 523 
 TRP   0.023   0.001   TRP A 664 
 HIS   0.018   0.001   HIS A 613 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 8672)
  covalent geometry    : angle       0.65219 (11736)
  hydrogen bonds       : bond        0.04345 (  338)
  hydrogen bonds       : angle       5.50450 ( 1005)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 184
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  329 ARG cc_start: 0.7715 (mtp85) cc_final: 0.7430 (ptm160)
REVERT: A  344 MET cc_start: 0.4964 (mmm) cc_final: 0.4525 (mmm)
REVERT: A  476 THR cc_start: 0.8363 (m) cc_final: 0.8105 (p)
REVERT: A  581 GLU cc_start: 0.7218 (tp30) cc_final: 0.6868 (tm-30)
REVERT: A  660 SER cc_start: 0.7514 (m) cc_final: 0.7298 (p)
REVERT: A  788 ASN cc_start: 0.7562 (t0) cc_final: 0.7301 (t0)
REVERT: A  837 ASP cc_start: 0.7968 (t0) cc_final: 0.7546 (t0)
REVERT: A  971 LEU cc_start: 0.6118 (pp) cc_final: 0.5812 (pp)
REVERT: A 1005 LYS cc_start: 0.9193 (pttt) cc_final: 0.8834 (tttp)
REVERT: F   28 ASP cc_start: 0.7934 (p0) cc_final: 0.7286 (p0)
REVERT: F   60 ARG cc_start: 0.7252 (tmm160) cc_final: 0.6846 (ptm160)
REVERT: F   67 ILE cc_start: 0.6541 (OUTLIER) cc_final: 0.6019 (mp)
REVERT: G   90 SER cc_start: 0.6624 (m) cc_final: 0.6384 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 184
  average time/residue: 0.1090
  time to fit residues: 26.6171
Evaluate side-chains
  143 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 10 optimal weight:    9.9990
   chunk 77 optimal weight:    7.9990
   chunk 30 optimal weight:    0.8980
   chunk 104 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 81 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 336 HIS
A 431 HIS
A 969 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.181838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.148094 restraints weight = 17453.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.150975 restraints weight = 11317.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.152867 restraints weight = 8218.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.154336 restraints weight = 6559.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.155324 restraints weight = 5566.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.4132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6235
moved from start:          0.4104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8672  Z= 0.167
  Angle     :  0.614   7.831  11736  Z= 0.312
  Chirality :  0.041   0.134   1332
  Planarity :  0.004   0.036   1486
  Dihedral  :  4.008  21.086   1141
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.49 (0.26), residues: 1049
  helix:  1.48 (0.26), residues: 425
  sheet: -0.63 (0.40), residues: 172
  loop : -0.29 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 746 
 TYR   0.023   0.002   TYR A 172 
 PHE   0.014   0.002   PHE A 523 
 TRP   0.021   0.002   TRP A 744 
 HIS   0.012   0.002   HIS A 613 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 8672)
  covalent geometry    : angle       0.61356 (11736)
  hydrogen bonds       : bond        0.04029 (  338)
  hydrogen bonds       : angle       5.11967 ( 1005)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  329 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7452 (mtm180)
REVERT: A  344 MET cc_start: 0.5065 (mmm) cc_final: 0.4602 (mmm)
REVERT: A  350 MET cc_start: 0.7186 (ptt) cc_final: 0.6693 (ptt)
REVERT: A  435 LEU cc_start: 0.8778 (mt) cc_final: 0.8285 (tp)
REVERT: A  581 GLU cc_start: 0.7090 (tp30) cc_final: 0.6759 (tm-30)
REVERT: A  660 SER cc_start: 0.7618 (m) cc_final: 0.7284 (p)
REVERT: A  661 LEU cc_start: 0.7765 (mp) cc_final: 0.7368 (mt)
REVERT: A  788 ASN cc_start: 0.7581 (t0) cc_final: 0.7257 (m-40)
REVERT: A  827 ASN cc_start: 0.8238 (t0) cc_final: 0.7963 (t0)
REVERT: A  837 ASP cc_start: 0.8217 (t0) cc_final: 0.7620 (t70)
REVERT: A  909 ASP cc_start: 0.7065 (t70) cc_final: 0.6832 (t0)
REVERT: A  971 LEU cc_start: 0.6267 (pp) cc_final: 0.5915 (pp)
REVERT: A  990 LEU cc_start: 0.8444 (tt) cc_final: 0.8196 (tt)
REVERT: A 1005 LYS cc_start: 0.9174 (pttt) cc_final: 0.8837 (tttm)
REVERT: F   28 ASP cc_start: 0.7815 (p0) cc_final: 0.7381 (p0)
REVERT: F   60 ARG cc_start: 0.7466 (tmm160) cc_final: 0.7125 (tmm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.1081
  time to fit residues: 23.4909
Evaluate side-chains
  135 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 97 optimal weight:    0.0670
   chunk 104 optimal weight:    4.9990
   chunk 44 optimal weight:    0.3980
   chunk 57 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0980
   chunk 9 optimal weight:   10.0000
   chunk 86 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
A 771 HIS
A 856 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.181797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.148600 restraints weight = 17763.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.151455 restraints weight = 11370.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.153525 restraints weight = 8225.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.155006 restraints weight = 6481.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.155939 restraints weight = 5440.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.4144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6232
moved from start:          0.4503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8672  Z= 0.113
  Angle     :  0.556   6.297  11736  Z= 0.280
  Chirality :  0.039   0.140   1332
  Planarity :  0.004   0.053   1486
  Dihedral  :  3.847  22.015   1141
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.59 (0.26), residues: 1049
  helix:  1.59 (0.27), residues: 422
  sheet: -0.63 (0.39), residues: 172
  loop : -0.24 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 893 
 TYR   0.009   0.001   TYR A 998 
 PHE   0.011   0.001   PHE A 523 
 TRP   0.017   0.001   TRP A 744 
 HIS   0.011   0.001   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 8672)
  covalent geometry    : angle       0.55585 (11736)
  hydrogen bonds       : bond        0.03362 (  338)
  hydrogen bonds       : angle       4.80889 ( 1005)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  344 MET cc_start: 0.5082 (mmm) cc_final: 0.4707 (mmm)
REVERT: A  350 MET cc_start: 0.7329 (ptt) cc_final: 0.6874 (ptt)
REVERT: A  431 HIS cc_start: 0.6980 (t70) cc_final: 0.6602 (t-90)
REVERT: A  435 LEU cc_start: 0.8781 (mt) cc_final: 0.8183 (tp)
REVERT: A  476 THR cc_start: 0.8255 (m) cc_final: 0.7944 (p)
REVERT: A  581 GLU cc_start: 0.6974 (tp30) cc_final: 0.6627 (tm-30)
REVERT: A  619 LYS cc_start: 0.8538 (tmtt) cc_final: 0.8321 (tptt)
REVERT: A  660 SER cc_start: 0.7749 (m) cc_final: 0.7511 (p)
REVERT: A  661 LEU cc_start: 0.7828 (mp) cc_final: 0.7624 (mp)
REVERT: A  771 HIS cc_start: 0.6723 (m90) cc_final: 0.6510 (m-70)
REVERT: A  780 GLU cc_start: 0.5459 (tm-30) cc_final: 0.5229 (tm-30)
REVERT: A  788 ASN cc_start: 0.7658 (t0) cc_final: 0.7363 (m-40)
REVERT: A  813 MET cc_start: 0.7681 (ttt) cc_final: 0.7432 (mmp)
REVERT: A  827 ASN cc_start: 0.8212 (t0) cc_final: 0.7990 (t0)
REVERT: A  874 ASP cc_start: 0.5391 (t70) cc_final: 0.5147 (t70)
REVERT: A  909 ASP cc_start: 0.6887 (t70) cc_final: 0.6659 (t70)
REVERT: A  971 LEU cc_start: 0.6218 (pp) cc_final: 0.5912 (pp)
REVERT: A  990 LEU cc_start: 0.8431 (tt) cc_final: 0.8171 (tt)
REVERT: A 1005 LYS cc_start: 0.9252 (pttt) cc_final: 0.9046 (ptpp)
REVERT: F   28 ASP cc_start: 0.7722 (p0) cc_final: 0.7371 (p0)
REVERT: F   88 ASP cc_start: 0.7904 (t0) cc_final: 0.7628 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.1095
  time to fit residues: 23.2605
Evaluate side-chains
  136 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 10 optimal weight:    9.9990
   chunk 5 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 76 optimal weight:    8.9990
   chunk 12 optimal weight:    0.0000
   chunk 98 optimal weight:    0.0470
   chunk 42 optimal weight:    0.3980
   chunk 101 optimal weight:    0.0980
   overall best weight:    0.5084

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

Flipped N/Q/H residues before XYZ refinement:
F  97 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.180709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.144563 restraints weight = 17811.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.147743 restraints weight = 11433.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.149825 restraints weight = 8240.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.151508 restraints weight = 6531.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.152490 restraints weight = 5517.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.4100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6312
moved from start:          0.4948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8672  Z= 0.111
  Angle     :  0.553   8.078  11736  Z= 0.278
  Chirality :  0.039   0.148   1332
  Planarity :  0.004   0.046   1486
  Dihedral  :  3.831  22.314   1141
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.68 (0.27), residues: 1049
  helix:  1.52 (0.27), residues: 422
  sheet: -0.56 (0.36), residues: 200
  loop :  0.03 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 984 
 TYR   0.010   0.001   TYR A 810 
 PHE   0.018   0.001   PHE A 333 
 TRP   0.014   0.001   TRP A 273 
 HIS   0.007   0.001   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8672)
  covalent geometry    : angle       0.55348 (11736)
  hydrogen bonds       : bond        0.03274 (  338)
  hydrogen bonds       : angle       4.76188 ( 1005)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  344 MET cc_start: 0.5114 (mmm) cc_final: 0.4825 (mmm)
REVERT: A  433 GLU cc_start: 0.7418 (tm-30) cc_final: 0.7108 (tm-30)
REVERT: A  435 LEU cc_start: 0.8797 (mt) cc_final: 0.8293 (tp)
REVERT: A  463 CYS cc_start: 0.6542 (m) cc_final: 0.6215 (m)
REVERT: A  476 THR cc_start: 0.8284 (m) cc_final: 0.7872 (p)
REVERT: A  608 SER cc_start: 0.8287 (p) cc_final: 0.8073 (p)
REVERT: A  661 LEU cc_start: 0.7830 (mp) cc_final: 0.7611 (mp)
REVERT: A  664 TRP cc_start: 0.8387 (t-100) cc_final: 0.8179 (t-100)
REVERT: A  771 HIS cc_start: 0.6726 (m90) cc_final: 0.6512 (m-70)
REVERT: A  837 ASP cc_start: 0.8116 (t0) cc_final: 0.7763 (t70)
REVERT: A  874 ASP cc_start: 0.5429 (t70) cc_final: 0.5093 (t70)
REVERT: A  971 LEU cc_start: 0.6176 (pp) cc_final: 0.5835 (pp)
REVERT: A  990 LEU cc_start: 0.8461 (tt) cc_final: 0.8149 (tt)
REVERT: A 1005 LYS cc_start: 0.9244 (pttt) cc_final: 0.9037 (ptpp)
REVERT: F   88 ASP cc_start: 0.7937 (t0) cc_final: 0.7632 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.0837
  time to fit residues: 17.7243
Evaluate side-chains
  139 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0980
   chunk 8 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 73 optimal weight:    0.5980
   chunk 104 optimal weight:    5.9990
   chunk 94 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 788 ASN
A 793 HIS
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 856 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.179033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.142965 restraints weight = 17521.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.145975 restraints weight = 11389.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.148132 restraints weight = 8344.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.149432 restraints weight = 6654.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.150131 restraints weight = 5707.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.4068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6388
moved from start:          0.5308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8672  Z= 0.119
  Angle     :  0.567   8.283  11736  Z= 0.284
  Chirality :  0.039   0.131   1332
  Planarity :  0.003   0.040   1486
  Dihedral  :  3.789  22.591   1141
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.71 %
    Favored  : 98.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.63 (0.27), residues: 1049
  helix:  1.43 (0.26), residues: 425
  sheet: -0.69 (0.36), residues: 200
  loop :  0.11 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 351 
 TYR   0.010   0.001   TYR A 765 
 PHE   0.015   0.001   PHE A 819 
 TRP   0.009   0.001   TRP A 744 
 HIS   0.005   0.001   HIS G  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 8672)
  covalent geometry    : angle       0.56712 (11736)
  hydrogen bonds       : bond        0.03474 (  338)
  hydrogen bonds       : angle       4.60044 ( 1005)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 159
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  344 MET cc_start: 0.5191 (mmm) cc_final: 0.4913 (mmm)
REVERT: A  353 ASN cc_start: 0.7821 (t0) cc_final: 0.7443 (t0)
REVERT: A  433 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7163 (tm-30)
REVERT: A  435 LEU cc_start: 0.8837 (mt) cc_final: 0.8366 (tp)
REVERT: A  476 THR cc_start: 0.8333 (m) cc_final: 0.8000 (p)
REVERT: A  581 GLU cc_start: 0.7368 (pp20) cc_final: 0.6804 (pp20)
REVERT: A  780 GLU cc_start: 0.5691 (tm-30) cc_final: 0.5392 (tm-30)
REVERT: A  837 ASP cc_start: 0.8133 (t0) cc_final: 0.7589 (t70)
REVERT: A  874 ASP cc_start: 0.5466 (t70) cc_final: 0.5184 (t70)
REVERT: A  990 LEU cc_start: 0.8500 (tt) cc_final: 0.8197 (tt)
REVERT: A 1005 LYS cc_start: 0.9247 (pttt) cc_final: 0.9020 (ptpp)
REVERT: F   88 ASP cc_start: 0.8079 (t0) cc_final: 0.7832 (t0)
REVERT: G   26 TYR cc_start: 0.7385 (m-80) cc_final: 0.7158 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 159
  average time/residue: 0.0976
  time to fit residues: 21.1408
Evaluate side-chains
  139 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 100 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 76 optimal weight:    0.4980
   chunk 72 optimal weight:    4.9990
   chunk 92 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 84 optimal weight:    0.0470
   chunk 0 optimal weight:   20.0000
   chunk 95 optimal weight:    2.9990
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
A 759 HIS
** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.178091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.143848 restraints weight = 17684.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.146758 restraints weight = 11441.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.148805 restraints weight = 8272.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.150228 restraints weight = 6550.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.151001 restraints weight = 5531.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.4077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6366
moved from start:          0.5629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8672  Z= 0.119
  Angle     :  0.588   7.852  11736  Z= 0.292
  Chirality :  0.040   0.167   1332
  Planarity :  0.003   0.037   1486
  Dihedral  :  3.798  22.402   1141
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.58 (0.27), residues: 1049
  helix:  1.38 (0.26), residues: 425
  sheet: -0.73 (0.36), residues: 200
  loop :  0.11 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 984 
 TYR   0.017   0.001   TYR A 576 
 PHE   0.009   0.001   PHE A 471 
 TRP   0.029   0.001   TRP A 744 
 HIS   0.008   0.001   HIS A 759 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 8672)
  covalent geometry    : angle       0.58819 (11736)
  hydrogen bonds       : bond        0.03487 (  338)
  hydrogen bonds       : angle       4.56204 ( 1005)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  344 MET cc_start: 0.5171 (mmm) cc_final: 0.4872 (mmm)
REVERT: A  353 ASN cc_start: 0.7857 (t0) cc_final: 0.7555 (t0)
REVERT: A  356 LEU cc_start: 0.8316 (tt) cc_final: 0.7995 (tt)
REVERT: A  435 LEU cc_start: 0.8854 (mt) cc_final: 0.8506 (tp)
REVERT: A  581 GLU cc_start: 0.7273 (pp20) cc_final: 0.6706 (pp20)
REVERT: A  837 ASP cc_start: 0.8112 (t0) cc_final: 0.7507 (t70)
REVERT: A  874 ASP cc_start: 0.5547 (t70) cc_final: 0.5194 (t70)
REVERT: A  894 TYR cc_start: 0.6901 (m-80) cc_final: 0.6647 (m-80)
REVERT: A  990 LEU cc_start: 0.8518 (tt) cc_final: 0.8194 (tt)
REVERT: A 1005 LYS cc_start: 0.9189 (pttt) cc_final: 0.8926 (ptpp)
REVERT: F   42 LYS cc_start: 0.8803 (pttt) cc_final: 0.8330 (pttm)
REVERT: F   88 ASP cc_start: 0.8082 (t0) cc_final: 0.7825 (t0)
REVERT: G   26 TYR cc_start: 0.7374 (m-80) cc_final: 0.7124 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.0966
  time to fit residues: 20.9155
Evaluate side-chains
  147 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9980
   chunk 90 optimal weight:    0.0980
   chunk 16 optimal weight:    7.9990
   chunk 73 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0770
   chunk 20 optimal weight:    0.6980
   chunk 100 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 88 optimal weight:    3.9990
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
A 759 HIS
** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 788 ASN
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.175617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.141705 restraints weight = 17244.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.144558 restraints weight = 10980.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.146551 restraints weight = 7886.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 61)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.147998 restraints weight = 6213.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.148761 restraints weight = 5229.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.4052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6367
moved from start:          0.5873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8672  Z= 0.119
  Angle     :  0.604   9.671  11736  Z= 0.299
  Chirality :  0.040   0.164   1332
  Planarity :  0.004   0.039   1486
  Dihedral  :  3.858  22.152   1141
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.53 (0.27), residues: 1049
  helix:  1.30 (0.26), residues: 426
  sheet: -0.76 (0.36), residues: 201
  loop :  0.11 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 432 
 TYR   0.027   0.001   TYR A 810 
 PHE   0.008   0.001   PHE A 333 
 TRP   0.021   0.001   TRP A 744 
 HIS   0.008   0.001   HIS A 759 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 8672)
  covalent geometry    : angle       0.60391 (11736)
  hydrogen bonds       : bond        0.03347 (  338)
  hydrogen bonds       : angle       4.51447 ( 1005)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  344 MET cc_start: 0.5236 (mmm) cc_final: 0.4948 (mmm)
REVERT: A  353 ASN cc_start: 0.7943 (t0) cc_final: 0.7660 (t0)
REVERT: A  356 LEU cc_start: 0.8367 (tt) cc_final: 0.8090 (tt)
REVERT: A  431 HIS cc_start: 0.7190 (t70) cc_final: 0.6973 (t70)
REVERT: A  435 LEU cc_start: 0.8883 (mt) cc_final: 0.8316 (tp)
REVERT: A  581 GLU cc_start: 0.7286 (pp20) cc_final: 0.6743 (pp20)
REVERT: A  810 TYR cc_start: 0.7176 (m-80) cc_final: 0.6627 (m-80)
REVERT: A  822 MET cc_start: 0.7680 (mpp) cc_final: 0.7373 (mpp)
REVERT: A  837 ASP cc_start: 0.8066 (t0) cc_final: 0.7484 (t70)
REVERT: A  874 ASP cc_start: 0.5626 (t70) cc_final: 0.5223 (t70)
REVERT: A  894 TYR cc_start: 0.6944 (m-80) cc_final: 0.6713 (m-80)
REVERT: A 1005 LYS cc_start: 0.9179 (pttt) cc_final: 0.8923 (ptpp)
REVERT: F   88 ASP cc_start: 0.8119 (t0) cc_final: 0.7872 (t0)
REVERT: G   26 TYR cc_start: 0.7566 (m-80) cc_final: 0.7254 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.0940
  time to fit residues: 20.0878
Evaluate side-chains
  152 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 73 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0770
   chunk 24 optimal weight:    0.1980
   chunk 101 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   chunk 82 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
** A 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 788 ASN
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  46 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.175577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.141338 restraints weight = 17438.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.144249 restraints weight = 11079.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.146201 restraints weight = 7933.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 63)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.147674 restraints weight = 6258.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.148496 restraints weight = 5257.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.4051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6385
moved from start:          0.6139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   8672  Z= 0.121
  Angle     :  0.622  10.649  11736  Z= 0.308
  Chirality :  0.040   0.139   1332
  Planarity :  0.004   0.039   1486
  Dihedral  :  3.895  22.009   1141
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.52 (0.27), residues: 1049
  helix:  1.27 (0.26), residues: 426
  sheet: -0.69 (0.36), residues: 200
  loop :  0.09 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 432 
 TYR   0.024   0.001   TYR A 810 
 PHE   0.014   0.001   PHE A 333 
 TRP   0.039   0.002   TRP A 367 
 HIS   0.004   0.001   HIS G  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8672)
  covalent geometry    : angle       0.62203 (11736)
  hydrogen bonds       : bond        0.03308 (  338)
  hydrogen bonds       : angle       4.56421 ( 1005)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  344 MET cc_start: 0.5304 (mmm) cc_final: 0.4991 (mmm)
REVERT: A  353 ASN cc_start: 0.8008 (t0) cc_final: 0.7768 (t0)
REVERT: A  356 LEU cc_start: 0.8388 (tt) cc_final: 0.8165 (tt)
REVERT: A  435 LEU cc_start: 0.8978 (mt) cc_final: 0.8538 (tp)
REVERT: A  476 THR cc_start: 0.8451 (m) cc_final: 0.8018 (p)
REVERT: A  581 GLU cc_start: 0.7245 (pp20) cc_final: 0.6704 (pp20)
REVERT: A  619 LYS cc_start: 0.8651 (tptp) cc_final: 0.8363 (tptt)
REVERT: A  754 ASP cc_start: 0.7486 (m-30) cc_final: 0.7275 (m-30)
REVERT: A  810 TYR cc_start: 0.7285 (m-80) cc_final: 0.6793 (m-80)
REVERT: A  822 MET cc_start: 0.7650 (mpp) cc_final: 0.7348 (mpp)
REVERT: A  837 ASP cc_start: 0.8015 (t0) cc_final: 0.7428 (t70)
REVERT: A  874 ASP cc_start: 0.5695 (t70) cc_final: 0.5269 (t70)
REVERT: A  994 ARG cc_start: 0.6787 (ttm-80) cc_final: 0.6181 (mtp-110)
REVERT: A 1005 LYS cc_start: 0.9203 (pttt) cc_final: 0.8942 (ptpp)
REVERT: F   38 THR cc_start: 0.8858 (t) cc_final: 0.8651 (p)
REVERT: F   88 ASP cc_start: 0.8095 (t0) cc_final: 0.7839 (t0)
REVERT: G   26 TYR cc_start: 0.7602 (m-80) cc_final: 0.7260 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.1135
  time to fit residues: 24.0818
Evaluate side-chains
  148 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 8 optimal weight:    0.0070
   chunk 103 optimal weight:    0.2980
   chunk 38 optimal weight:    0.8980
   chunk 78 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.8000

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

Flipped N/Q/H residues before XYZ refinement:
** A 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 788 ASN
G  14 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.173291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.139182 restraints weight = 17332.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.142037 restraints weight = 11096.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.144074 restraints weight = 7946.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.145361 restraints weight = 6242.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.146415 restraints weight = 5288.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6428
moved from start:          0.6412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8672  Z= 0.144
  Angle     :  0.656  10.807  11736  Z= 0.325
  Chirality :  0.040   0.138   1332
  Planarity :  0.004   0.047   1486
  Dihedral  :  4.065  22.490   1141
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.51 (0.27), residues: 1049
  helix:  1.28 (0.26), residues: 426
  sheet: -0.72 (0.35), residues: 197
  loop :  0.06 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 994 
 TYR   0.021   0.002   TYR A 810 
 PHE   0.009   0.001   PHE A 333 
 TRP   0.047   0.002   TRP A 367 
 HIS   0.006   0.001   HIS G  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8672)
  covalent geometry    : angle       0.65596 (11736)
  hydrogen bonds       : bond        0.03559 (  338)
  hydrogen bonds       : angle       4.61676 ( 1005)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 ASN cc_start: 0.8020 (t0) cc_final: 0.7795 (t0)
REVERT: A  356 LEU cc_start: 0.8447 (tt) cc_final: 0.8240 (tt)
REVERT: A  435 LEU cc_start: 0.8911 (mt) cc_final: 0.8397 (tt)
REVERT: A  476 THR cc_start: 0.8423 (m) cc_final: 0.8087 (p)
REVERT: A  581 GLU cc_start: 0.7318 (pp20) cc_final: 0.6791 (pp20)
REVERT: A  810 TYR cc_start: 0.7103 (m-80) cc_final: 0.6791 (m-80)
REVERT: A  822 MET cc_start: 0.7637 (mpp) cc_final: 0.7321 (mpp)
REVERT: A  837 ASP cc_start: 0.7974 (t0) cc_final: 0.7405 (t70)
REVERT: A  874 ASP cc_start: 0.5853 (t70) cc_final: 0.5421 (t70)
REVERT: A  909 ASP cc_start: 0.6965 (t70) cc_final: 0.6762 (t70)
REVERT: A 1005 LYS cc_start: 0.9166 (pttt) cc_final: 0.8931 (ptpp)
REVERT: F   28 ASP cc_start: 0.7572 (p0) cc_final: 0.7270 (p0)
REVERT: F   38 THR cc_start: 0.8881 (t) cc_final: 0.8652 (p)
REVERT: F   42 LYS cc_start: 0.8519 (pttt) cc_final: 0.8252 (pttt)
REVERT: F   60 ARG cc_start: 0.7527 (tmm160) cc_final: 0.7323 (ptm160)
REVERT: G   26 TYR cc_start: 0.7549 (m-80) cc_final: 0.7246 (m-80)
REVERT: G   43 ASP cc_start: 0.5692 (t0) cc_final: 0.5361 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.1168
  time to fit residues: 25.3643
Evaluate side-chains
  149 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0050
   chunk 57 optimal weight:    0.4980
   chunk 41 optimal weight:    0.7980
   chunk 0 optimal weight:   30.0000
   chunk 44 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 85 optimal weight:    0.4980
   chunk 78 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.4794

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

Flipped N/Q/H residues before XYZ refinement:
A 376 GLN
** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 788 ASN
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.174224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.140341 restraints weight = 17331.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.143222 restraints weight = 11031.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.145101 restraints weight = 7891.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 70)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.146632 restraints weight = 6208.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.147517 restraints weight = 5204.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.4034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6404
moved from start:          0.6581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8672  Z= 0.121
  Angle     :  0.645  10.694  11736  Z= 0.322
  Chirality :  0.040   0.139   1332
  Planarity :  0.005   0.147   1486
  Dihedral  :  4.056  22.029   1141
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    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:  0.50 (0.27), residues: 1049
  helix:  1.20 (0.26), residues: 426
  sheet: -0.54 (0.36), residues: 203
  loop :  0.05 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 351 
 TYR   0.024   0.001   TYR A 894 
 PHE   0.079   0.002   PHE A 347 
 TRP   0.049   0.002   TRP A 367 
 HIS   0.003   0.001   HIS A 493 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8672)
  covalent geometry    : angle       0.64512 (11736)
  hydrogen bonds       : bond        0.03439 (  338)
  hydrogen bonds       : angle       4.61382 ( 1005)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1638.11 seconds
wall clock time: 28 minutes 49.52 seconds (1729.52 seconds total)