Starting phenix.real_space_refine
on Tue Jul 29 06:38:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8atv_15664/07_2025/8atv_15664.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8atv_15664/07_2025/8atv_15664.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.39
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8atv_15664/07_2025/8atv_15664.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8atv_15664/07_2025/8atv_15664.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8atv_15664/07_2025/8atv_15664.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8atv_15664/07_2025/8atv_15664.cif"
  }
  resolution = 3.39
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      61      5.49       5
     S      35      5.16       5
     C    6950      2.51       5
     N    1943      2.21       5
     O    2172      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11161
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2733
          Classifications: {'peptide': 334}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 19, 'TRANS': 314}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "A"
      Number of atoms: 7199
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 923, 7191
          Classifications: {'peptide': 923}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 63}
          Link IDs: {'PTRANS': 44, 'TRANS': 878}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 218
          Unresolved non-hydrogen angles: 266
          Unresolved non-hydrogen dihedrals: 172
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 95
      Conformer: "B"
        Number of residues, atoms: 923, 7191
          Classifications: {'peptide': 923}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 63}
          Link IDs: {'PTRANS': 44, 'TRANS': 878}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 218
          Unresolved non-hydrogen angles: 266
          Unresolved non-hydrogen dihedrals: 172
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 95
          bond proxies already assigned to first conformer: 7343
    Chain: "N"
      Number of atoms: 560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 560
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
    Chain: "T"
      Number of atoms: 548
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 548
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
    Chain: "C"
      Number of atoms: 89
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 89
          Classifications: {'RNA': 4}
          Modifications used: {'rna3p_pur': 4}
          Link IDs: {'rna3p': 3}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 10.34, per 1000 atoms: 0.93
  Number of scatterers: 11161
  At special positions: 0
  Unit cell: (102.82, 117.37, 119.31, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      35     16.00
     P      61     15.00
     O    2172      8.00
     N    1943      7.00
     C    6950      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.59
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2380

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 11 sheets defined
      58.3% alpha, 8.9% beta
      21 base pairs and 40 stacking pairs defined.
    Time for finding SS restraints: 4.09
  Creating SS restraints...
    Processing helix  chain 'B' and resid 7 through 12
    Processing helix  chain 'B' and resid 25 through 37
    Processing helix  chain 'B' and resid 37 through 42
      removed outlier: 4.161A  pdb=" N   THR B  41 " --> pdb=" O   ASP B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 47
    Processing helix  chain 'B' and resid 58 through 69
    Processing helix  chain 'B' and resid 79 through 91
    Processing helix  chain 'B' and resid 104 through 113
      removed outlier: 4.308A  pdb=" N   TYR B 108 " --> pdb=" O   ASP B 104 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   SER B 109 " --> pdb=" O   TRP B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 157
      removed outlier: 3.782A  pdb=" N   ILE B 147 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 181
    Processing helix  chain 'B' and resid 190 through 199
    Processing helix  chain 'B' and resid 212 through 216
      removed outlier: 3.504A  pdb=" N   GLY B 215 " --> pdb=" O   GLU B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 225
    Processing helix  chain 'B' and resid 230 through 234
      removed outlier: 3.663A  pdb=" N   GLU B 233 " --> pdb=" O   SER B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 267
    Processing helix  chain 'B' and resid 273 through 282
      removed outlier: 5.741A  pdb=" N   MET B 278 " --> pdb=" O   ASN B 275 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   ASP B 279 " --> pdb=" O   THR B 276 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   GLY B 282 " --> pdb=" O   ASP B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 293
    Processing helix  chain 'B' and resid 296 through 300
    Processing helix  chain 'B' and resid 307 through 321
    Processing helix  chain 'A' and resid 388 through 395
    Processing helix  chain 'A' and resid 397 through 412
    Processing helix  chain 'A' and resid 412 through 421
    Processing helix  chain 'A' and resid 422 through 441
    Processing helix  chain 'A' and resid 448 through 478
      Proline residue:  A 463  - end of helix
      removed outlier: 3.870A  pdb=" N   GLU A 478 " --> pdb=" O   SER A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 486 through 497
      removed outlier: 3.820A  pdb=" N   THR A 491 " --> pdb=" O   ASN A 487 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ASN A 492 " --> pdb=" O   LYS A 488 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLY A 495 " --> pdb=" O   THR A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 519
    Processing helix  chain 'A' and resid 531 through 555
      removed outlier: 3.645A  pdb=" N   ILE A 536 " --> pdb=" O   ALA A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 612
    Processing helix  chain 'A' and resid 652 through 660
      removed outlier: 4.207A  pdb=" N   GLN A 658 " --> pdb=" O   THR A 654 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 668
    Processing helix  chain 'A' and resid 703 through 717
      removed outlier: 3.864A  pdb=" N   VAL A 707 " --> pdb=" O   SER A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 720 through 731
    Processing helix  chain 'A' and resid 737 through 751
      removed outlier: 3.853A  pdb=" N   GLY A 751 " --> pdb=" O   VAL A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 775 through 813
      removed outlier: 3.500A  pdb=" N   THR A 803 " --> pdb=" O   ASN A 799 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 842 through 848
    Processing helix  chain 'A' and resid 860 through 873
    Processing helix  chain 'A' and resid 879 through 890
    Processing helix  chain 'A' and resid 890 through 900
    Processing helix  chain 'A' and resid 907 through 911
    Processing helix  chain 'A' and resid 913 through 929
    Processing helix  chain 'A' and resid 932 through 935
    Processing helix  chain 'A' and resid 948 through 959
    Processing helix  chain 'A' and resid 960 through 967
    Processing helix  chain 'A' and resid 977 through 994
    Processing helix  chain 'A' and resid 998 through 1004
      removed outlier: 3.720A  pdb=" N   LEU A1004 " --> pdb=" O   ASN A1000 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1009 through 1021
      removed outlier: 4.145A  pdb=" N   VAL A1021 " --> pdb=" O   VAL A1017 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1025 through 1038
      removed outlier: 3.687A  pdb=" N   GLN A1036 " --> pdb=" O   GLN A1032 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1047 through 1066
    Processing helix  chain 'A' and resid 1067 through 1085
    Processing helix  chain 'A' and resid 1090 through 1094
      removed outlier: 3.545A  pdb=" N   GLU A1093 " --> pdb=" O   ASP A1090 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   LYS A1094 " --> pdb=" O   VAL A1091 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1090 through 1094'
    Processing helix  chain 'A' and resid 1149 through 1180
      Proline residue:  A1158  - end of helix
      removed outlier: 3.629A  pdb=" N   ILE A1162 " --> pdb=" O   PRO A1158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1197 through 1213
    Processing helix  chain 'A' and resid 1216 through 1229
    Processing helix  chain 'A' and resid 1242 through 1260
      removed outlier: 3.596A  pdb=" N   ILE A1248 " --> pdb=" O   LEU A1244 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE A1249 " --> pdb=" O   ALA A1245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1264 through 1281
      removed outlier: 3.581A  pdb=" N   LEU A1279 " --> pdb=" O   ARG A1275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1293
    Processing helix  chain 'A' and resid 1297 through 1301
    Processing helix  chain 'A' and resid 1339 through 1346
      removed outlier: 3.506A  pdb=" N   LEU A1343 " --> pdb=" O   VAL A1340 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ASN A1345 " --> pdb=" O   VAL A1342 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.924A  pdb=" N   TYR B  73 " --> pdb=" O   GLN B  96 " (cutoff:3.500A)
      removed outlier: 8.068A  pdb=" N   LEU B  98 " --> pdb=" O   TYR B  73 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   LEU B  75 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   LYS B  49 " --> pdb=" O   LEU B 133 " (cutoff:3.500A)
      removed outlier: 7.858A  pdb=" N   VAL B 135 " --> pdb=" O   LYS B  49 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   LEU B  51 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   ASN B 137 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   LEU B  53 " --> pdb=" O   ASN B 137 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   LYS B 167 " --> pdb=" O   PHE B 132 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   GLU B 246 " --> pdb=" O   LEU B 204 " (cutoff:3.500A)
      removed outlier: 6.069A  pdb=" N   LEU B 204 " --> pdb=" O   GLU B 246 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   ASP B 248 " --> pdb=" O   THR B 202 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   THR B 202 " --> pdb=" O   ASP B 248 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 528 through 530
    Processing sheet with id=AA3, first strand: chain 'A' and resid 613 through 619
      removed outlier: 3.637A  pdb=" N   GLY A 629 " --> pdb=" O   VAL A 616 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 680 through 684
      removed outlier: 4.485A  pdb=" N   TRP A 682 " --> pdb=" O   SER A 687 " (cutoff:3.500A)
      removed outlier: 7.770A  pdb=" N   SER A 687 " --> pdb=" O   TRP A 682 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 698 through 699
    Processing sheet with id=AA6, first strand: chain 'A' and resid 734 through 736
    Processing sheet with id=AA7, first strand: chain 'A' and resid 855 through 856
    Processing sheet with id=AA8, first strand: chain 'A' and resid 942 through 945
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1087 through 1088
      removed outlier: 3.546A  pdb=" N   LEU A1238 " --> pdb=" O   MET A1321 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   MET A1321 " --> pdb=" O   LEU A1238 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1109 through 1111
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1127 through 1131
      removed outlier: 3.521A  pdb=" N   ILE A1139 " --> pdb=" O   LYS A1128 " (cutoff:3.500A)

    539 hydrogen bonds defined for protein.
    1544 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      47 hydrogen bonds
      94 hydrogen bond angles
      0 basepair planarities
      21 basepair parallelities
      40 stacking parallelities
  Total time for adding SS restraints: 6.09

  Time building geometry restraints manager: 3.67 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: 3129
        1.34 -     1.45: 2167
        1.45 -     1.57: 6081
        1.57 -     1.69: 112
        1.69 -     1.81: 59
  Bond restraints: 11548
  Sorted by residual:
  bond pdb=" O3'  DT T  14 "
       pdb=" P    DG T  15 "
    ideal  model  delta    sigma   weight residual
    1.607  1.471  0.136 1.50e-02 4.44e+03 8.26e+01
  bond pdb=" O3'  DA T  13 "
       pdb=" P    DT T  14 "
    ideal  model  delta    sigma   weight residual
    1.607  1.494  0.113 1.50e-02 4.44e+03 5.67e+01
  bond pdb=" O3'  DC T  25 "
       pdb=" P    DA T  26 "
    ideal  model  delta    sigma   weight residual
    1.607  1.510  0.097 1.50e-02 4.44e+03 4.17e+01
  bond pdb=" O3'  DT N 112 "
       pdb=" P    DG N 113 "
    ideal  model  delta    sigma   weight residual
    1.607  1.687 -0.080 1.50e-02 4.44e+03 2.86e+01
  bond pdb=" O3'  DA N 133 "
       pdb=" P    DT N 134 "
    ideal  model  delta    sigma   weight residual
    1.607  1.528  0.079 1.50e-02 4.44e+03 2.77e+01
  ... (remaining 11543 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.63: 15707
        2.63 -     5.26: 176
        5.26 -     7.89: 19
        7.89 -    10.52: 10
       10.52 -    13.15: 2
  Bond angle restraints: 15914
  Sorted by residual:
  angle pdb=" C5'  DA N 130 "
        pdb=" C4'  DA N 130 "
        pdb=" O4'  DA N 130 "
      ideal   model   delta    sigma   weight residual
     109.40  117.79   -8.39 1.50e+00 4.44e-01 3.13e+01
  angle pdb=" C5'  DT T  34 "
        pdb=" C4'  DT T  34 "
        pdb=" O4'  DT T  34 "
      ideal   model   delta    sigma   weight residual
     109.40  116.99   -7.59 1.50e+00 4.44e-01 2.56e+01
  angle pdb=" C   LEU A 755 "
        pdb=" CA  LEU A 755 "
        pdb=" CB  LEU A 755 "
      ideal   model   delta    sigma   weight residual
     117.23  110.74    6.49 1.36e+00 5.41e-01 2.28e+01
  angle pdb=" C3'  DT T  14 "
        pdb=" O3'  DT T  14 "
        pdb=" P    DG T  15 "
      ideal   model   delta    sigma   weight residual
     120.20  127.00   -6.80 1.50e+00 4.44e-01 2.06e+01
  angle pdb=" C3'  DT N 112 "
        pdb=" O3'  DT N 112 "
        pdb=" P    DG N 113 "
      ideal   model   delta    sigma   weight residual
     120.20  126.82   -6.62 1.50e+00 4.44e-01 1.95e+01
  ... (remaining 15909 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.58: 6265
       27.58 -    55.17: 488
       55.17 -    82.75: 51
       82.75 -   110.34: 6
      110.34 -   137.92: 2
  Dihedral angle restraints: 6812
    sinusoidal: 3137
      harmonic: 3675
  Sorted by residual:
  dihedral pdb=" O3A GTP C 201 "
           pdb=" O3B GTP C 201 "
           pdb=" PB  GTP C 201 "
           pdb=" PG  GTP C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     303.79  165.87  137.92     1      2.00e+01 2.50e-03 4.18e+01
  dihedral pdb=" C8  GTP C 201 "
           pdb=" C1' GTP C 201 "
           pdb=" N9  GTP C 201 "
           pdb=" O4' GTP C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -12.68  117.28     1      2.00e+01 2.50e-03 3.50e+01
  dihedral pdb=" O3B GTP C 201 "
           pdb=" O3A GTP C 201 "
           pdb=" PB  GTP C 201 "
           pdb=" PA  GTP C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -68.92 -166.09   97.17     1      2.00e+01 2.50e-03 2.70e+01
  ... (remaining 6809 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 1711
       0.106 -    0.212: 45
       0.212 -    0.318: 3
       0.318 -    0.424: 2
       0.424 -    0.530: 1
  Chirality restraints: 1762
  Sorted by residual:
  chirality pdb=" P    DT N 127 "
            pdb=" OP1  DT N 127 "
            pdb=" OP2  DT N 127 "
            pdb=" O5'  DT N 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.88   -0.53 2.00e-01 2.50e+01 7.01e+00
  chirality pdb=" C4'  DA N 130 "
            pdb=" C5'  DA N 130 "
            pdb=" O4'  DA N 130 "
            pdb=" C3'  DA N 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.11   -0.42 2.00e-01 2.50e+01 4.37e+00
  chirality pdb=" C3'  DG N 108 "
            pdb=" C4'  DG N 108 "
            pdb=" O3'  DG N 108 "
            pdb=" C2'  DG N 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.32   -0.34 2.00e-01 2.50e+01 2.84e+00
  ... (remaining 1759 not shown)

  Planarity restraints: 1828
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 119 "    0.028 5.00e-02 4.00e+02   4.22e-02 2.84e+00
        pdb=" N   PRO B 120 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B 120 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 120 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 703 "   -0.027 5.00e-02 4.00e+02   4.11e-02 2.70e+00
        pdb=" N   PRO A 704 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 704 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 704 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 775 "    0.026 5.00e-02 4.00e+02   3.90e-02 2.43e+00
        pdb=" N   PRO A 776 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 776 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 776 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1825 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 399
        2.72 -     3.26: 10573
        3.26 -     3.81: 18947
        3.81 -     4.35: 23018
        4.35 -     4.90: 38372
  Nonbonded interactions: 91309
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 487 "
            pdb=" OG1 THR A 491 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" OD1 ASP B 257 "
            pdb=" N   ASN B 258 "
     model   vdw
     2.177 3.120
  nonbonded pdb=" O   PRO B 102 "
            pdb=" OH  TYR B 108 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" NE2 GLN A 416 "
            pdb=" OE1 GLU A 420 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" O   PHE B  90 "
            pdb=" OG  SER B  93 "
     model   vdw
     2.264 3.040
  ... (remaining 91304 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.140
  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:          0.520
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     38.210
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.100
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
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   0.136  11549  Z= 0.238
  Angle     :  0.695  13.149  15914  Z= 0.372
  Chirality :  0.048   0.530   1762
  Planarity :  0.004   0.042   1828
  Dihedral  : 18.012 137.923   4432
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.24), residues: 1250
  helix:  1.67 (0.20), residues: 697
  sheet:  0.70 (0.54), residues: 93
  loop : -0.92 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 864 
 HIS   0.007   0.001   HIS A1057 
 PHE   0.012   0.001   PHE A 886 
 TYR   0.014   0.001   TYR B 161 
 ARG   0.003   0.000   ARG A1220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13915 (  586)
  hydrogen bonds       : angle       5.32629 ( 1638)
  covalent geometry    : bond        0.00441 (11548)
  covalent geometry    : angle       0.69520 (15914)
  Misc. bond           : bond        0.05346 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 1.213 
Fit side-chains
REVERT: A  467 GLU cc_start: 0.6632 (tp30) cc_final: 0.6321 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.2542
  time to fit residues: 59.1469
Evaluate side-chains
  138 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 1.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 97 optimal weight:    9.9990
   chunk 54 optimal weight:    0.0770
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 52 optimal weight:   10.0000
   chunk 101 optimal weight:    8.9990
   chunk 39 optimal weight:    0.0970
   chunk 61 optimal weight:    6.9990
   chunk 75 optimal weight:    9.9990
   chunk 117 optimal weight:   30.0000
   overall best weight:    1.8338

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

Flipped N/Q/H residues before XYZ refinement:
A 449 ASN
A 658 GLN
A 890 HIS
A 966 GLN
A1032 GLN
A1231 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.166747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.132975 restraints weight = 16216.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 1.76
r_work: 0.3245 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3113 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3094
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3094
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.0894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11549  Z= 0.129
  Angle     :  0.560   8.090  15914  Z= 0.301
  Chirality :  0.040   0.166   1762
  Planarity :  0.004   0.040   1828
  Dihedral  : 18.176 109.849   2047
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  4.92 %
    Favored  : 94.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.24), residues: 1250
  helix:  1.94 (0.20), residues: 691
  sheet:  0.94 (0.55), residues: 93
  loop : -0.80 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1110 
 HIS   0.007   0.001   HIS A1057 
 PHE   0.013   0.001   PHE A 886 
 TYR   0.018   0.001   TYR A1229 
 ARG   0.003   0.000   ARG A1220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04682 (  586)
  hydrogen bonds       : angle       4.02373 ( 1638)
  covalent geometry    : bond        0.00283 (11548)
  covalent geometry    : angle       0.55991 (15914)
  Misc. bond           : bond        0.00064 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 163
  time to evaluate  : 1.213 
Fit side-chains
REVERT: B   25 ASN cc_start: 0.7111 (t0) cc_final: 0.6834 (t0)
REVERT: A  461 MET cc_start: 0.8697 (tmm) cc_final: 0.8092 (ttt)
REVERT: A  467 GLU cc_start: 0.7434 (tp30) cc_final: 0.7134 (tp30)
REVERT: A  888 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7019 (mt-10)
REVERT: A 1351 SER cc_start: 0.7249 (m) cc_final: 0.6662 (p)
  outliers start: 6
  outliers final: 4
  residues processed: 163
  average time/residue: 0.2603
  time to fit residues: 59.3022
Evaluate side-chains
  147 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 143
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  630 GLU
Chi-restraints excluded: chain A residue 1054 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 57 optimal weight:    7.9990
   chunk 13 optimal weight:    6.9990
   chunk 59 optimal weight:    0.8980
   chunk 37 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 43 optimal weight:   20.0000
   chunk 10 optimal weight:    0.3980
   chunk 107 optimal weight:    7.9990
   chunk 128 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   overall best weight:    4.0586

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

Flipped N/Q/H residues before XYZ refinement:
A 966 GLN
A1032 GLN
A1231 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.163899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.129801 restraints weight = 22742.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 2.15
r_work: 0.3161 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3150
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3150 r_free = 0.3150    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3150 r_free = 0.3150    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3150
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.1063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  11549  Z= 0.166
  Angle     :  0.578   8.705  15914  Z= 0.308
  Chirality :  0.041   0.189   1762
  Planarity :  0.005   0.048   1828
  Dihedral  : 18.348 108.976   2047
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  6.53 %
    Favored  : 92.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.24), residues: 1250
  helix:  1.73 (0.20), residues: 696
  sheet:  0.76 (0.53), residues: 103
  loop : -0.99 (0.28), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 864 
 HIS   0.007   0.001   HIS A 943 
 PHE   0.013   0.001   PHE A 886 
 TYR   0.016   0.002   TYR A 496 
 ARG   0.002   0.000   ARG A1250 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04785 (  586)
  hydrogen bonds       : angle       4.01667 ( 1638)
  covalent geometry    : bond        0.00383 (11548)
  covalent geometry    : angle       0.57780 (15914)
  Misc. bond           : bond        0.00034 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 149
  time to evaluate  : 1.247 
Fit side-chains
REVERT: B   25 ASN cc_start: 0.7049 (t0) cc_final: 0.6752 (t0)
REVERT: B  214 LYS cc_start: 0.8172 (mmtm) cc_final: 0.7863 (mmtm)
REVERT: A  461 MET cc_start: 0.8724 (tmm) cc_final: 0.8172 (ttt)
REVERT: A  468 GLU cc_start: 0.8112 (tp30) cc_final: 0.7872 (tp30)
REVERT: A  527 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6938 (mm-30)
REVERT: A 1019 THR cc_start: 0.8914 (m) cc_final: 0.8587 (m)
  outliers start: 12
  outliers final: 11
  residues processed: 152
  average time/residue: 0.2586
  time to fit residues: 55.4432
Evaluate side-chains
  159 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 148
  time to evaluate  : 1.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain B residue  309 ASP
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  630 GLU
Chi-restraints excluded: chain A residue  696 THR
Chi-restraints excluded: chain A residue 1054 LEU
Chi-restraints excluded: chain A residue 1231 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 119 optimal weight:    0.6980
   chunk 86 optimal weight:    9.9990
   chunk 124 optimal weight:    7.9990
   chunk 66 optimal weight:    4.9990
   chunk 120 optimal weight:   10.0000
   chunk 1 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 27 optimal weight:    9.9990
   chunk 77 optimal weight:    7.9990
   chunk 99 optimal weight:    6.9990
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
B  96 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.165122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.132029 restraints weight = 16255.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 1.58
r_work: 0.3221 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3090 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3074
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3074
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.1172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11549  Z= 0.138
  Angle     :  0.555   8.619  15914  Z= 0.297
  Chirality :  0.039   0.160   1762
  Planarity :  0.004   0.050   1828
  Dihedral  : 18.354 108.375   2047
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  8.81 %
    Favored  : 90.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.24), residues: 1250
  helix:  1.80 (0.20), residues: 697
  sheet:  0.80 (0.52), residues: 103
  loop : -0.96 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 864 
 HIS   0.006   0.001   HIS A1057 
 PHE   0.013   0.001   PHE A 886 
 TYR   0.016   0.001   TYR A 496 
 ARG   0.003   0.000   ARG A1220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04411 (  586)
  hydrogen bonds       : angle       3.92855 ( 1638)
  covalent geometry    : bond        0.00310 (11548)
  covalent geometry    : angle       0.55548 (15914)
  Misc. bond           : bond        0.00036 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 149
  time to evaluate  : 1.238 
Fit side-chains
REVERT: B   25 ASN cc_start: 0.7173 (t0) cc_final: 0.6852 (t0)
REVERT: B  168 MET cc_start: 0.8104 (mmm) cc_final: 0.7784 (tpt)
REVERT: B  214 LYS cc_start: 0.8174 (mmtm) cc_final: 0.7939 (mmtm)
REVERT: A  461 MET cc_start: 0.8776 (tmm) cc_final: 0.8309 (ttt)
REVERT: A  527 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7107 (mm-30)
REVERT: A  988 LYS cc_start: 0.7108 (tmtt) cc_final: 0.6780 (tppt)
REVERT: A 1019 THR cc_start: 0.8910 (m) cc_final: 0.8627 (m)
REVERT: A 1351 SER cc_start: 0.7356 (m) cc_final: 0.6759 (p)
  outliers start: 9
  outliers final: 6
  residues processed: 151
  average time/residue: 0.2490
  time to fit residues: 53.7999
Evaluate side-chains
  153 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 147
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain A residue  502 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 20 optimal weight:    6.9990
   chunk 91 optimal weight:    0.0770
   chunk 93 optimal weight:    7.9990
   chunk 8 optimal weight:   20.0000
   chunk 31 optimal weight:    0.8980
   chunk 60 optimal weight:   10.0000
   chunk 40 optimal weight:    0.8980
   chunk 68 optimal weight:    9.9990
   chunk 25 optimal weight:    4.9990
   chunk 121 optimal weight:   40.0000
   overall best weight:    2.7742

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

Flipped N/Q/H residues before XYZ refinement:
A1231 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.164898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.130950 restraints weight = 16268.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 1.84
r_work: 0.3226 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3098 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3083
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3083
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.1319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11549  Z= 0.135
  Angle     :  0.541   8.598  15914  Z= 0.290
  Chirality :  0.039   0.142   1762
  Planarity :  0.004   0.053   1828
  Dihedral  : 18.364 107.505   2047
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  9.66 %
    Favored  : 89.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.24), residues: 1250
  helix:  1.88 (0.20), residues: 691
  sheet:  0.76 (0.52), residues: 103
  loop : -0.89 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 864 
 HIS   0.006   0.001   HIS A1057 
 PHE   0.012   0.001   PHE A 886 
 TYR   0.016   0.001   TYR A 496 
 ARG   0.003   0.000   ARG A1220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04238 (  586)
  hydrogen bonds       : angle       3.85629 ( 1638)
  covalent geometry    : bond        0.00304 (11548)
  covalent geometry    : angle       0.54118 (15914)
  Misc. bond           : bond        0.00038 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 152
  time to evaluate  : 1.188 
Fit side-chains
REVERT: B   25 ASN cc_start: 0.7235 (t0) cc_final: 0.6905 (t0)
REVERT: B  168 MET cc_start: 0.8167 (mmm) cc_final: 0.7845 (tpt)
REVERT: A  461 MET cc_start: 0.8815 (tmm) cc_final: 0.8485 (ttt)
REVERT: A  527 GLU cc_start: 0.7290 (mm-30) cc_final: 0.7054 (mm-30)
REVERT: A  988 LYS cc_start: 0.7299 (tmtt) cc_final: 0.6924 (tppt)
REVERT: A 1019 THR cc_start: 0.8929 (m) cc_final: 0.8685 (m)
  outliers start: 12
  outliers final: 8
  residues processed: 155
  average time/residue: 0.2524
  time to fit residues: 55.8594
Evaluate side-chains
  153 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 145
  time to evaluate  : 1.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain B residue  309 ASP
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  696 THR
Chi-restraints excluded: chain A residue  794 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    3.9990
   chunk 93 optimal weight:   10.0000
   chunk 77 optimal weight:    6.9990
   chunk 99 optimal weight:   10.0000
   chunk 21 optimal weight:    8.9990
   chunk 82 optimal weight:    9.9990
   chunk 33 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
A1231 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.163853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.130040 restraints weight = 18088.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 1.82
r_work: 0.3210 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3065
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3065
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.1398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  11549  Z= 0.153
  Angle     :  0.560   8.768  15914  Z= 0.300
  Chirality :  0.040   0.149   1762
  Planarity :  0.004   0.054   1828
  Dihedral  : 18.429 107.476   2047
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  9.85 %
    Favored  : 88.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.24), residues: 1250
  helix:  1.74 (0.20), residues: 697
  sheet:  0.68 (0.53), residues: 103
  loop : -0.96 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 864 
 HIS   0.006   0.001   HIS A1057 
 PHE   0.014   0.001   PHE A 886 
 TYR   0.016   0.001   TYR A 496 
 ARG   0.002   0.000   ARG A1220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04478 (  586)
  hydrogen bonds       : angle       3.90000 ( 1638)
  covalent geometry    : bond        0.00351 (11548)
  covalent geometry    : angle       0.56045 (15914)
  Misc. bond           : bond        0.00040 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 149
  time to evaluate  : 1.648 
Fit side-chains
REVERT: B   25 ASN cc_start: 0.7300 (t0) cc_final: 0.6954 (t0)
REVERT: B  168 MET cc_start: 0.8187 (mmm) cc_final: 0.7887 (tpt)
REVERT: A  461 MET cc_start: 0.8858 (tmm) cc_final: 0.8523 (ttt)
REVERT: A  527 GLU cc_start: 0.7281 (mm-30) cc_final: 0.7059 (mm-30)
REVERT: A  988 LYS cc_start: 0.7198 (tmtt) cc_final: 0.6859 (tppt)
REVERT: A 1019 THR cc_start: 0.8867 (m) cc_final: 0.8613 (m)
  outliers start: 15
  outliers final: 11
  residues processed: 153
  average time/residue: 0.2676
  time to fit residues: 59.3104
Evaluate side-chains
  158 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain B residue  309 ASP
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  630 GLU
Chi-restraints excluded: chain A residue  696 THR
Chi-restraints excluded: chain A residue  794 SER
Chi-restraints excluded: chain A residue 1231 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 61 optimal weight:    8.9990
   chunk 41 optimal weight:    6.9990
   chunk 44 optimal weight:    0.6980
   chunk 81 optimal weight:   20.0000
   chunk 87 optimal weight:    9.9990
   chunk 108 optimal weight:   10.0000
   chunk 88 optimal weight:    0.7980
   chunk 16 optimal weight:   20.0000
   chunk 116 optimal weight:    7.9990
   chunk 123 optimal weight:   30.0000
   chunk 94 optimal weight:    7.9990
   overall best weight:    4.8986

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

Flipped N/Q/H residues before XYZ refinement:
A1231 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.162595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.128930 restraints weight = 17764.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 1.80
r_work: 0.3171 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3159
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3159 r_free = 0.3159    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3159 r_free = 0.3159    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3159
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.1484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11549  Z= 0.185
  Angle     :  0.595   8.970  15914  Z= 0.317
  Chirality :  0.041   0.167   1762
  Planarity :  0.005   0.059   1828
  Dihedral  : 18.543 108.335   2047
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 10.89 %
    Favored  : 87.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.24), residues: 1250
  helix:  1.61 (0.20), residues: 697
  sheet:  0.72 (0.52), residues: 101
  loop : -1.08 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 455 
 HIS   0.007   0.001   HIS A 943 
 PHE   0.014   0.001   PHE A 886 
 TYR   0.016   0.002   TYR A 496 
 ARG   0.003   0.000   ARG A1220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04887 (  586)
  hydrogen bonds       : angle       4.01906 ( 1638)
  covalent geometry    : bond        0.00430 (11548)
  covalent geometry    : angle       0.59546 (15914)
  Misc. bond           : bond        0.00036 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 146
  time to evaluate  : 1.153 
Fit side-chains
REVERT: B   25 ASN cc_start: 0.7144 (t0) cc_final: 0.6815 (t0)
REVERT: A  461 MET cc_start: 0.8857 (tmm) cc_final: 0.8481 (ttt)
REVERT: A  527 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6814 (mm-30)
REVERT: A  988 LYS cc_start: 0.7074 (tmtt) cc_final: 0.6773 (tppt)
  outliers start: 14
  outliers final: 12
  residues processed: 149
  average time/residue: 0.2518
  time to fit residues: 53.2068
Evaluate side-chains
  152 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 140
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain B residue  309 ASP
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  630 GLU
Chi-restraints excluded: chain A residue  696 THR
Chi-restraints excluded: chain A residue  794 SER
Chi-restraints excluded: chain A residue 1054 LEU
Chi-restraints excluded: chain A residue 1233 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 34 optimal weight:   10.0000
   chunk 97 optimal weight:    8.9990
   chunk 68 optimal weight:    0.0870
   chunk 40 optimal weight:    0.9980
   chunk 44 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   chunk 63 optimal weight:   10.0000
   chunk 24 optimal weight:    7.9990
   chunk 96 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    2.6164

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

Flipped N/Q/H residues before XYZ refinement:
A 890 HIS
A1231 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.164825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.130885 restraints weight = 17700.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 1.74
r_work: 0.3222 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3094 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3079
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3079
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.1473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11549  Z= 0.135
  Angle     :  0.545   8.576  15914  Z= 0.291
  Chirality :  0.039   0.167   1762
  Planarity :  0.004   0.055   1828
  Dihedral  : 18.353 107.352   2047
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 11.55 %
    Favored  : 87.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.24), residues: 1250
  helix:  1.84 (0.20), residues: 690
  sheet:  0.75 (0.52), residues: 101
  loop : -0.95 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 455 
 HIS   0.006   0.001   HIS A1057 
 PHE   0.013   0.001   PHE A 886 
 TYR   0.015   0.001   TYR A 496 
 ARG   0.003   0.000   ARG A1220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04237 (  586)
  hydrogen bonds       : angle       3.86728 ( 1638)
  covalent geometry    : bond        0.00304 (11548)
  covalent geometry    : angle       0.54535 (15914)
  Misc. bond           : bond        0.00042 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 148
  time to evaluate  : 1.137 
Fit side-chains
REVERT: B   25 ASN cc_start: 0.7193 (t0) cc_final: 0.6830 (t0)
REVERT: B   85 PHE cc_start: 0.7921 (t80) cc_final: 0.7647 (t80)
REVERT: B  168 MET cc_start: 0.8128 (mmm) cc_final: 0.7838 (tpt)
REVERT: A  461 MET cc_start: 0.8849 (tmm) cc_final: 0.8490 (ttt)
REVERT: A  527 GLU cc_start: 0.7242 (mm-30) cc_final: 0.7021 (mm-30)
REVERT: A  988 LYS cc_start: 0.7104 (tmtt) cc_final: 0.6768 (tppt)
REVERT: A 1019 THR cc_start: 0.9074 (m) cc_final: 0.8814 (m)
  outliers start: 11
  outliers final: 9
  residues processed: 150
  average time/residue: 0.2551
  time to fit residues: 53.8909
Evaluate side-chains
  153 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 144
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain B residue  309 ASP
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  696 THR
Chi-restraints excluded: chain A residue  794 SER
Chi-restraints excluded: chain A residue 1231 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 42 optimal weight:   30.0000
   chunk 47 optimal weight:   20.0000
   chunk 26 optimal weight:    4.9990
   chunk 126 optimal weight:   10.0000
   chunk 58 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   chunk 125 optimal weight:   10.0000
   chunk 36 optimal weight:    8.9990
   chunk 113 optimal weight:    9.9990
   chunk 33 optimal weight:    0.1980
   overall best weight:    3.6186

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

Flipped N/Q/H residues before XYZ refinement:
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1231 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.163695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.130103 restraints weight = 18459.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 1.82
r_work: 0.3192 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3175
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3175
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.1520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11549  Z= 0.155
  Angle     :  0.563   8.724  15914  Z= 0.300
  Chirality :  0.040   0.160   1762
  Planarity :  0.004   0.057   1828
  Dihedral  : 18.355 107.343   2047
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 11.84 %
    Favored  : 86.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.24), residues: 1250
  helix:  1.78 (0.20), residues: 690
  sheet:  0.67 (0.52), residues: 101
  loop : -1.00 (0.27), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 864 
 HIS   0.006   0.001   HIS A 943 
 PHE   0.014   0.001   PHE A 886 
 TYR   0.016   0.001   TYR A 496 
 ARG   0.003   0.000   ARG A1220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04488 (  586)
  hydrogen bonds       : angle       3.90434 ( 1638)
  covalent geometry    : bond        0.00356 (11548)
  covalent geometry    : angle       0.56274 (15914)
  Misc. bond           : bond        0.00038 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 141
  time to evaluate  : 1.129 
Fit side-chains
REVERT: B   25 ASN cc_start: 0.7076 (t0) cc_final: 0.6747 (t0)
REVERT: B   85 PHE cc_start: 0.7913 (t80) cc_final: 0.7642 (t80)
REVERT: B  168 MET cc_start: 0.7980 (mmm) cc_final: 0.7694 (tpt)
REVERT: A  461 MET cc_start: 0.8820 (tmm) cc_final: 0.8496 (ttt)
REVERT: A  527 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6834 (mm-30)
REVERT: A  988 LYS cc_start: 0.7064 (tmtt) cc_final: 0.6746 (tppt)
  outliers start: 13
  outliers final: 13
  residues processed: 144
  average time/residue: 0.2555
  time to fit residues: 52.3213
Evaluate side-chains
  153 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 140
  time to evaluate  : 1.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain B residue  309 ASP
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  630 GLU
Chi-restraints excluded: chain A residue  696 THR
Chi-restraints excluded: chain A residue  794 SER
Chi-restraints excluded: chain A residue 1018 MET
Chi-restraints excluded: chain A residue 1054 LEU
Chi-restraints excluded: chain A residue 1231 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   chunk 54 optimal weight:    8.9990
   chunk 123 optimal weight:   50.0000
   chunk 16 optimal weight:   10.0000
   chunk 3 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 91 optimal weight:   10.0000
   chunk 98 optimal weight:    6.9990
   chunk 76 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1231 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.162930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.129507 restraints weight = 22985.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 2.09
r_work: 0.3166 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3155
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3155 r_free = 0.3155    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3155 r_free = 0.3155    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3155
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11549  Z= 0.173
  Angle     :  0.579   8.839  15914  Z= 0.308
  Chirality :  0.040   0.164   1762
  Planarity :  0.005   0.058   1828
  Dihedral  : 18.388 107.572   2047
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 11.93 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.24), residues: 1250
  helix:  1.71 (0.20), residues: 690
  sheet:  0.59 (0.51), residues: 101
  loop : -1.04 (0.27), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 864 
 HIS   0.006   0.001   HIS A 943 
 PHE   0.013   0.001   PHE A 886 
 TYR   0.016   0.002   TYR A 496 
 ARG   0.003   0.000   ARG A1220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04683 (  586)
  hydrogen bonds       : angle       3.95850 ( 1638)
  covalent geometry    : bond        0.00401 (11548)
  covalent geometry    : angle       0.57866 (15914)
  Misc. bond           : bond        0.00035 (    1)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 143
  time to evaluate  : 1.444 
Fit side-chains
REVERT: B   25 ASN cc_start: 0.7110 (t0) cc_final: 0.6772 (t0)
REVERT: B  168 MET cc_start: 0.7995 (mmm) cc_final: 0.7691 (tpt)
REVERT: A  461 MET cc_start: 0.8845 (tmm) cc_final: 0.8510 (ttt)
REVERT: A  527 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6848 (mm-30)
REVERT: A  988 LYS cc_start: 0.7022 (tmtt) cc_final: 0.6720 (tppt)
  outliers start: 13
  outliers final: 12
  residues processed: 146
  average time/residue: 0.3549
  time to fit residues: 74.2590
Evaluate side-chains
  155 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 143
  time to evaluate  : 1.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue  133 LEU
Chi-restraints excluded: chain B residue  276 THR
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain B residue  309 ASP
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  630 GLU
Chi-restraints excluded: chain A residue  696 THR
Chi-restraints excluded: chain A residue  794 SER
Chi-restraints excluded: chain A residue 1018 MET
Chi-restraints excluded: chain A residue 1054 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   chunk 52 optimal weight:    6.9990
   chunk 13 optimal weight:    4.9990
   chunk 39 optimal weight:    7.9990
   chunk 22 optimal weight:   20.0000
   chunk 40 optimal weight:    5.9990
   chunk 51 optimal weight:   10.0000
   chunk 11 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   chunk 88 optimal weight:    2.9990
   overall best weight:    4.1788

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

Flipped N/Q/H residues before XYZ refinement:
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.163002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.128981 restraints weight = 16397.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 1.88
r_work: 0.3191 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3049
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3049 r_free = 0.3049    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3049 r_free = 0.3049    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3049
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.1605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11549  Z= 0.167
  Angle     :  0.572   8.832  15914  Z= 0.305
  Chirality :  0.040   0.156   1762
  Planarity :  0.005   0.057   1828
  Dihedral  : 18.409 107.614   2047
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 12.12 %
    Favored  : 86.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.24), residues: 1250
  helix:  1.70 (0.20), residues: 691
  sheet:  0.54 (0.51), residues: 101
  loop : -1.05 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 864 
 HIS   0.006   0.001   HIS A 943 
 PHE   0.013   0.001   PHE A 886 
 TYR   0.015   0.002   TYR A 496 
 ARG   0.003   0.000   ARG A1220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04657 (  586)
  hydrogen bonds       : angle       3.96183 ( 1638)
  covalent geometry    : bond        0.00386 (11548)
  covalent geometry    : angle       0.57225 (15914)
  Misc. bond           : bond        0.00038 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6798.59 seconds
wall clock time: 120 minutes 17.86 seconds (7217.86 seconds total)