Starting phenix.real_space_refine
on Sat Aug 23 09:48:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c5s_16442/08_2025/8c5s_16442.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c5s_16442/08_2025/8c5s_16442.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c5s_16442/08_2025/8c5s_16442.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c5s_16442/08_2025/8c5s_16442.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c5s_16442/08_2025/8c5s_16442.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c5s_16442/08_2025/8c5s_16442.map"
  }
  resolution = 3.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      65      5.49       5
     S      36      5.16       5
     C    7038      2.51       5
     N    1960      2.21       5
     O    2213      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11312
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2758
          Classifications: {'peptide': 336}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 19, 'TRANS': 316}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 7244
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 924, 7244
          Classifications: {'peptide': 924}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 50}
          Link IDs: {'PTRANS': 44, 'TRANS': 879}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 172
          Unresolved non-hydrogen angles: 209
          Unresolved non-hydrogen dihedrals: 135
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 6, 'ARG:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 80
    Chain: "N"
      Number of atoms: 580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 580
          Classifications: {'DNA': 28}
          Link IDs: {'rna3p': 27}
    Chain: "T"
      Number of atoms: 569
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 569
          Classifications: {'DNA': 28}
          Link IDs: {'rna3p': 27}
    Chain: "C"
      Number of atoms: 129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 129
          Classifications: {'RNA': 6}
          Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 2}
          Link IDs: {'rna3p': 5}
    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: 2.08, per 1000 atoms: 0.18
  Number of scatterers: 11312
  At special positions: 0
  Unit cell: (104.76, 116.4, 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      36     16.00
     P      65     15.00
     O    2213      8.00
     N    1960      7.00
     C    7038      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: 0.81
  Conformation dependent library (CDL) restraints added in 376.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2384

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 10 sheets defined
      57.1% alpha, 7.5% beta
      23 base pairs and 46 stacking pairs defined.
    Time for finding SS restraints: 1.32
  Creating SS restraints...
    Processing helix  chain 'B' and resid 7 through 14
      removed outlier: 3.686A  pdb=" N   LEU B  14 " --> pdb=" O   ASP B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 37
      removed outlier: 3.607A  pdb=" N   TYR B  29 " --> pdb=" O   ASN B  25 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ASP B  37 " --> pdb=" O   PHE B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 42
      removed outlier: 4.122A  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 90
    Processing helix  chain 'B' and resid 104 through 113
      removed outlier: 4.098A  pdb=" N   TYR B 108 " --> pdb=" O   ASP B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 157
      removed outlier: 3.830A  pdb=" N   ILE B 147 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLY B 155 " --> pdb=" O   LEU B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 164
      removed outlier: 3.576A  pdb=" N   PHE B 163 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 181
    Processing helix  chain 'B' and resid 190 through 200
    Processing helix  chain 'B' and resid 210 through 215
    Processing helix  chain 'B' and resid 217 through 225
      removed outlier: 4.070A  pdb=" N   GLU B 222 " --> pdb=" O   SER B 218 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   GLU B 223 " --> pdb=" O   GLN B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 234
      removed outlier: 3.617A  pdb=" N   ILE B 234 " --> pdb=" O   ALA B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 266
    Processing helix  chain 'B' and resid 273 through 278
      removed outlier: 3.578A  pdb=" N   VAL B 277 " --> pdb=" O   PRO B 273 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   MET B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 273 through 278'
    Processing helix  chain 'B' and resid 279 through 281
      No H-bonds generated for 'chain 'B' and resid 279 through 281'
    Processing helix  chain 'B' and resid 284 through 293
      removed outlier: 3.618A  pdb=" N   TYR B 288 " --> pdb=" O   GLY B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 300
      removed outlier: 3.557A  pdb=" N   LEU B 299 " --> pdb=" O   ASP B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 320
      removed outlier: 3.548A  pdb=" N   GLU B 320 " --> pdb=" O   LYS B 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 395
    Processing helix  chain 'A' and resid 397 through 421
      removed outlier: 5.057A  pdb=" N   ASP A 414 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   ARG A 415 " --> pdb=" O   PHE A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 442
      removed outlier: 4.138A  pdb=" N   ALA A 440 " --> pdb=" O   GLU A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 474
      Proline residue:  A 463  - end of helix
    Processing helix  chain 'A' and resid 487 through 492
    Processing helix  chain 'A' and resid 492 through 501
      Proline residue:  A 498  - end of helix
      removed outlier: 3.525A  pdb=" N   THR A 501 " --> pdb=" O   GLY A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 517
    Processing helix  chain 'A' and resid 531 through 552
      removed outlier: 3.571A  pdb=" N   LEU A 552 " --> pdb=" O   SER A 548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 612
    Processing helix  chain 'A' and resid 652 through 662
    Processing helix  chain 'A' and resid 703 through 717
      removed outlier: 4.074A  pdb=" N   VAL A 707 " --> pdb=" O   SER A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 731
    Processing helix  chain 'A' and resid 738 through 749
    Processing helix  chain 'A' and resid 775 through 813
      removed outlier: 3.568A  pdb=" N   LEU A 779 " --> pdb=" O   ASP A 775 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 842 through 848
      removed outlier: 3.588A  pdb=" N   LEU A 848 " --> pdb=" O   MET A 844 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 872
    Processing helix  chain 'A' and resid 879 through 889
    Processing helix  chain 'A' and resid 890 through 900
      removed outlier: 3.526A  pdb=" N   ASN A 900 " --> pdb=" O   ASP A 896 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 907 through 911
    Processing helix  chain 'A' and resid 913 through 930
    Processing helix  chain 'A' and resid 948 through 959
    Processing helix  chain 'A' and resid 961 through 966
    Processing helix  chain 'A' and resid 977 through 994
    Processing helix  chain 'A' and resid 998 through 1004
    Processing helix  chain 'A' and resid 1009 through 1021
      removed outlier: 4.068A  pdb=" N   VAL A1013 " --> pdb=" O   THR A1009 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   VAL A1021 " --> pdb=" O   VAL A1017 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1025 through 1036
    Processing helix  chain 'A' and resid 1037 through 1041
      removed outlier: 3.926A  pdb=" N   PHE A1041 " --> pdb=" O   SER A1038 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1047 through 1063
    Processing helix  chain 'A' and resid 1067 through 1085
      removed outlier: 3.514A  pdb=" N   LEU A1071 " --> pdb=" O   HIS A1067 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ILE A1072 " --> pdb=" O   SER A1068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1149 through 1180
      removed outlier: 3.995A  pdb=" N   GLN A1153 " --> pdb=" O   ASN A1149 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   LYS A1154 " --> pdb=" O   ALA A1150 " (cutoff:3.500A)
      Proline residue:  A1158  - end of helix
      removed outlier: 3.833A  pdb=" N   ALA A1167 " --> pdb=" O   HIS A1163 " (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 1257
    Processing helix  chain 'A' and resid 1264 through 1281
      removed outlier: 3.697A  pdb=" N   SER A1281 " --> pdb=" O   GLU A1277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1292
    Processing helix  chain 'A' and resid 1295 through 1300
    Processing helix  chain 'A' and resid 1305 through 1311
      removed outlier: 3.834A  pdb=" N   GLU A1310 " --> pdb=" O   LEU A1306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1339 through 1345
      removed outlier: 3.557A  pdb=" N   VAL A1342 " --> pdb=" O   ASP A1339 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ASN A1345 " --> pdb=" O   VAL A1342 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 99
      removed outlier: 3.647A  pdb=" N   GLU B  77 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   SER B  74 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LEU B  76 " --> pdb=" O   ASP B  52 " (cutoff:3.500A)
      removed outlier: 10.435A  pdb=" N   LYS B 165 " --> pdb=" O   ASP B 130 " (cutoff:3.500A)
      removed outlier: 7.382A  pdb=" N   PHE B 132 " --> pdb=" O   LYS B 165 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   LYS B 167 " --> pdb=" O   PHE B 132 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ALA B 206 " --> pdb=" O   LEU B 244 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   GLU B 246 " --> pdb=" O   LEU B 204 " (cutoff:3.500A)
      removed outlier: 6.032A  pdb=" N   LEU B 204 " --> pdb=" O   GLU B 246 " (cutoff:3.500A)
      removed outlier: 9.263A  pdb=" N   ILE B 227 " --> pdb=" O   LYS B 203 " (cutoff:3.500A)
      removed outlier: 7.238A  pdb=" N   ILE B 205 " --> pdb=" O   ILE B 227 " (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 614 through 616
    Processing sheet with id=AA4, first strand: chain 'A' and resid 818 through 819
    Processing sheet with id=AA5, first strand: chain 'A' and resid 822 through 824
    Processing sheet with id=AA6, first strand: chain 'A' and resid 855 through 856
      removed outlier: 3.969A  pdb=" N   LYS A 855 " --> pdb=" O   SER A 938 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   SER A 938 " --> pdb=" O   LYS A 855 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 942 through 944
      removed outlier: 3.648A  pdb=" N   THR A1193 " --> pdb=" O   VAL A 942 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1087 through 1088
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1109 through 1111
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1127 through 1131

    508 hydrogen bonds defined for protein.
    1461 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      51 hydrogen bonds
      102 hydrogen bond angles
      0 basepair planarities
      23 basepair parallelities
      46 stacking parallelities
  Total time for adding SS restraints: 2.04

  Time building geometry restraints manager: 1.04 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: 3140
        1.34 -     1.45: 2231
        1.45 -     1.57: 6142
        1.57 -     1.69: 133
        1.69 -     1.81: 62
  Bond restraints: 11708
  Sorted by residual:
  bond pdb=" O3'  DC T  24 "
       pdb=" P    DG T  25 "
    ideal  model  delta    sigma   weight residual
    1.607  1.728 -0.121 1.50e-02 4.44e+03 6.56e+01
  bond pdb=" O3'  DT N 135 "
       pdb=" P    DG N 136 "
    ideal  model  delta    sigma   weight residual
    1.607  1.495  0.112 1.50e-02 4.44e+03 5.56e+01
  bond pdb=" O3'  DC T  17 "
       pdb=" P    DA T  18 "
    ideal  model  delta    sigma   weight residual
    1.607  1.499  0.108 1.50e-02 4.44e+03 5.16e+01
  bond pdb=" O3'  DA T  31 "
       pdb=" P    DT T  32 "
    ideal  model  delta    sigma   weight residual
    1.607  1.506  0.101 1.50e-02 4.44e+03 4.56e+01
  bond pdb=" O3'  DA T  34 "
       pdb=" P    DA T  35 "
    ideal  model  delta    sigma   weight residual
    1.607  1.523  0.084 1.50e-02 4.44e+03 3.15e+01
  ... (remaining 11703 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.50: 15979
        4.50 -     9.00: 129
        9.00 -    13.50: 24
       13.50 -    18.00: 5
       18.00 -    22.50: 3
  Bond angle restraints: 16140
  Sorted by residual:
  angle pdb=" C3'  DA T  35 "
        pdb=" O3'  DA T  35 "
        pdb=" P    DT T  36 "
      ideal   model   delta    sigma   weight residual
     120.20   99.37   20.83 1.50e+00 4.44e-01 1.93e+02
  angle pdb=" C3'   A C 104 "
        pdb=" O3'   A C 104 "
        pdb=" P     A C 105 "
      ideal   model   delta    sigma   weight residual
     120.20  101.23   18.97 1.50e+00 4.44e-01 1.60e+02
  angle pdb=" C3'  DC T  17 "
        pdb=" O3'  DC T  17 "
        pdb=" P    DA T  18 "
      ideal   model   delta    sigma   weight residual
     120.20  135.17  -14.97 1.50e+00 4.44e-01 9.96e+01
  angle pdb=" O3'  DG N 136 "
        pdb=" C3'  DG N 136 "
        pdb=" C2'  DG N 136 "
      ideal   model   delta    sigma   weight residual
     111.50   98.40   13.10 1.50e+00 4.44e-01 7.62e+01
  angle pdb=" C3'  DT T  19 "
        pdb=" O3'  DT T  19 "
        pdb=" P    DT T  20 "
      ideal   model   delta    sigma   weight residual
     120.20  107.31   12.89 1.50e+00 4.44e-01 7.38e+01
  ... (remaining 16135 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.06: 6440
       30.06 -    60.11: 443
       60.11 -    90.17: 25
       90.17 -   120.22: 2
      120.22 -   150.28: 4
  Dihedral angle restraints: 6914
    sinusoidal: 3234
      harmonic: 3680
  Sorted by residual:
  dihedral pdb=" O5' GTP C 201 "
           pdb=" O3A GTP C 201 "
           pdb=" PA  GTP C 201 "
           pdb=" PB  GTP C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -85.88   55.19 -141.07     1      2.00e+01 2.50e-03 4.27e+01
  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  167.39  136.40     1      2.00e+01 2.50e-03 4.14e+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  -18.61  123.20     1      2.00e+01 2.50e-03 3.71e+01
  ... (remaining 6911 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.134: 1716
       0.134 -    0.268: 32
       0.268 -    0.402: 7
       0.402 -    0.536: 25
       0.536 -    0.670: 8
  Chirality restraints: 1788
  Sorted by residual:
  chirality pdb=" C1'  DG T  16 "
            pdb=" O4'  DG T  16 "
            pdb=" C2'  DG T  16 "
            pdb=" N9   DG T  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    1.75    0.67 2.00e-01 2.50e+01 1.12e+01
  chirality pdb=" P    DT N 109 "
            pdb=" OP1  DT N 109 "
            pdb=" OP2  DT N 109 "
            pdb=" O5'  DT N 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.97   -0.62 2.00e-01 2.50e+01 9.69e+00
  chirality pdb=" P    DC T  10 "
            pdb=" OP1  DC T  10 "
            pdb=" OP2  DC T  10 "
            pdb=" O5'  DC T  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.97   -0.62 2.00e-01 2.50e+01 9.64e+00
  ... (remaining 1785 not shown)

  Planarity restraints: 1841
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 900 "   -0.056 5.00e-02 4.00e+02   8.44e-02 1.14e+01
        pdb=" N   PRO A 901 "    0.146 5.00e-02 4.00e+02
        pdb=" CA  PRO A 901 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 901 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 767 "    0.057 5.00e-02 4.00e+02   8.34e-02 1.11e+01
        pdb=" N   PRO A 768 "   -0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO A 768 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 768 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 462 "   -0.032 5.00e-02 4.00e+02   4.87e-02 3.79e+00
        pdb=" N   PRO A 463 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A 463 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 463 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1838 not shown)

  Histogram of nonbonded interaction distances:
        1.84 -     2.45: 34
        2.45 -     3.07: 7210
        3.07 -     3.68: 17158
        3.68 -     4.29: 25016
        4.29 -     4.90: 40963
  Nonbonded interactions: 90381
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN B 336 "
            pdb=" N2   DG T  25 "
     model   vdw
     1.842 3.120
  nonbonded pdb=" O   ASN A 900 "
            pdb=" OD1 ASN A 900 "
     model   vdw
     2.082 3.040
  nonbonded pdb=" OG1 THR A1132 "
            pdb=" O   GLN A1135 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OE1 GLN A 944 "
            pdb=" OG  SER A1351 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OG  SER A 794 "
            pdb=" N7   DG T  25 "
     model   vdw
     2.267 3.120
  ... (remaining 90376 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.110
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.210
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
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      :  0.007   0.121  11709  Z= 0.348
  Angle     :  1.037  22.496  16140  Z= 0.543
  Chirality :  0.087   0.670   1788
  Planarity :  0.005   0.084   1841
  Dihedral  : 18.483 150.277   4530
  Min Nonbonded Distance : 1.842

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.24), residues: 1252
  helix:  1.71 (0.21), residues: 649
  sheet: -0.89 (0.49), residues: 111
  loop : -1.04 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 264 
 TYR   0.024   0.001   TYR B 161 
 PHE   0.029   0.001   PHE A1338 
 TRP   0.023   0.001   TRP A 915 
 HIS   0.004   0.001   HIS A1169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00658 (11708)
  covalent geometry    : angle       1.03711 (16140)
  hydrogen bonds       : bond        0.14756 (  559)
  hydrogen bonds       : angle       6.18565 ( 1563)
  Misc. bond           : bond        0.01822 (    1)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  476 LEU cc_start: 0.6034 (mt) cc_final: 0.5205 (tt)
REVERT: A 1005 LYS cc_start: 0.7467 (tmmt) cc_final: 0.7193 (tttp)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.0933
  time to fit residues: 24.4518
Evaluate side-chains
  150 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:   10.9990
   chunk 66 optimal weight:    9.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:   40.0000
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    7.9990
   chunk 35 optimal weight:    7.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 137 ASN
B 187 HIS
A 492 ASN
A 900 ASN
A 987 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.157943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.130315 restraints weight = 15505.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.130907 restraints weight = 11819.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.132281 restraints weight = 9871.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.134268 restraints weight = 8308.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.134411 restraints weight = 7133.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.1238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  11709  Z= 0.230
  Angle     :  0.648   9.564  16140  Z= 0.344
  Chirality :  0.043   0.147   1788
  Planarity :  0.005   0.059   1841
  Dihedral  : 20.048 170.885   2103
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.87 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  :  8.29 %
    Favored  : 89.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.24), residues: 1252
  helix:  1.53 (0.21), residues: 662
  sheet: -0.92 (0.46), residues: 129
  loop : -1.22 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 883 
 TYR   0.023   0.002   TYR B 161 
 PHE   0.020   0.002   PHE A1161 
 TRP   0.016   0.002   TRP A 915 
 HIS   0.011   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 (11708)
  covalent geometry    : angle       0.64774 (16140)
  hydrogen bonds       : bond        0.05709 (  559)
  hydrogen bonds       : angle       4.69806 ( 1563)
  Misc. bond           : bond        0.00081 (    1)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 151
  time to evaluate  : 0.270 
Fit side-chains
REVERT: B  137 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8534 (t0)
REVERT: B  321 TRP cc_start: 0.8079 (t60) cc_final: 0.7091 (t60)
REVERT: A  439 LYS cc_start: 0.6578 (tttt) cc_final: 0.6185 (tttt)
  outliers start: 21
  outliers final: 15
  residues processed: 164
  average time/residue: 0.0906
  time to fit residues: 21.2131
Evaluate side-chains
  156 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  137 ASN
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain B residue  187 HIS
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  472 CYS
Chi-restraints excluded: chain A residue  512 THR
Chi-restraints excluded: chain A residue  784 LEU
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  996 LYS
Chi-restraints excluded: chain A residue 1096 PHE
Chi-restraints excluded: chain A residue 1146 ASN
Chi-restraints excluded: chain A residue 1186 SER
Chi-restraints excluded: chain A residue 1189 ASP
Chi-restraints excluded: chain A residue 1235 ILE
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1350 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 62 optimal weight:    6.9990
   chunk 14 optimal weight:    8.9990
   chunk 33 optimal weight:    9.9990
   chunk 86 optimal weight:    5.9990
   chunk 24 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 44 optimal weight:    0.4980
   chunk 89 optimal weight:    5.9990
   chunk 34 optimal weight:    0.5980
   overall best weight:    3.4186

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

Flipped N/Q/H residues before XYZ refinement:
B 137 ASN
A 900 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.157277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.130535 restraints weight = 15503.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.131768 restraints weight = 13175.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.133143 restraints weight = 11973.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.133490 restraints weight = 9451.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.133731 restraints weight = 8676.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.1438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11709  Z= 0.155
  Angle     :  0.583   8.852  16140  Z= 0.307
  Chirality :  0.039   0.143   1788
  Planarity :  0.005   0.053   1841
  Dihedral  : 19.551 148.872   2103
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.07 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 12.21 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.24), residues: 1252
  helix:  1.60 (0.21), residues: 664
  sheet: -0.95 (0.44), residues: 129
  loop : -1.23 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 264 
 TYR   0.026   0.001   TYR B 161 
 PHE   0.016   0.001   PHE A1338 
 TRP   0.016   0.001   TRP A 915 
 HIS   0.011   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (11708)
  covalent geometry    : angle       0.58317 (16140)
  hydrogen bonds       : bond        0.04738 (  559)
  hydrogen bonds       : angle       4.43912 ( 1563)
  Misc. bond           : bond        0.00095 (    1)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 149
  time to evaluate  : 0.255 
Fit side-chains
REVERT: B  247 MET cc_start: 0.8443 (mmt) cc_final: 0.7958 (tpp)
REVERT: B  321 TRP cc_start: 0.8026 (t60) cc_final: 0.7464 (t60)
  outliers start: 23
  outliers final: 18
  residues processed: 162
  average time/residue: 0.0892
  time to fit residues: 20.9309
Evaluate side-chains
  163 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 145
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  472 CYS
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  692 TYR
Chi-restraints excluded: chain A residue  784 LEU
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  991 GLU
Chi-restraints excluded: chain A residue  996 LYS
Chi-restraints excluded: chain A residue 1096 PHE
Chi-restraints excluded: chain A residue 1146 ASN
Chi-restraints excluded: chain A residue 1186 SER
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1189 ASP
Chi-restraints excluded: chain A residue 1235 ILE
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1350 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 125 optimal weight:   10.0000
   chunk 24 optimal weight:    6.9990
   chunk 29 optimal weight:    9.9990
   chunk 65 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 72 optimal weight:    8.9990
   chunk 86 optimal weight:   10.0000
   chunk 4 optimal weight:    0.1980
   chunk 48 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   chunk 40 optimal weight:    9.9990
   overall best weight:    2.8386

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

Flipped N/Q/H residues before XYZ refinement:
B 137 ASN
A 900 ASN
A 968 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.158520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.132245 restraints weight = 15499.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.133137 restraints weight = 12985.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.133971 restraints weight = 11169.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.134690 restraints weight = 9737.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.134943 restraints weight = 8836.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11709  Z= 0.139
  Angle     :  0.566   9.328  16140  Z= 0.296
  Chirality :  0.039   0.141   1788
  Planarity :  0.004   0.053   1841
  Dihedral  : 19.103 136.287   2103
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.47 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 13.42 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.24), residues: 1252
  helix:  1.71 (0.21), residues: 664
  sheet: -0.96 (0.43), residues: 129
  loop : -1.23 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 264 
 TYR   0.023   0.001   TYR B 161 
 PHE   0.016   0.001   PHE A1338 
 TRP   0.019   0.001   TRP A 915 
 HIS   0.006   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (11708)
  covalent geometry    : angle       0.56557 (16140)
  hydrogen bonds       : bond        0.04321 (  559)
  hydrogen bonds       : angle       4.31373 ( 1563)
  Misc. bond           : bond        0.00085 (    1)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 154
  time to evaluate  : 0.237 
Fit side-chains
REVERT: B  137 ASN cc_start: 0.8973 (OUTLIER) cc_final: 0.8522 (t0)
REVERT: B  247 MET cc_start: 0.8424 (mmt) cc_final: 0.7980 (tpp)
REVERT: B  321 TRP cc_start: 0.8005 (t60) cc_final: 0.7207 (t60)
REVERT: A  420 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7202 (tm-30)
REVERT: A  503 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7614 (mp)
REVERT: A 1215 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7410 (t)
  outliers start: 28
  outliers final: 19
  residues processed: 172
  average time/residue: 0.0856
  time to fit residues: 21.5525
Evaluate side-chains
  166 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 143
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  137 ASN
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain A residue  472 CYS
Chi-restraints excluded: chain A residue  503 ILE
Chi-restraints excluded: chain A residue  602 SER
Chi-restraints excluded: chain A residue  651 ILE
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain A residue  784 LEU
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  991 GLU
Chi-restraints excluded: chain A residue  996 LYS
Chi-restraints excluded: chain A residue 1096 PHE
Chi-restraints excluded: chain A residue 1146 ASN
Chi-restraints excluded: chain A residue 1186 SER
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1189 ASP
Chi-restraints excluded: chain A residue 1215 VAL
Chi-restraints excluded: chain A residue 1235 ILE
Chi-restraints excluded: chain A residue 1296 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 101 optimal weight:    0.6980
   chunk 39 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 73 optimal weight:    4.9990
   chunk 80 optimal weight:    9.9990
   chunk 19 optimal weight:    0.8980
   chunk 7 optimal weight:    7.9990
   chunk 16 optimal weight:    7.9990
   chunk 47 optimal weight:    8.9990
   chunk 89 optimal weight:    5.9990
   overall best weight:    2.7184

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

Flipped N/Q/H residues before XYZ refinement:
B 137 ASN
A 900 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.159053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.132728 restraints weight = 15389.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.133448 restraints weight = 13122.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.134395 restraints weight = 11684.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.134570 restraints weight = 9980.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.136236 restraints weight = 9414.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11709  Z= 0.138
  Angle     :  0.559   9.690  16140  Z= 0.292
  Chirality :  0.038   0.143   1788
  Planarity :  0.004   0.053   1841
  Dihedral  : 18.977 135.869   2103
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.31 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 14.54 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.24), residues: 1252
  helix:  1.77 (0.21), residues: 664
  sheet: -0.96 (0.43), residues: 129
  loop : -1.23 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 264 
 TYR   0.028   0.001   TYR B 161 
 PHE   0.018   0.001   PHE A1338 
 TRP   0.017   0.001   TRP A 915 
 HIS   0.005   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (11708)
  covalent geometry    : angle       0.55910 (16140)
  hydrogen bonds       : bond        0.04184 (  559)
  hydrogen bonds       : angle       4.24587 ( 1563)
  Misc. bond           : bond        0.00071 (    1)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 156
  time to evaluate  : 0.288 
Fit side-chains
REVERT: B  114 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7501 (mp0)
REVERT: B  137 ASN cc_start: 0.9003 (OUTLIER) cc_final: 0.8642 (t0)
REVERT: B  247 MET cc_start: 0.8427 (mmt) cc_final: 0.7931 (tpp)
REVERT: B  321 TRP cc_start: 0.8022 (t60) cc_final: 0.7435 (t60)
REVERT: A  420 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7230 (tm-30)
REVERT: A  519 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6908 (pp)
REVERT: A 1215 VAL cc_start: 0.7697 (OUTLIER) cc_final: 0.7429 (t)
REVERT: A 1271 PHE cc_start: 0.4844 (m-80) cc_final: 0.3979 (t80)
  outliers start: 27
  outliers final: 19
  residues processed: 172
  average time/residue: 0.0838
  time to fit residues: 21.2598
Evaluate side-chains
  172 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  137 ASN
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain B residue  233 GLU
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain A residue  472 CYS
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  602 SER
Chi-restraints excluded: chain A residue  651 ILE
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain A residue  784 LEU
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  991 GLU
Chi-restraints excluded: chain A residue  996 LYS
Chi-restraints excluded: chain A residue 1096 PHE
Chi-restraints excluded: chain A residue 1146 ASN
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1189 ASP
Chi-restraints excluded: chain A residue 1215 VAL
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1350 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 34 optimal weight:    7.9990
   chunk 49 optimal weight:   30.0000
   chunk 103 optimal weight:    3.9990
   chunk 86 optimal weight:    9.9990
   chunk 61 optimal weight:    8.9990
   chunk 74 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9990
   chunk 82 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 52 optimal weight:    8.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 137 ASN
B 287 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.155509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.128238 restraints weight = 15658.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.129333 restraints weight = 12893.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.130547 restraints weight = 10924.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.130749 restraints weight = 9267.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.131073 restraints weight = 8667.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  11709  Z= 0.223
  Angle     :  0.625   9.312  16140  Z= 0.329
  Chirality :  0.041   0.148   1788
  Planarity :  0.005   0.055   1841
  Dihedral  : 19.046 136.207   2103
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.03 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 14.63 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.24), residues: 1252
  helix:  1.60 (0.21), residues: 662
  sheet: -1.00 (0.43), residues: 129
  loop : -1.33 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 264 
 TYR   0.015   0.002   TYR B  42 
 PHE   0.019   0.002   PHE A1338 
 TRP   0.017   0.002   TRP A 915 
 HIS   0.005   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00525 (11708)
  covalent geometry    : angle       0.62539 (16140)
  hydrogen bonds       : bond        0.04975 (  559)
  hydrogen bonds       : angle       4.42570 ( 1563)
  Misc. bond           : bond        0.00046 (    1)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 146
  time to evaluate  : 0.363 
Fit side-chains
REVERT: B  114 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7539 (mp0)
REVERT: B  137 ASN cc_start: 0.9012 (OUTLIER) cc_final: 0.8757 (t0)
REVERT: B  247 MET cc_start: 0.8476 (mmt) cc_final: 0.8092 (tpp)
REVERT: B  321 TRP cc_start: 0.8099 (t60) cc_final: 0.7599 (t60)
REVERT: A  461 MET cc_start: 0.8009 (ttm) cc_final: 0.7195 (ttm)
REVERT: A 1215 VAL cc_start: 0.7690 (OUTLIER) cc_final: 0.7418 (t)
REVERT: A 1271 PHE cc_start: 0.4933 (m-80) cc_final: 0.3954 (t80)
  outliers start: 35
  outliers final: 21
  residues processed: 174
  average time/residue: 0.0856
  time to fit residues: 21.6526
Evaluate side-chains
  165 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 141
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  137 ASN
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  472 CYS
Chi-restraints excluded: chain A residue  602 SER
Chi-restraints excluded: chain A residue  651 ILE
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain A residue  784 LEU
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  991 GLU
Chi-restraints excluded: chain A residue  996 LYS
Chi-restraints excluded: chain A residue 1024 VAL
Chi-restraints excluded: chain A residue 1096 PHE
Chi-restraints excluded: chain A residue 1146 ASN
Chi-restraints excluded: chain A residue 1186 SER
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1189 ASP
Chi-restraints excluded: chain A residue 1215 VAL
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1350 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 57 optimal weight:   20.0000
   chunk 38 optimal weight:   10.0000
   chunk 51 optimal weight:    0.6980
   chunk 35 optimal weight:    5.9990
   chunk 29 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   chunk 61 optimal weight:    5.9990
   chunk 82 optimal weight:    9.9990
   chunk 105 optimal weight:    2.9990
   chunk 88 optimal weight:    7.9990
   overall best weight:    4.5388

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

Flipped N/Q/H residues before XYZ refinement:
B 137 ASN
B 287 GLN
A 639 GLN
A 987 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.156792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.129093 restraints weight = 15567.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.130490 restraints weight = 12470.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.131708 restraints weight = 9735.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.132488 restraints weight = 8570.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.133092 restraints weight = 7682.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  11709  Z= 0.181
  Angle     :  0.598   9.379  16140  Z= 0.314
  Chirality :  0.040   0.144   1788
  Planarity :  0.004   0.056   1841
  Dihedral  : 19.014 135.881   2103
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.39 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 16.03 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.24), residues: 1252
  helix:  1.59 (0.21), residues: 662
  sheet: -1.05 (0.43), residues: 129
  loop : -1.33 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 264 
 TYR   0.022   0.002   TYR B  73 
 PHE   0.021   0.001   PHE A1338 
 TRP   0.019   0.002   TRP A 915 
 HIS   0.006   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (11708)
  covalent geometry    : angle       0.59840 (16140)
  hydrogen bonds       : bond        0.04674 (  559)
  hydrogen bonds       : angle       4.38506 ( 1563)
  Misc. bond           : bond        0.00055 (    1)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 147
  time to evaluate  : 0.328 
Fit side-chains
REVERT: B  114 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7507 (mp0)
REVERT: B  137 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8404 (t0)
REVERT: B  247 MET cc_start: 0.8513 (mmt) cc_final: 0.8066 (tpp)
REVERT: B  321 TRP cc_start: 0.8081 (t60) cc_final: 0.7483 (t60)
REVERT: A  420 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7289 (tm-30)
REVERT: A 1051 SER cc_start: 0.7508 (t) cc_final: 0.7172 (p)
REVERT: A 1215 VAL cc_start: 0.7686 (OUTLIER) cc_final: 0.7414 (t)
REVERT: A 1271 PHE cc_start: 0.4911 (m-80) cc_final: 0.3906 (t80)
  outliers start: 29
  outliers final: 20
  residues processed: 167
  average time/residue: 0.0857
  time to fit residues: 21.0823
Evaluate side-chains
  169 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  137 ASN
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain A residue  472 CYS
Chi-restraints excluded: chain A residue  602 SER
Chi-restraints excluded: chain A residue  607 MET
Chi-restraints excluded: chain A residue  651 ILE
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain A residue  784 LEU
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  991 GLU
Chi-restraints excluded: chain A residue  996 LYS
Chi-restraints excluded: chain A residue 1096 PHE
Chi-restraints excluded: chain A residue 1146 ASN
Chi-restraints excluded: chain A residue 1186 SER
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1189 ASP
Chi-restraints excluded: chain A residue 1215 VAL
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1350 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 108 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9980
   chunk 31 optimal weight:    8.9990
   chunk 1 optimal weight:    7.9990
   chunk 61 optimal weight:    3.9990
   chunk 125 optimal weight:   10.0000
   chunk 71 optimal weight:    3.9990
   chunk 56 optimal weight:    8.9990
   chunk 12 optimal weight:   10.0000
   chunk 46 optimal weight:    8.9990
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
B 137 ASN
B 287 GLN
A 900 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.156331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.129034 restraints weight = 15474.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.130264 restraints weight = 12783.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.131764 restraints weight = 11186.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.132270 restraints weight = 8775.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.132401 restraints weight = 8126.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.2019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11709  Z= 0.174
  Angle     :  0.598   9.151  16140  Z= 0.314
  Chirality :  0.040   0.145   1788
  Planarity :  0.004   0.055   1841
  Dihedral  : 18.990 135.587   2103
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.71 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 15.94 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.24), residues: 1252
  helix:  1.57 (0.21), residues: 664
  sheet: -1.05 (0.42), residues: 129
  loop : -1.33 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 264 
 TYR   0.020   0.001   TYR B  73 
 PHE   0.024   0.001   PHE A1338 
 TRP   0.021   0.002   TRP A 915 
 HIS   0.005   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (11708)
  covalent geometry    : angle       0.59777 (16140)
  hydrogen bonds       : bond        0.04600 (  559)
  hydrogen bonds       : angle       4.36014 ( 1563)
  Misc. bond           : bond        0.00056 (    1)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 146
  time to evaluate  : 0.246 
Fit side-chains
REVERT: B  114 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7522 (mp0)
REVERT: B  137 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8396 (t0)
REVERT: B  247 MET cc_start: 0.8543 (mmt) cc_final: 0.8027 (tpp)
REVERT: B  321 TRP cc_start: 0.8088 (t60) cc_final: 0.7654 (t60)
REVERT: A  420 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7293 (tm-30)
REVERT: A 1051 SER cc_start: 0.7558 (t) cc_final: 0.7211 (p)
REVERT: A 1215 VAL cc_start: 0.7744 (OUTLIER) cc_final: 0.7449 (t)
REVERT: A 1271 PHE cc_start: 0.4795 (m-80) cc_final: 0.3789 (t80)
  outliers start: 33
  outliers final: 24
  residues processed: 168
  average time/residue: 0.0913
  time to fit residues: 22.4941
Evaluate side-chains
  173 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 145
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  137 ASN
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain A residue  472 CYS
Chi-restraints excluded: chain A residue  602 SER
Chi-restraints excluded: chain A residue  651 ILE
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain A residue  784 LEU
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  991 GLU
Chi-restraints excluded: chain A residue  996 LYS
Chi-restraints excluded: chain A residue 1024 VAL
Chi-restraints excluded: chain A residue 1096 PHE
Chi-restraints excluded: chain A residue 1146 ASN
Chi-restraints excluded: chain A residue 1186 SER
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1189 ASP
Chi-restraints excluded: chain A residue 1215 VAL
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1350 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 26 optimal weight:    9.9990
   chunk 54 optimal weight:    7.9990
   chunk 102 optimal weight:    1.9990
   chunk 112 optimal weight:    7.9990
   chunk 90 optimal weight:   20.0000
   chunk 115 optimal weight:    6.9990
   chunk 119 optimal weight:   30.0000
   chunk 65 optimal weight:    0.0060
   chunk 124 optimal weight:    6.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    3.4004

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

Flipped N/Q/H residues before XYZ refinement:
B 137 ASN
B 287 GLN
A 900 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.157377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.129948 restraints weight = 15377.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.131284 restraints weight = 11542.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.132478 restraints weight = 9684.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.134007 restraints weight = 8157.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.134191 restraints weight = 6958.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.2038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11709  Z= 0.155
  Angle     :  0.589   8.978  16140  Z= 0.308
  Chirality :  0.039   0.151   1788
  Planarity :  0.004   0.055   1841
  Dihedral  : 18.939 135.336   2103
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.55 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 16.40 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.24), residues: 1252
  helix:  1.60 (0.21), residues: 665
  sheet: -1.04 (0.42), residues: 129
  loop : -1.32 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 264 
 TYR   0.021   0.001   TYR B  73 
 PHE   0.023   0.001   PHE A1338 
 TRP   0.027   0.001   TRP A 915 
 HIS   0.005   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (11708)
  covalent geometry    : angle       0.58902 (16140)
  hydrogen bonds       : bond        0.04389 (  559)
  hydrogen bonds       : angle       4.29682 ( 1563)
  Misc. bond           : bond        0.00059 (    1)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 147
  time to evaluate  : 0.268 
Fit side-chains
REVERT: B  114 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7468 (mp0)
REVERT: B  137 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8386 (t0)
REVERT: B  321 TRP cc_start: 0.8122 (t60) cc_final: 0.7693 (t60)
REVERT: A  420 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7292 (tm-30)
REVERT: A 1051 SER cc_start: 0.7443 (t) cc_final: 0.7113 (p)
REVERT: A 1215 VAL cc_start: 0.7736 (OUTLIER) cc_final: 0.7461 (t)
REVERT: A 1271 PHE cc_start: 0.4796 (m-80) cc_final: 0.3808 (t80)
  outliers start: 31
  outliers final: 24
  residues processed: 168
  average time/residue: 0.0927
  time to fit residues: 22.8466
Evaluate side-chains
  172 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 144
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  137 ASN
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain A residue  472 CYS
Chi-restraints excluded: chain A residue  602 SER
Chi-restraints excluded: chain A residue  651 ILE
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain A residue  784 LEU
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  991 GLU
Chi-restraints excluded: chain A residue  996 LYS
Chi-restraints excluded: chain A residue 1024 VAL
Chi-restraints excluded: chain A residue 1096 PHE
Chi-restraints excluded: chain A residue 1146 ASN
Chi-restraints excluded: chain A residue 1186 SER
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1189 ASP
Chi-restraints excluded: chain A residue 1215 VAL
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1350 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 35 optimal weight:    5.9990
   chunk 100 optimal weight:    0.0010
   chunk 10 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 93 optimal weight:    5.9990
   chunk 116 optimal weight:   20.0000
   chunk 115 optimal weight:    5.9990
   chunk 99 optimal weight:    8.9990
   chunk 64 optimal weight:    6.9990
   overall best weight:    2.7592

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

Flipped N/Q/H residues before XYZ refinement:
B 137 ASN
B 287 GLN
A 900 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.158255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.130401 restraints weight = 15436.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.132594 restraints weight = 12299.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.134073 restraints weight = 9297.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.134736 restraints weight = 7880.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.135037 restraints weight = 7182.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11709  Z= 0.141
  Angle     :  0.579   8.813  16140  Z= 0.302
  Chirality :  0.039   0.148   1788
  Planarity :  0.004   0.054   1841
  Dihedral  : 18.880 135.028   2103
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.55 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 16.78 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.24), residues: 1252
  helix:  1.64 (0.21), residues: 671
  sheet: -1.09 (0.43), residues: 125
  loop : -1.30 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 264 
 TYR   0.022   0.001   TYR B  73 
 PHE   0.022   0.001   PHE A1338 
 TRP   0.031   0.002   TRP A 915 
 HIS   0.005   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (11708)
  covalent geometry    : angle       0.57875 (16140)
  hydrogen bonds       : bond        0.04212 (  559)
  hydrogen bonds       : angle       4.23116 ( 1563)
  Misc. bond           : bond        0.00060 (    1)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 147
  time to evaluate  : 0.388 
Fit side-chains
REVERT: B  114 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7493 (mp0)
REVERT: B  137 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8371 (t0)
REVERT: B  321 TRP cc_start: 0.8111 (t60) cc_final: 0.7710 (t60)
REVERT: A  420 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7308 (tm-30)
REVERT: A 1051 SER cc_start: 0.7359 (t) cc_final: 0.7058 (p)
REVERT: A 1215 VAL cc_start: 0.7759 (OUTLIER) cc_final: 0.7472 (t)
REVERT: A 1271 PHE cc_start: 0.4830 (m-80) cc_final: 0.3890 (t80)
  outliers start: 30
  outliers final: 23
  residues processed: 167
  average time/residue: 0.0985
  time to fit residues: 23.6540
Evaluate side-chains
  170 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 143
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  137 ASN
Chi-restraints excluded: chain B residue  174 SER
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  414 ASP
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain A residue  472 CYS
Chi-restraints excluded: chain A residue  602 SER
Chi-restraints excluded: chain A residue  651 ILE
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  683 VAL
Chi-restraints excluded: chain A residue  784 LEU
Chi-restraints excluded: chain A residue  927 VAL
Chi-restraints excluded: chain A residue  969 LEU
Chi-restraints excluded: chain A residue  991 GLU
Chi-restraints excluded: chain A residue  996 LYS
Chi-restraints excluded: chain A residue 1024 VAL
Chi-restraints excluded: chain A residue 1096 PHE
Chi-restraints excluded: chain A residue 1146 ASN
Chi-restraints excluded: chain A residue 1186 SER
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1189 ASP
Chi-restraints excluded: chain A residue 1215 VAL
Chi-restraints excluded: chain A residue 1296 THR
Chi-restraints excluded: chain A residue 1350 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 5 optimal weight:    0.4980
   chunk 51 optimal weight:    0.6980
   chunk 8 optimal weight:    6.9990
   chunk 35 optimal weight:    5.9990
   chunk 75 optimal weight:    4.9990
   chunk 125 optimal weight:   10.0000
   chunk 128 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 79 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   chunk 31 optimal weight:    0.5980
   overall best weight:    2.5584

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

Flipped N/Q/H residues before XYZ refinement:
B 137 ASN
B 287 GLN
A 900 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.158755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.131766 restraints weight = 15429.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.132957 restraints weight = 11453.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.134088 restraints weight = 9389.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.135276 restraints weight = 8060.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.135327 restraints weight = 7320.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11709  Z= 0.136
  Angle     :  0.574   8.716  16140  Z= 0.299
  Chirality :  0.039   0.149   1788
  Planarity :  0.004   0.052   1841
  Dihedral  : 18.836 134.767   2103
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.63 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 17.24 %
    Favored  : 80.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.24), residues: 1252
  helix:  1.66 (0.21), residues: 672
  sheet: -1.05 (0.43), residues: 125
  loop : -1.28 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 264 
 TYR   0.022   0.001   TYR B  73 
 PHE   0.036   0.001   PHE A1338 
 TRP   0.034   0.002   TRP A 915 
 HIS   0.005   0.001   HIS B 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (11708)
  covalent geometry    : angle       0.57448 (16140)
  hydrogen bonds       : bond        0.04109 (  559)
  hydrogen bonds       : angle       4.18900 ( 1563)
  Misc. bond           : bond        0.00060 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1374.14 seconds
wall clock time: 24 minutes 39.23 seconds (1479.23 seconds total)