Starting phenix.real_space_refine
on Wed Aug  5 03:40:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w4r_65642/08_2026/9w4r_65642.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w4r_65642/08_2026/9w4r_65642.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w4r_65642/08_2026/9w4r_65642.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w4r_65642/08_2026/9w4r_65642.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w4r_65642/08_2026/9w4r_65642.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w4r_65642/08_2026/9w4r_65642.map"
  }
  resolution = 3.78
  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=   0.055 sd=   0.628
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      4      6.06       5
     P      57      5.49       5
     S      49      5.16       5
     C    5099      2.51       5
     N    1446      2.21       5
     O    1654      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8309
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 6095
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 749, 6095
          Classifications: {'peptide': 749}
          Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 708}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 993
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 993
          Classifications: {'peptide': 130}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 122}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1217
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 1217
          Classifications: {'RNA': 57}
          Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 3, 'rna3p_pur': 24, 'rna3p_pyr': 23}
          Link IDs: {'rna2p': 10, 'rna3p': 46}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    288  SG  CYS A 306      50.930  67.911  59.045  1.00181.30           S
  ATOM    311  SG  CYS A 309      48.624  65.345  60.705  1.00180.62           S
  ATOM   3436  SG  CYS A 915      34.298  59.396  80.911  1.00238.58           S
  ATOM   3456  SG  CYS A 918      37.390  57.503  80.161  1.00239.63           S
  ATOM   3533  SG  CYS A 928      34.433  55.800  81.899  1.00258.85           S
  ATOM   6796  SG  CYS B 139      46.390  57.123  40.122  1.00236.31           S
  ATOM   6822  SG  CYS B 142      48.248  56.702  36.902  1.00243.32           S
  ATOM   6895  SG  CYS B 152      49.745  55.484  40.274  1.00232.15           S
  ATOM   6966  SG  CYS B 161      46.626  70.546  28.879  1.00289.80           S
  ATOM   6993  SG  CYS B 164      49.136  72.453  26.862  1.00313.30           S
  ATOM   7064  SG  CYS B 174      45.362  73.229  26.491  1.00298.22           S

  Time building chain proxies: 1.96, per 1000 atoms: 0.24
  Number of scatterers: 8309
  At special positions: 0
  Unit cell: (80.925, 117.03, 136.95, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      4     29.99
     S      49     16.00
     P      57     15.00
     O    1654      8.00
     N    1446      7.00
     C    5099      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 238.9 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A2001 "
        pdb="ZN    ZN A2001 " - pdb=" ND1 HIS A 328 "
        pdb="ZN    ZN A2001 " - pdb=" NE2 HIS A 322 "
        pdb="ZN    ZN A2001 " - pdb=" SG  CYS A 306 "
        pdb="ZN    ZN A2001 " - pdb=" SG  CYS A 309 "
      pdb="  ZN A2002 "
        pdb="ZN    ZN A2002 " - pdb=" NE2 HIS A 923 "
        pdb="ZN    ZN A2002 " - pdb=" SG  CYS A 915 "
        pdb="ZN    ZN A2002 " - pdb=" SG  CYS A 918 "
        pdb="ZN    ZN A2002 " - pdb=" SG  CYS A 928 "
      pdb="  ZN B1001 "
        pdb="ZN    ZN B1001 " - pdb=" ND1 HIS B 147 "
        pdb="ZN    ZN B1001 " - pdb=" SG  CYS B 139 "
        pdb="ZN    ZN B1001 " - pdb=" SG  CYS B 152 "
        pdb="ZN    ZN B1001 " - pdb=" SG  CYS B 142 "
      pdb="  ZN B1002 "
        pdb="ZN    ZN B1002 " - pdb=" NE2 HIS B 169 "
        pdb="ZN    ZN B1002 " - pdb=" SG  CYS B 161 "
        pdb="ZN    ZN B1002 " - pdb=" SG  CYS B 164 "
        pdb="ZN    ZN B1002 " - pdb=" SG  CYS B 174 "
      Number of angles added : 11


  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1658

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 7 sheets defined
      44.1% alpha, 14.4% beta
      11 base pairs and 27 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 274 through 286
      removed outlier: 3.601A  pdb=" N   LYS A 278 " --> pdb=" O   ARG A 274 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   GLU A 282 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   ARG A 283 " --> pdb=" O   GLN A 279 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   LEU A 284 " --> pdb=" O   ALA A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 324
    Processing helix  chain 'A' and resid 325 through 341
    Processing helix  chain 'A' and resid 342 through 344
      No H-bonds generated for 'chain 'A' and resid 342 through 344'
    Processing helix  chain 'A' and resid 348 through 366
      removed outlier: 4.108A  pdb=" N   HIS A 366 " --> pdb=" O   LEU A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 391
      removed outlier: 3.724A  pdb=" N   PHE A 390 " --> pdb=" O   VAL A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 404
    Processing helix  chain 'A' and resid 424 through 439
    Processing helix  chain 'A' and resid 473 through 490
    Processing helix  chain 'A' and resid 492 through 506
      removed outlier: 3.881A  pdb=" N   VAL A 497 " --> pdb=" O   PHE A 493 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   LEU A 498 " --> pdb=" O   ILE A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 515
    Processing helix  chain 'A' and resid 518 through 533
    Processing helix  chain 'A' and resid 551 through 557
      removed outlier: 3.520A  pdb=" N   MET A 554 " --> pdb=" O   PRO A 551 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   ASP A 555 " --> pdb=" O   LYS A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 643
      removed outlier: 3.616A  pdb=" N   LEU A 637 " --> pdb=" O   TRP A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 689 through 708
    Processing helix  chain 'A' and resid 901 through 907
      removed outlier: 4.243A  pdb=" N   LEU A 905 " --> pdb=" O   ASP A 901 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 944 through 961
      removed outlier: 3.617A  pdb=" N   CYS A 958 " --> pdb=" O   VAL A 954 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   PHE A 959 " --> pdb=" O   CYS A 955 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 965 through 987
    Processing helix  chain 'A' and resid 997 through 1000
    Processing helix  chain 'A' and resid 1026 through 1041
    Processing helix  chain 'A' and resid 1077 through 1092
      removed outlier: 3.790A  pdb=" N   ASP A1092 " --> pdb=" O   TYR A1088 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1092 through 1109
      removed outlier: 4.233A  pdb=" N   GLN A1096 " --> pdb=" O   ASP A1092 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1113 through 1117
    Processing helix  chain 'A' and resid 1120 through 1135
    Processing helix  chain 'A' and resid 1184 through 1196
    Processing helix  chain 'A' and resid 1216 through 1221
    Processing helix  chain 'A' and resid 1222 through 1225
    Processing helix  chain 'A' and resid 1239 through 1243
    Processing helix  chain 'A' and resid 1244 through 1261
    Processing helix  chain 'A' and resid 1272 through 1277
    Processing helix  chain 'B' and resid 111 through 115
      removed outlier: 3.750A  pdb=" N   VAL B 115 " --> pdb=" O   PRO B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 174
    Processing sheet with id=AA1, first strand: chain 'A' and resid 289 through 291
    Processing sheet with id=AA2, first strand: chain 'A' and resid 395 through 399
      removed outlier: 3.939A  pdb=" N   ASN A 414 " --> pdb=" O   TYR A 399 " (cutoff:3.500A)
      removed outlier: 5.409A  pdb=" N   VAL A 413 " --> pdb=" O   ARG A 468 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   SER A 470 " --> pdb=" O   VAL A 413 " (cutoff:3.500A)
      removed outlier: 5.791A  pdb=" N   ILE A 415 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   ARG A 459 " --> pdb=" O   ASP A 444 " (cutoff:3.500A)
      removed outlier: 5.312A  pdb=" N   ASP A 444 " --> pdb=" O   ARG A 459 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 559 through 563
      removed outlier: 4.095A  pdb=" N   LYS A 569 " --> pdb=" O   LYS A 560 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   ILE A 562 " --> pdb=" O   PHE A 567 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   PHE A 567 " --> pdb=" O   ILE A 562 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 649 through 650
      removed outlier: 4.711A  pdb=" N   LEU A 659 " --> pdb=" O   VAL A 650 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 674 through 675
      removed outlier: 4.385A  pdb=" N   ASP A 675 " --> pdb=" O   SER A 678 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 991 through 996
      removed outlier: 3.955A  pdb=" N   ASP A1011 " --> pdb=" O   PHE A 996 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   LEU A1010 " --> pdb=" O   ASP A1070 " (cutoff:3.500A)
      removed outlier: 7.310A  pdb=" N   SER A1072 " --> pdb=" O   LEU A1010 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ILE A1012 " --> pdb=" O   SER A1072 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   ILE A1057 " --> pdb=" O   PRO A1049 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   LYS A1059 " --> pdb=" O   ILE A1047 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ILE A1047 " --> pdb=" O   LYS A1059 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 47
      removed outlier: 6.094A  pdb=" N   GLY B  40 " --> pdb=" O   ARG B  61 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   ARG B  61 " --> pdb=" O   GLY B  40 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   GLY B  42 " --> pdb=" O   THR B  59 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   THR B  59 " --> pdb=" O   GLY B  42 " (cutoff:3.500A)
      removed outlier: 5.314A  pdb=" N   CYS B  44 " --> pdb=" O   SER B  57 " (cutoff:3.500A)
      removed outlier: 5.769A  pdb=" N   SER B  57 " --> pdb=" O   CYS B  44 " (cutoff:3.500A)
      removed outlier: 10.287A  pdb=" N   PHE B  53 " --> pdb=" O   VAL B  72 " (cutoff:3.500A)
      removed outlier: 11.415A  pdb=" N   VAL B  72 " --> pdb=" O   PHE B  53 " (cutoff:3.500A)
      removed outlier: 9.136A  pdb=" N   PHE B  55 " --> pdb=" O   VAL B  70 " (cutoff:3.500A)
      removed outlier: 10.210A  pdb=" N   VAL B  70 " --> pdb=" O   PHE B  55 " (cutoff:3.500A)
      removed outlier: 9.860A  pdb=" N   SER B  57 " --> pdb=" O   PRO B  68 " (cutoff:3.500A)
      removed outlier: 5.960A  pdb=" N   THR B  59 " --> pdb=" O   LEU B  66 " (cutoff:3.500A)
      removed outlier: 4.704A  pdb=" N   LEU B 104 " --> pdb=" O   ASP B  71 " (cutoff:3.500A)
      removed outlier: 5.069A  pdb=" N   HIS B  75 " --> pdb=" O   SER B 106 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   ARG B 108 " --> pdb=" O   HIS B  75 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   THR B  96 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   VAL B 109 " --> pdb=" O   GLU B  94 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   GLU B  94 " --> pdb=" O   VAL B 109 " (cutoff:3.500A)

    305 hydrogen bonds defined for protein.
    855 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      24 hydrogen bonds
      36 hydrogen bond angles
      0 basepair planarities
      11 basepair parallelities
      27 stacking parallelities
  Total time for adding SS restraints: 1.44

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1857
        1.33 -     1.45: 2024
        1.45 -     1.57: 4548
        1.57 -     1.69: 112
        1.69 -     1.81: 66
  Bond restraints: 8607
  Sorted by residual:
  bond pdb=" C   ILE A 494 "
       pdb=" N   PRO A 495 "
    ideal  model  delta    sigma   weight residual
    1.337  1.374 -0.037 1.24e-02 6.50e+03 8.88e+00
  bond pdb=" C   PRO A1137 "
       pdb=" N   PRO A1138 "
    ideal  model  delta    sigma   weight residual
    1.332  1.362 -0.030 1.12e-02 7.97e+03 7.32e+00
  bond pdb=" CB  VAL A 497 "
       pdb=" CG2 VAL A 497 "
    ideal  model  delta    sigma   weight residual
    1.521  1.448  0.073 3.30e-02 9.18e+02 4.85e+00
  bond pdb=" C5    C C  41 "
       pdb=" C6    C C  41 "
    ideal  model  delta    sigma   weight residual
    1.339  1.326  0.013 8.00e-03 1.56e+04 2.84e+00
  bond pdb=" N9    A C  25 "
       pdb=" C4    A C  25 "
    ideal  model  delta    sigma   weight residual
    1.374  1.364  0.010 6.00e-03 2.78e+04 2.64e+00
  ... (remaining 8602 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 11256
        1.67 -     3.34: 547
        3.34 -     5.01: 57
        5.01 -     6.69: 16
        6.69 -     8.36: 3
  Bond angle restraints: 11879
  Sorted by residual:
  angle pdb=" O5'   G C  50 "
        pdb=" C5'   G C  50 "
        pdb=" C4'   G C  50 "
      ideal   model   delta    sigma   weight residual
     109.40  113.48   -4.08 8.00e-01 1.56e+00 2.61e+01
  angle pdb=" N1    C C  41 "
        pdb=" C6    C C  41 "
        pdb=" C5    C C  41 "
      ideal   model   delta    sigma   weight residual
     121.00  123.44   -2.44 5.00e-01 4.00e+00 2.38e+01
  angle pdb=" O5'   G C  28 "
        pdb=" C5'   G C  28 "
        pdb=" C4'   G C  28 "
      ideal   model   delta    sigma   weight residual
     109.40  113.22   -3.82 8.00e-01 1.56e+00 2.28e+01
  angle pdb=" N1    C C  68 "
        pdb=" C6    C C  68 "
        pdb=" C5    C C  68 "
      ideal   model   delta    sigma   weight residual
     121.00  123.37   -2.37 5.00e-01 4.00e+00 2.25e+01
  angle pdb=" N1    U C  16 "
        pdb=" C6    U C  16 "
        pdb=" C5    U C  16 "
      ideal   model   delta    sigma   weight residual
     122.70  124.80   -2.10 5.00e-01 4.00e+00 1.77e+01
  ... (remaining 11874 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.97: 4917
       25.97 -    51.94: 278
       51.94 -    77.91: 99
       77.91 -   103.87: 7
      103.87 -   129.84: 1
  Dihedral angle restraints: 5302
    sinusoidal: 2743
      harmonic: 2559
  Sorted by residual:
  dihedral pdb=" CA  ASP A 287 "
           pdb=" C   ASP A 287 "
           pdb=" N   HIS A 288 "
           pdb=" CA  HIS A 288 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.16   25.84     0      5.00e+00 4.00e-02 2.67e+01
  dihedral pdb=" CA  HIS B 148 "
           pdb=" C   HIS B 148 "
           pdb=" N   ALA B 149 "
           pdb=" CA  ALA B 149 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.69  -22.31     0      5.00e+00 4.00e-02 1.99e+01
  dihedral pdb=" CA  ALA A 620 "
           pdb=" C   ALA A 620 "
           pdb=" N   LEU A 621 "
           pdb=" CA  LEU A 621 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.13   21.87     0      5.00e+00 4.00e-02 1.91e+01
  ... (remaining 5299 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1106
       0.066 -    0.131: 214
       0.131 -    0.197: 31
       0.197 -    0.262: 2
       0.262 -    0.328: 1
  Chirality restraints: 1354
  Sorted by residual:
  chirality pdb=" CB  ILE A1229 "
            pdb=" CA  ILE A1229 "
            pdb=" CG1 ILE A1229 "
            pdb=" CG2 ILE A1229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.33 2.00e-01 2.50e+01 2.68e+00
  chirality pdb=" CB  VAL A 653 "
            pdb=" CA  VAL A 653 "
            pdb=" CG1 VAL A 653 "
            pdb=" CG2 VAL A 653 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.25 2.00e-01 2.50e+01 1.62e+00
  chirality pdb=" CB  ILE A 360 "
            pdb=" CA  ILE A 360 "
            pdb=" CG1 ILE A 360 "
            pdb=" CG2 ILE A 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 1351 not shown)

  Planarity restraints: 1302
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A1055 "   -0.045 5.00e-02 4.00e+02   6.76e-02 7.32e+00
        pdb=" N   PRO A1056 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A1056 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A1056 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 675 "   -0.044 5.00e-02 4.00e+02   6.58e-02 6.93e+00
        pdb=" N   PRO A 676 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO A 676 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 676 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A1264 "    0.036 5.00e-02 4.00e+02   5.51e-02 4.87e+00
        pdb=" N   PRO A1265 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A1265 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A1265 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1299 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2170
        2.80 -     3.33: 7811
        3.33 -     3.85: 15878
        3.85 -     4.38: 18035
        4.38 -     4.90: 27897
  Nonbonded interactions: 71791
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN B  48 "
            pdb=" O2'   A C  37 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" O   ILE A1111 "
            pdb=" OH  TYR A1124 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   GLY A1004 "
            pdb=" OH  TYR A1100 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   LYS A 385 "
            pdb=" OG1 THR A 389 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O   MET A 525 "
            pdb=" OH  TYR A 640 "
     model   vdw
     2.296 3.040
  ... (remaining 71786 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:             0.200
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.920
  Find NCS groups from input model:        0.030
  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:0.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073   8623  Z= 0.226
  Angle     :  0.809   8.358  11890  Z= 0.559
  Chirality :  0.053   0.328   1354
  Planarity :  0.006   0.068   1302
  Dihedral  : 17.160 129.842   3644
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  :  9.18 %
    Favored  : 87.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.27), residues: 867
  helix:  0.19 (0.27), residues: 318
  sheet: -1.37 (0.47), residues: 97
  loop : -0.95 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 654 
 TYR   0.015   0.002   TYR A 502 
 PHE   0.026   0.002   PHE A 493 
 TRP   0.023   0.002   TRP A 503 
 HIS   0.010   0.001   HIS B 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.23 ( 8607)
  covalent geometry    : angle       0.80318 /  0.56 (11879)
  hydrogen bonds       : bond        0.17410 / 11.72 (  329)
  hydrogen bonds       : angle       6.52873 /  4.82 (  891)
  metal coordination   : bond        0.00977 /  0.51 (   16)
  metal coordination   : angle       3.39377 /  2.46 (   11)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 183
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 LYS cc_start: 0.9049 (tttp) cc_final: 0.8518 (tptp)
REVERT: A  327 ARG cc_start: 0.8572 (ttt90) cc_final: 0.8115 (tpm170)
REVERT: A  329 LYS cc_start: 0.8478 (mttt) cc_final: 0.8220 (mttt)
REVERT: A  377 GLN cc_start: 0.9407 (tt0) cc_final: 0.9103 (tm-30)
REVERT: A  381 GLU cc_start: 0.9302 (mt-10) cc_final: 0.8816 (pt0)
REVERT: A  404 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8063 (t)
REVERT: A  444 ASP cc_start: 0.8989 (m-30) cc_final: 0.8789 (m-30)
REVERT: A  447 SER cc_start: 0.8721 (p) cc_final: 0.8505 (p)
REVERT: A  459 ARG cc_start: 0.8860 (tpp80) cc_final: 0.8641 (tpp80)
REVERT: A  493 PHE cc_start: 0.7654 (t80) cc_final: 0.6925 (t80)
REVERT: A  521 CYS cc_start: 0.8685 (m) cc_final: 0.8254 (m)
REVERT: A  649 TYR cc_start: 0.8079 (m-80) cc_final: 0.7803 (m-80)
REVERT: A  661 ARG cc_start: 0.6364 (mmm160) cc_final: 0.4618 (mmm-85)
REVERT: A  679 VAL cc_start: 0.7329 (OUTLIER) cc_final: 0.7118 (t)
REVERT: A  932 PHE cc_start: 0.8645 (m-80) cc_final: 0.8257 (m-10)
REVERT: A  959 PHE cc_start: 0.8457 (t80) cc_final: 0.8250 (t80)
REVERT: A 1105 PHE cc_start: 0.8830 (m-80) cc_final: 0.8287 (m-80)
REVERT: A 1127 MET cc_start: 0.8616 (ptm) cc_final: 0.8322 (ptm)
REVERT: A 1214 LEU cc_start: 0.8968 (mt) cc_final: 0.8762 (mt)
REVERT: A 1252 MET cc_start: 0.9025 (mmm) cc_final: 0.8729 (mmm)
REVERT: B   84 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7990 (m-80)
  outliers start: 29
  outliers final: 8
  residues processed: 205
  average time/residue: 0.1292
  time to fit residues: 33.0348
Evaluate side-chains
  140 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  556 ASP
Chi-restraints excluded: chain A residue  670 ARG
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue 1226 CYS
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  147 HIS
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  160 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:   30.0000
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    8.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:   50.0000
   overall best weight:    5.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 331 ASN
A1046 ASN
** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  39 HIS
** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.104639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.079363 restraints weight = 41582.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.081952 restraints weight = 25243.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.083647 restraints weight = 17726.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 69)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.084731 restraints weight = 13759.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.085484 restraints weight = 11445.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.2583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063   8623  Z= 0.259
  Angle     :  0.848  34.306  11890  Z= 0.408
  Chirality :  0.046   0.221   1354
  Planarity :  0.007   0.112   1302
  Dihedral  : 18.377 140.296   1850
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 25.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 16.33 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.04 (0.28), residues: 867
  helix: -0.19 (0.26), residues: 332
  sheet: -1.68 (0.48), residues: 102
  loop : -0.72 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 699 
 TYR   0.014   0.002   TYR A 695 
 PHE   0.023   0.002   PHE A 406 
 TRP   0.037   0.003   TRP A1189 
 HIS   0.007   0.002   HIS A1041 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00547 /  0.26 ( 8607)
  covalent geometry    : angle       0.76596 /  0.40 (11879)
  hydrogen bonds       : bond        0.07713 /  5.14 (  329)
  hydrogen bonds       : angle       5.85430 /  4.34 (  891)
  metal coordination   : bond        0.02098 /  1.46 (   16)
  metal coordination   : angle      11.95402 /  9.25 (   11)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 133
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 LEU cc_start: 0.9429 (tp) cc_final: 0.9205 (tp)
REVERT: A  284 LEU cc_start: 0.9416 (mm) cc_final: 0.8869 (tp)
REVERT: A  324 LYS cc_start: 0.9148 (tttp) cc_final: 0.8380 (tptp)
REVERT: A  327 ARG cc_start: 0.8403 (ttt90) cc_final: 0.8083 (tpm170)
REVERT: A  329 LYS cc_start: 0.8136 (mttt) cc_final: 0.7908 (mmtt)
REVERT: A  361 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8742 (pt0)
REVERT: A  404 THR cc_start: 0.8665 (p) cc_final: 0.8297 (t)
REVERT: A  414 ASN cc_start: 0.6491 (m110) cc_final: 0.5921 (m-40)
REVERT: A  493 PHE cc_start: 0.7659 (t80) cc_final: 0.7004 (t80)
REVERT: A  506 LEU cc_start: 0.9073 (tt) cc_final: 0.8855 (pp)
REVERT: A  521 CYS cc_start: 0.8521 (m) cc_final: 0.8109 (m)
REVERT: A  619 LEU cc_start: 0.5890 (OUTLIER) cc_final: 0.5572 (tt)
REVERT: A  649 TYR cc_start: 0.8179 (m-80) cc_final: 0.7887 (m-80)
REVERT: A  661 ARG cc_start: 0.6477 (mmm160) cc_final: 0.5705 (mmm-85)
REVERT: A  679 VAL cc_start: 0.7627 (OUTLIER) cc_final: 0.7375 (t)
REVERT: A  943 MET cc_start: 0.7373 (mmt) cc_final: 0.6989 (mmp)
REVERT: A 1128 VAL cc_start: 0.9447 (OUTLIER) cc_final: 0.9123 (t)
REVERT: A 1194 ARG cc_start: 0.9394 (ttp-110) cc_final: 0.9107 (ttm110)
REVERT: A 1212 LYS cc_start: 0.9069 (pptt) cc_final: 0.8807 (ptmm)
REVERT: A 1222 TRP cc_start: 0.7652 (m100) cc_final: 0.7205 (m100)
REVERT: B  159 LYS cc_start: 0.8637 (tppt) cc_final: 0.8392 (tptp)
  outliers start: 29
  outliers final: 14
  residues processed: 155
  average time/residue: 0.1194
  time to fit residues: 23.3897
Evaluate side-chains
  133 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  520 TYR
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  635 GLU
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  926 ASN
Chi-restraints excluded: chain A residue  944 THR
Chi-restraints excluded: chain A residue  971 ASN
Chi-restraints excluded: chain A residue 1073 LEU
Chi-restraints excluded: chain A residue 1128 VAL
Chi-restraints excluded: chain A residue 1192 LEU
Chi-restraints excluded: chain A residue 1226 CYS
Chi-restraints excluded: chain A residue 1249 ASN
Chi-restraints excluded: chain B residue  160 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 52 optimal weight:   40.0000
   chunk 73 optimal weight:    0.3980
   chunk 42 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 63 optimal weight:    6.9990
   chunk 1 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 18 optimal weight:    8.9990
   chunk 17 optimal weight:   10.0000
   chunk 85 optimal weight:   20.0000
   overall best weight:    2.8386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 317 GLN
A 532 GLN
A 688 ASN
** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.105702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.080412 restraints weight = 40976.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.083072 restraints weight = 24823.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.084815 restraints weight = 17359.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.085927 restraints weight = 13414.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.086682 restraints weight = 11071.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.3090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   8623  Z= 0.176
  Angle     :  0.745  24.675  11890  Z= 0.368
  Chirality :  0.044   0.259   1354
  Planarity :  0.006   0.087   1302
  Dihedral  : 18.254 143.099   1834
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 24.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 17.09 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.95 (0.28), residues: 867
  helix: -0.14 (0.27), residues: 332
  sheet: -1.57 (0.47), residues: 102
  loop : -0.67 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 699 
 TYR   0.017   0.002   TYR A 502 
 PHE   0.037   0.002   PHE A 406 
 TRP   0.015   0.002   TRP A 503 
 HIS   0.007   0.001   HIS A1062 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00388 /  0.18 ( 8607)
  covalent geometry    : angle       0.69571 /  0.36 (11879)
  hydrogen bonds       : bond        0.06700 /  4.48 (  329)
  hydrogen bonds       : angle       5.65899 /  4.23 (  891)
  metal coordination   : bond        0.01464 /  0.98 (   16)
  metal coordination   : angle       8.75195 /  6.59 (   11)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 129
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 LEU cc_start: 0.9291 (tp) cc_final: 0.9019 (tp)
REVERT: A  284 LEU cc_start: 0.9387 (mm) cc_final: 0.8837 (tp)
REVERT: A  324 LYS cc_start: 0.9138 (tttp) cc_final: 0.8341 (tptp)
REVERT: A  327 ARG cc_start: 0.8375 (ttt90) cc_final: 0.8085 (tpm170)
REVERT: A  329 LYS cc_start: 0.8310 (mttt) cc_final: 0.7928 (mmtt)
REVERT: A  404 THR cc_start: 0.8667 (p) cc_final: 0.8226 (t)
REVERT: A  414 ASN cc_start: 0.6345 (m110) cc_final: 0.5760 (m-40)
REVERT: A  493 PHE cc_start: 0.7557 (t80) cc_final: 0.6800 (t80)
REVERT: A  521 CYS cc_start: 0.8488 (m) cc_final: 0.8051 (m)
REVERT: A  649 TYR cc_start: 0.8107 (m-80) cc_final: 0.7879 (m-80)
REVERT: A  661 ARG cc_start: 0.6391 (mmm160) cc_final: 0.4940 (mmm160)
REVERT: A  668 LYS cc_start: 0.8747 (mptt) cc_final: 0.8508 (mptt)
REVERT: A  679 VAL cc_start: 0.7566 (OUTLIER) cc_final: 0.7339 (t)
REVERT: A  943 MET cc_start: 0.7048 (mmt) cc_final: 0.6689 (mmp)
REVERT: A 1071 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8930 (mm)
REVERT: A 1187 GLU cc_start: 0.9299 (tp30) cc_final: 0.8887 (tm-30)
REVERT: A 1196 TYR cc_start: 0.8588 (m-80) cc_final: 0.7940 (m-80)
REVERT: A 1212 LYS cc_start: 0.9158 (pptt) cc_final: 0.8919 (ptmm)
REVERT: A 1222 TRP cc_start: 0.7567 (m100) cc_final: 0.7361 (m100)
REVERT: A 1250 PHE cc_start: 0.9231 (t80) cc_final: 0.8843 (m-80)
REVERT: A 1252 MET cc_start: 0.8995 (mmm) cc_final: 0.8279 (mmm)
REVERT: B  159 LYS cc_start: 0.8641 (tppt) cc_final: 0.8378 (tptp)
  outliers start: 29
  outliers final: 18
  residues processed: 151
  average time/residue: 0.1224
  time to fit residues: 23.1901
Evaluate side-chains
  134 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  520 TYR
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  635 GLU
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  926 ASN
Chi-restraints excluded: chain A residue  944 THR
Chi-restraints excluded: chain A residue 1071 ILE
Chi-restraints excluded: chain A residue 1073 LEU
Chi-restraints excluded: chain A residue 1128 VAL
Chi-restraints excluded: chain A residue 1192 LEU
Chi-restraints excluded: chain A residue 1226 CYS
Chi-restraints excluded: chain A residue 1249 ASN
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  160 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 52 optimal weight:   20.0000
   chunk 76 optimal weight:   40.0000
   chunk 12 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 47 optimal weight:    5.9990
   chunk 32 optimal weight:    0.5980
   chunk 73 optimal weight:    2.9990
   chunk 81 optimal weight:    7.9990
   chunk 69 optimal weight:   10.0000
   chunk 49 optimal weight:    7.9990
   chunk 91 optimal weight:   40.0000
   overall best weight:    4.7188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 148 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.103668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.078170 restraints weight = 42220.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.080812 restraints weight = 25278.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.082515 restraints weight = 17628.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 69)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.083598 restraints weight = 13617.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.084311 restraints weight = 11318.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.3555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081   8623  Z= 0.218
  Angle     :  0.777  24.446  11890  Z= 0.383
  Chirality :  0.044   0.253   1354
  Planarity :  0.006   0.082   1302
  Dihedral  : 18.276 144.471   1834
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 28.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 18.49 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.28), residues: 867
  helix: -0.21 (0.26), residues: 332
  sheet: -1.85 (0.47), residues: 104
  loop : -0.62 (0.32), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 699 
 TYR   0.010   0.002   TYR A1130 
 PHE   0.025   0.002   PHE A 406 
 TRP   0.014   0.002   TRP A 503 
 HIS   0.007   0.001   HIS B 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00476 /  0.22 ( 8607)
  covalent geometry    : angle       0.73500 /  0.38 (11879)
  hydrogen bonds       : bond        0.06604 /  4.45 (  329)
  hydrogen bonds       : angle       5.74759 /  4.27 (  891)
  metal coordination   : bond        0.01857 /  1.28 (   16)
  metal coordination   : angle       8.31094 /  6.27 (   11)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 124
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 LYS cc_start: 0.9147 (tttp) cc_final: 0.8368 (tptp)
REVERT: A  327 ARG cc_start: 0.8386 (ttt90) cc_final: 0.7851 (tpp-160)
REVERT: A  329 LYS cc_start: 0.8316 (mttt) cc_final: 0.7959 (mmtt)
REVERT: A  404 THR cc_start: 0.8773 (p) cc_final: 0.8423 (p)
REVERT: A  406 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7735 (m-80)
REVERT: A  414 ASN cc_start: 0.6450 (m110) cc_final: 0.5848 (m-40)
REVERT: A  493 PHE cc_start: 0.7477 (t80) cc_final: 0.6872 (t80)
REVERT: A  521 CYS cc_start: 0.8501 (m) cc_final: 0.8052 (m)
REVERT: A  565 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8622 (mm-30)
REVERT: A  638 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8595 (ttmt)
REVERT: A  661 ARG cc_start: 0.6650 (mmm160) cc_final: 0.6347 (mmm160)
REVERT: A  932 PHE cc_start: 0.8846 (m-10) cc_final: 0.8259 (m-10)
REVERT: A  943 MET cc_start: 0.7333 (mmt) cc_final: 0.6870 (mmp)
REVERT: A 1127 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8274 (ptp)
REVERT: A 1187 GLU cc_start: 0.9261 (tp30) cc_final: 0.8925 (tm-30)
REVERT: A 1189 TRP cc_start: 0.9134 (t-100) cc_final: 0.8912 (t-100)
REVERT: A 1196 TYR cc_start: 0.8717 (m-80) cc_final: 0.8517 (m-80)
REVERT: A 1197 THR cc_start: 0.7518 (OUTLIER) cc_final: 0.7170 (p)
REVERT: A 1212 LYS cc_start: 0.9194 (pptt) cc_final: 0.8966 (ptmm)
REVERT: A 1222 TRP cc_start: 0.7630 (m100) cc_final: 0.7429 (m100)
REVERT: A 1250 PHE cc_start: 0.9239 (t80) cc_final: 0.8993 (m-80)
REVERT: A 1252 MET cc_start: 0.9205 (mmm) cc_final: 0.8467 (mmm)
REVERT: B  159 LYS cc_start: 0.8702 (tppt) cc_final: 0.8457 (tptp)
  outliers start: 30
  outliers final: 16
  residues processed: 148
  average time/residue: 0.1234
  time to fit residues: 23.1420
Evaluate side-chains
  132 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  406 PHE
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  520 TYR
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  635 GLU
Chi-restraints excluded: chain A residue  638 LYS
Chi-restraints excluded: chain A residue  944 THR
Chi-restraints excluded: chain A residue  971 ASN
Chi-restraints excluded: chain A residue 1073 LEU
Chi-restraints excluded: chain A residue 1127 MET
Chi-restraints excluded: chain A residue 1128 VAL
Chi-restraints excluded: chain A residue 1192 LEU
Chi-restraints excluded: chain A residue 1197 THR
Chi-restraints excluded: chain A residue 1226 CYS
Chi-restraints excluded: chain A residue 1249 ASN
Chi-restraints excluded: chain B residue  154 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 61 optimal weight:   10.0000
   chunk 86 optimal weight:    8.9990
   chunk 13 optimal weight:    9.9990
   chunk 72 optimal weight:    8.9990
   chunk 63 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 83 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.104152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.078774 restraints weight = 41174.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.081387 restraints weight = 24877.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.083012 restraints weight = 17538.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.084096 restraints weight = 13711.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.084819 restraints weight = 11336.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.3743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   8623  Z= 0.176
  Angle     :  0.755  21.235  11890  Z= 0.375
  Chirality :  0.044   0.264   1354
  Planarity :  0.006   0.071   1302
  Dihedral  : 18.226 144.214   1829
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 26.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 19.90 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.29), residues: 867
  helix: -0.23 (0.26), residues: 330
  sheet: -1.80 (0.51), residues: 94
  loop : -0.58 (0.32), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 699 
 TYR   0.032   0.002   TYR A 649 
 PHE   0.030   0.002   PHE A 528 
 TRP   0.015   0.002   TRP A 503 
 HIS   0.009   0.001   HIS B 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00390 /  0.17 ( 8607)
  covalent geometry    : angle       0.72298 /  0.37 (11879)
  hydrogen bonds       : bond        0.06185 /  4.18 (  329)
  hydrogen bonds       : angle       5.73703 /  4.27 (  891)
  metal coordination   : bond        0.01436 /  0.99 (   16)
  metal coordination   : angle       7.18589 /  5.39 (   11)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 LEU cc_start: 0.9303 (tp) cc_final: 0.9025 (pp)
REVERT: A  284 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.8906 (tp)
REVERT: A  324 LYS cc_start: 0.9120 (tttp) cc_final: 0.8349 (tptm)
REVERT: A  329 LYS cc_start: 0.8389 (mttt) cc_final: 0.7888 (mmtt)
REVERT: A  404 THR cc_start: 0.8792 (p) cc_final: 0.8484 (p)
REVERT: A  414 ASN cc_start: 0.6403 (m110) cc_final: 0.5798 (m-40)
REVERT: A  493 PHE cc_start: 0.7440 (t80) cc_final: 0.6948 (t80)
REVERT: A  521 CYS cc_start: 0.8443 (m) cc_final: 0.8004 (m)
REVERT: A  565 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8576 (mm-30)
REVERT: A  932 PHE cc_start: 0.8812 (m-10) cc_final: 0.8245 (m-10)
REVERT: A  943 MET cc_start: 0.7213 (mmt) cc_final: 0.6811 (mmp)
REVERT: A 1098 LEU cc_start: 0.9661 (mm) cc_final: 0.9401 (mm)
REVERT: A 1196 TYR cc_start: 0.8654 (m-80) cc_final: 0.8155 (m-10)
REVERT: A 1212 LYS cc_start: 0.9170 (pptt) cc_final: 0.8963 (ptmm)
REVERT: A 1250 PHE cc_start: 0.9271 (t80) cc_final: 0.8869 (m-80)
REVERT: A 1252 MET cc_start: 0.9184 (mmm) cc_final: 0.8418 (mmm)
REVERT: B  159 LYS cc_start: 0.8707 (tppt) cc_final: 0.8469 (tptp)
  outliers start: 25
  outliers final: 16
  residues processed: 129
  average time/residue: 0.1188
  time to fit residues: 19.3561
Evaluate side-chains
  126 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  390 PHE
Chi-restraints excluded: chain A residue  520 TYR
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  635 GLU
Chi-restraints excluded: chain A residue  944 THR
Chi-restraints excluded: chain A residue 1073 LEU
Chi-restraints excluded: chain A residue 1127 MET
Chi-restraints excluded: chain A residue 1192 LEU
Chi-restraints excluded: chain A residue 1226 CYS
Chi-restraints excluded: chain A residue 1229 ILE
Chi-restraints excluded: chain A residue 1249 ASN
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  154 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 83 optimal weight:   10.0000
   chunk 88 optimal weight:   30.0000
   chunk 47 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9990
   chunk 21 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 35 optimal weight:    9.9990
   chunk 54 optimal weight:    9.9990
   chunk 50 optimal weight:    9.9990
   overall best weight:    3.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.103334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.077749 restraints weight = 40941.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.080348 restraints weight = 24837.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.082110 restraints weight = 17399.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 71)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.083179 restraints weight = 13425.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.083937 restraints weight = 11118.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.3980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086   8623  Z= 0.194
  Angle     :  0.758  19.215  11890  Z= 0.382
  Chirality :  0.045   0.260   1354
  Planarity :  0.006   0.071   1302
  Dihedral  : 18.252 143.777   1829
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 28.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 21.68 %
    Favored  : 75.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.29), residues: 867
  helix: -0.32 (0.26), residues: 337
  sheet: -1.92 (0.50), residues: 98
  loop : -0.65 (0.33), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1194 
 TYR   0.020   0.002   TYR A 649 
 PHE   0.049   0.002   PHE A 406 
 TRP   0.053   0.003   TRP A1189 
 HIS   0.011   0.002   HIS B 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00427 /  0.19 ( 8607)
  covalent geometry    : angle       0.73183 /  0.38 (11879)
  hydrogen bonds       : bond        0.06193 /  4.19 (  329)
  hydrogen bonds       : angle       5.69417 /  4.23 (  891)
  metal coordination   : bond        0.01559 /  1.09 (   16)
  metal coordination   : angle       6.58949 /  4.98 (   11)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 LEU cc_start: 0.9270 (tp) cc_final: 0.9006 (pp)
REVERT: A  324 LYS cc_start: 0.9125 (tttp) cc_final: 0.8451 (tptm)
REVERT: A  414 ASN cc_start: 0.6471 (m110) cc_final: 0.5870 (m-40)
REVERT: A  493 PHE cc_start: 0.7268 (t80) cc_final: 0.6903 (t80)
REVERT: A  521 CYS cc_start: 0.8492 (m) cc_final: 0.8051 (m)
REVERT: A  565 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8673 (mm-30)
REVERT: A  679 VAL cc_start: 0.7609 (OUTLIER) cc_final: 0.7347 (t)
REVERT: A  932 PHE cc_start: 0.8853 (m-80) cc_final: 0.8283 (m-10)
REVERT: A 1187 GLU cc_start: 0.9175 (tp30) cc_final: 0.8735 (tm-30)
REVERT: A 1212 LYS cc_start: 0.9210 (pptt) cc_final: 0.8987 (ptmm)
REVERT: A 1250 PHE cc_start: 0.9347 (t80) cc_final: 0.8881 (m-80)
REVERT: A 1252 MET cc_start: 0.9189 (mmm) cc_final: 0.8461 (mmm)
REVERT: B  159 LYS cc_start: 0.8717 (tppt) cc_final: 0.8480 (tptp)
  outliers start: 20
  outliers final: 15
  residues processed: 129
  average time/residue: 0.1217
  time to fit residues: 19.7032
Evaluate side-chains
  122 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  520 TYR
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  944 THR
Chi-restraints excluded: chain A residue 1040 ARG
Chi-restraints excluded: chain A residue 1073 LEU
Chi-restraints excluded: chain A residue 1226 CYS
Chi-restraints excluded: chain A residue 1229 ILE
Chi-restraints excluded: chain A residue 1249 ASN
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  170 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 67 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 46 optimal weight:    8.9990
   chunk 15 optimal weight:    5.9990
   chunk 71 optimal weight:   20.0000
   chunk 69 optimal weight:    5.9990
   chunk 12 optimal weight:   20.0000
   chunk 13 optimal weight:    6.9990
   chunk 48 optimal weight:    6.9990
   chunk 61 optimal weight:    7.9990
   chunk 87 optimal weight:   30.0000
   overall best weight:    4.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.102350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.076603 restraints weight = 41705.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.079208 restraints weight = 25306.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.080907 restraints weight = 17798.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.081986 restraints weight = 13810.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.082753 restraints weight = 11434.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.4243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   8623  Z= 0.221
  Angle     :  0.799  17.930  11890  Z= 0.397
  Chirality :  0.045   0.358   1354
  Planarity :  0.006   0.074   1302
  Dihedral  : 18.311 143.127   1829
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 31.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 22.07 %
    Favored  : 75.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.29), residues: 867
  helix: -0.38 (0.26), residues: 336
  sheet: -1.81 (0.50), residues: 98
  loop : -0.67 (0.33), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 699 
 TYR   0.016   0.002   TYR A1205 
 PHE   0.026   0.002   PHE A 528 
 TRP   0.027   0.002   TRP A1189 
 HIS   0.013   0.002   HIS B 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00477 /  0.22 ( 8607)
  covalent geometry    : angle       0.77463 /  0.39 (11879)
  hydrogen bonds       : bond        0.06314 /  4.28 (  329)
  hydrogen bonds       : angle       5.76441 /  4.27 (  891)
  metal coordination   : bond        0.01983 /  1.38 (   16)
  metal coordination   : angle       6.51413 /  4.79 (   11)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 LEU cc_start: 0.9230 (tp) cc_final: 0.8954 (pp)
REVERT: A  284 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9193 (tp)
REVERT: A  324 LYS cc_start: 0.9096 (tttp) cc_final: 0.8493 (tptm)
REVERT: A  414 ASN cc_start: 0.6474 (m110) cc_final: 0.5834 (m-40)
REVERT: A  521 CYS cc_start: 0.8400 (m) cc_final: 0.8037 (m)
REVERT: A  565 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8719 (mm-30)
REVERT: A  932 PHE cc_start: 0.8910 (m-80) cc_final: 0.8308 (m-10)
REVERT: A 1187 GLU cc_start: 0.9212 (tp30) cc_final: 0.8781 (tm-30)
REVERT: A 1250 PHE cc_start: 0.9338 (t80) cc_final: 0.8873 (m-80)
REVERT: A 1252 MET cc_start: 0.9227 (mmm) cc_final: 0.8517 (mmm)
REVERT: B  159 LYS cc_start: 0.8731 (tppt) cc_final: 0.8523 (tptp)
  outliers start: 18
  outliers final: 15
  residues processed: 128
  average time/residue: 0.1130
  time to fit residues: 18.2140
Evaluate side-chains
  119 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  390 PHE
Chi-restraints excluded: chain A residue  520 TYR
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  944 THR
Chi-restraints excluded: chain A residue 1073 LEU
Chi-restraints excluded: chain A residue 1226 CYS
Chi-restraints excluded: chain A residue 1229 ILE
Chi-restraints excluded: chain A residue 1249 ASN
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  170 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 76 optimal weight:   30.0000
   chunk 11 optimal weight:    0.4980
   chunk 62 optimal weight:   10.0000
   chunk 43 optimal weight:    1.9990
   chunk 85 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 29 optimal weight:    8.9990
   chunk 24 optimal weight:    6.9990
   overall best weight:    1.8586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.104663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.079351 restraints weight = 41124.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.082008 restraints weight = 24823.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.083777 restraints weight = 17233.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.084932 restraints weight = 13238.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.085660 restraints weight = 11008.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.4323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8623  Z= 0.160
  Angle     :  0.816  16.241  11890  Z= 0.404
  Chirality :  0.046   0.341   1354
  Planarity :  0.006   0.060   1302
  Dihedral  : 18.280 142.526   1829
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 25.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 22.45 %
    Favored  : 74.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.04 (0.29), residues: 867
  helix: -0.24 (0.26), residues: 336
  sheet: -1.55 (0.52), residues: 98
  loop : -0.72 (0.33), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 283 
 TYR   0.025   0.002   TYR A1205 
 PHE   0.029   0.002   PHE A 528 
 TRP   0.021   0.002   TRP A1189 
 HIS   0.013   0.002   HIS B 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.16 ( 8607)
  covalent geometry    : angle       0.79720 /  0.40 (11879)
  hydrogen bonds       : bond        0.05758 /  3.91 (  329)
  hydrogen bonds       : angle       5.71061 /  4.22 (  891)
  metal coordination   : bond        0.01454 /  1.02 (   16)
  metal coordination   : angle       5.83484 /  4.24 (   11)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 LEU cc_start: 0.9288 (tp) cc_final: 0.9052 (pp)
REVERT: A  307 LYS cc_start: 0.9113 (mtmm) cc_final: 0.8786 (mtmt)
REVERT: A  324 LYS cc_start: 0.9035 (tttp) cc_final: 0.8455 (tptm)
REVERT: A  414 ASN cc_start: 0.6089 (m110) cc_final: 0.5566 (m-40)
REVERT: A  521 CYS cc_start: 0.8490 (m) cc_final: 0.8043 (m)
REVERT: A  565 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8661 (mm-30)
REVERT: A  679 VAL cc_start: 0.7534 (OUTLIER) cc_final: 0.7271 (t)
REVERT: A  932 PHE cc_start: 0.8842 (m-80) cc_final: 0.8394 (m-10)
REVERT: A 1187 GLU cc_start: 0.9183 (tp30) cc_final: 0.8788 (tm-30)
REVERT: A 1196 TYR cc_start: 0.8619 (m-80) cc_final: 0.7893 (m-10)
REVERT: A 1250 PHE cc_start: 0.9334 (t80) cc_final: 0.8873 (m-80)
REVERT: A 1252 MET cc_start: 0.9229 (mmm) cc_final: 0.8361 (mmm)
REVERT: B   58 MET cc_start: -0.1857 (ttt) cc_final: -0.2457 (tpp)
  outliers start: 22
  outliers final: 18
  residues processed: 128
  average time/residue: 0.1028
  time to fit residues: 16.9140
Evaluate side-chains
  124 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  390 PHE
Chi-restraints excluded: chain A residue  520 TYR
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  944 THR
Chi-restraints excluded: chain A residue 1040 ARG
Chi-restraints excluded: chain A residue 1073 LEU
Chi-restraints excluded: chain A residue 1105 PHE
Chi-restraints excluded: chain A residue 1192 LEU
Chi-restraints excluded: chain A residue 1226 CYS
Chi-restraints excluded: chain A residue 1249 ASN
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  170 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 84 optimal weight:   20.0000
   chunk 67 optimal weight:    7.9990
   chunk 14 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 39 optimal weight:    0.7980
   chunk 74 optimal weight:   50.0000
   chunk 27 optimal weight:    0.3980
   chunk 48 optimal weight:    0.9990
   chunk 57 optimal weight:   20.0000
   chunk 51 optimal weight:    9.9990
   overall best weight:    1.4386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 450 HIS
A 969 GLN
** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.105646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.079614 restraints weight = 41268.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.082276 restraints weight = 25103.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.084036 restraints weight = 17717.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.085176 restraints weight = 13786.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.085912 restraints weight = 11448.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.4498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   8623  Z= 0.164
  Angle     :  0.821  14.993  11890  Z= 0.414
  Chirality :  0.046   0.320   1354
  Planarity :  0.006   0.055   1302
  Dihedral  : 18.229 142.177   1829
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 25.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 23.09 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.29), residues: 867
  helix: -0.01 (0.27), residues: 330
  sheet: -1.41 (0.53), residues: 98
  loop : -0.80 (0.32), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 286 
 TYR   0.041   0.002   TYR A1205 
 PHE   0.034   0.002   PHE B 163 
 TRP   0.018   0.002   TRP A1189 
 HIS   0.013   0.002   HIS B 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00366 /  0.16 ( 8607)
  covalent geometry    : angle       0.80402 /  0.41 (11879)
  hydrogen bonds       : bond        0.05737 /  3.92 (  329)
  hydrogen bonds       : angle       5.60144 /  4.14 (  891)
  metal coordination   : bond        0.01313 /  0.91 (   16)
  metal coordination   : angle       5.44974 /  4.01 (   11)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 LEU cc_start: 0.9259 (tp) cc_final: 0.9039 (pp)
REVERT: A  324 LYS cc_start: 0.9024 (tttp) cc_final: 0.8513 (tptp)
REVERT: A  414 ASN cc_start: 0.6184 (m110) cc_final: 0.5741 (m110)
REVERT: A  493 PHE cc_start: 0.7446 (t80) cc_final: 0.7208 (t80)
REVERT: A  521 CYS cc_start: 0.8457 (m) cc_final: 0.8014 (m)
REVERT: A  565 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8660 (mm-30)
REVERT: A  656 GLN cc_start: 0.8512 (tm-30) cc_final: 0.7991 (tm-30)
REVERT: A  661 ARG cc_start: 0.7221 (mmt90) cc_final: 0.5619 (mmm160)
REVERT: A  679 VAL cc_start: 0.7521 (OUTLIER) cc_final: 0.7246 (t)
REVERT: A  698 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7420 (mp0)
REVERT: A  932 PHE cc_start: 0.8827 (m-80) cc_final: 0.8424 (m-10)
REVERT: A 1187 GLU cc_start: 0.9196 (tp30) cc_final: 0.8793 (tm-30)
REVERT: A 1196 TYR cc_start: 0.8607 (m-80) cc_final: 0.7965 (m-10)
REVERT: A 1250 PHE cc_start: 0.9316 (t80) cc_final: 0.8853 (m-80)
REVERT: A 1252 MET cc_start: 0.9190 (mmm) cc_final: 0.8330 (mmm)
REVERT: B   58 MET cc_start: 0.0659 (ttt) cc_final: -0.0522 (tpp)
REVERT: B  159 LYS cc_start: 0.7973 (tptp) cc_final: 0.7697 (tptp)
  outliers start: 21
  outliers final: 18
  residues processed: 124
  average time/residue: 0.0999
  time to fit residues: 15.9876
Evaluate side-chains
  123 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  390 PHE
Chi-restraints excluded: chain A residue  520 TYR
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  944 THR
Chi-restraints excluded: chain A residue 1040 ARG
Chi-restraints excluded: chain A residue 1073 LEU
Chi-restraints excluded: chain A residue 1105 PHE
Chi-restraints excluded: chain A residue 1192 LEU
Chi-restraints excluded: chain A residue 1226 CYS
Chi-restraints excluded: chain A residue 1249 ASN
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  170 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 79 optimal weight:   10.0000
   chunk 57 optimal weight:   20.0000
   chunk 82 optimal weight:   30.0000
   chunk 84 optimal weight:    0.1980
   chunk 68 optimal weight:   10.0000
   chunk 71 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0870
   chunk 8 optimal weight:    2.9990
   chunk 60 optimal weight:    9.9990
   chunk 67 optimal weight:    0.4980
   overall best weight:    1.3562

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.106121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.080650 restraints weight = 40481.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.083317 restraints weight = 24432.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.085080 restraints weight = 17099.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.086126 restraints weight = 13198.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.086965 restraints weight = 11073.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.4583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8623  Z= 0.157
  Angle     :  0.831  15.533  11890  Z= 0.421
  Chirality :  0.046   0.326   1354
  Planarity :  0.006   0.053   1302
  Dihedral  : 18.196 141.812   1829
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 24.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 23.47 %
    Favored  : 74.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.29), residues: 867
  helix:  0.07 (0.27), residues: 325
  sheet: -1.45 (0.53), residues: 98
  loop : -0.87 (0.32), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 699 
 TYR   0.050   0.002   TYR A1205 
 PHE   0.051   0.002   PHE A 406 
 TRP   0.017   0.002   TRP A 503 
 HIS   0.012   0.002   HIS B 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.16 ( 8607)
  covalent geometry    : angle       0.81431 /  0.42 (11879)
  hydrogen bonds       : bond        0.05623 /  3.86 (  329)
  hydrogen bonds       : angle       5.55487 /  4.09 (  891)
  metal coordination   : bond        0.01215 /  0.87 (   16)
  metal coordination   : angle       5.56116 /  4.22 (   11)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 LYS cc_start: 0.9003 (tttp) cc_final: 0.8509 (tptp)
REVERT: A  414 ASN cc_start: 0.6437 (m110) cc_final: 0.5968 (m110)
REVERT: A  423 MET cc_start: 0.8050 (pmm) cc_final: 0.7733 (pmm)
REVERT: A  521 CYS cc_start: 0.8486 (m) cc_final: 0.8040 (m)
REVERT: A  565 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8662 (mm-30)
REVERT: A  656 GLN cc_start: 0.8492 (tm-30) cc_final: 0.7962 (tm-30)
REVERT: A  661 ARG cc_start: 0.7345 (mmt90) cc_final: 0.5251 (mmm160)
REVERT: A  668 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8793 (mmtt)
REVERT: A  679 VAL cc_start: 0.7513 (OUTLIER) cc_final: 0.7255 (t)
REVERT: A  932 PHE cc_start: 0.8809 (m-80) cc_final: 0.8344 (m-10)
REVERT: A 1187 GLU cc_start: 0.9183 (tp30) cc_final: 0.8777 (tm-30)
REVERT: A 1250 PHE cc_start: 0.9280 (t80) cc_final: 0.8865 (m-80)
REVERT: A 1252 MET cc_start: 0.9238 (mmm) cc_final: 0.8558 (mmm)
REVERT: B   58 MET cc_start: -0.1392 (ttt) cc_final: -0.2132 (tpp)
REVERT: B  159 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7623 (tptp)
  outliers start: 17
  outliers final: 15
  residues processed: 112
  average time/residue: 0.1125
  time to fit residues: 15.9781
Evaluate side-chains
  114 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  520 TYR
Chi-restraints excluded: chain A residue  623 THR
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  944 THR
Chi-restraints excluded: chain A residue 1040 ARG
Chi-restraints excluded: chain A residue 1073 LEU
Chi-restraints excluded: chain A residue 1192 LEU
Chi-restraints excluded: chain A residue 1226 CYS
Chi-restraints excluded: chain A residue 1249 ASN
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  159 LYS
Chi-restraints excluded: chain B residue  170 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 88 optimal weight:   40.0000
   chunk 13 optimal weight:    6.9990
   chunk 77 optimal weight:   40.0000
   chunk 20 optimal weight:    0.8980
   chunk 72 optimal weight:   10.0000
   chunk 73 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    3.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.104617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.079116 restraints weight = 40725.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.081714 restraints weight = 24801.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.083449 restraints weight = 17414.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.084600 restraints weight = 13481.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 73)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.085324 restraints weight = 11210.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.4719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8623  Z= 0.176
  Angle     :  0.812  13.963  11890  Z= 0.410
  Chirality :  0.046   0.307   1354
  Planarity :  0.006   0.051   1302
  Dihedral  : 18.210 140.933   1829
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 27.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 23.98 %
    Favored  : 73.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.29), residues: 867
  helix:  0.05 (0.27), residues: 325
  sheet: -1.50 (0.53), residues: 98
  loop : -0.83 (0.32), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 699 
 TYR   0.046   0.002   TYR A1205 
 PHE   0.033   0.002   PHE A 406 
 TRP   0.016   0.002   TRP A1222 
 HIS   0.013   0.002   HIS B 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00385 /  0.18 ( 8607)
  covalent geometry    : angle       0.79620 /  0.41 (11879)
  hydrogen bonds       : bond        0.05699 /  3.91 (  329)
  hydrogen bonds       : angle       5.57685 /  4.08 (  891)
  metal coordination   : bond        0.01632 /  1.17 (   16)
  metal coordination   : angle       5.22496 /  3.92 (   11)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1918.81 seconds
wall clock time: 33 minutes 33.72 seconds (2013.72 seconds total)