Starting phenix.real_space_refine
on Sun Mar 10 21:50:07 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/03_2024/6yw7_10960_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/03_2024/6yw7_10960.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/03_2024/6yw7_10960.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/03_2024/6yw7_10960.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/03_2024/6yw7_10960_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/03_2024/6yw7_10960_updated.pdb"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     C    3596      2.51       5
     N    1798      2.21       5
     O      26      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 5426
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 396, 1188
          Classifications: {'peptide': 396}
          Incomplete info: {'n_c_alpha_c_only': 396}
          Link IDs: {'PTRANS': 26, 'TRANS': 369}
          Chain breaks: 2
          Unresolved chain link angles: 421
          Unresolved non-hydrogen bonds: 2072
          Unresolved non-hydrogen angles: 2818
          Unresolved non-hydrogen dihedrals: 1103
          Unresolved non-hydrogen chiralities: 481
          Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 9, 'TYR:plan': 18, 'ASN:plan1': 10, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 20, 'GLU:plan': 32, 'ARG:plan': 22}
          Unresolved non-hydrogen planarities: 818
    Chain: "D"
      Number of atoms: 852
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 852
          Classifications: {'peptide': 284}
          Incomplete info: {'n_c_alpha_c_only': 284}
          Link IDs: {'PTRANS': 9, 'TRANS': 274}
          Unresolved chain link angles: 292
          Unresolved non-hydrogen bonds: 1489
          Unresolved non-hydrogen angles: 2017
          Unresolved non-hydrogen dihedrals: 780
          Unresolved non-hydrogen chiralities: 346
          Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 11, 'TYR:plan': 12, 'ASN:plan1': 16, 'ASP:plan': 20, 'PHE:plan': 18, 'GLU:plan': 21, 'ARG:plan': 16}
          Unresolved non-hydrogen planarities: 620
    Chain: "E"
      Number of atoms: 510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 170, 510
          Classifications: {'peptide': 170}
          Incomplete info: {'n_c_alpha_c_only': 170}
          Link IDs: {'PTRANS': 11, 'TRANS': 158}
          Chain breaks: 1
          Unresolved chain link angles: 180
          Unresolved non-hydrogen bonds: 903
          Unresolved non-hydrogen angles: 1215
          Unresolved non-hydrogen dihedrals: 488
          Unresolved non-hydrogen chiralities: 202
          Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 342
    Chain: "B"
      Number of atoms: 858
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 858
          Classifications: {'peptide': 286}
          Incomplete info: {'n_c_alpha_c_only': 286}
          Link IDs: {'PTRANS': 14, 'TRANS': 271}
          Chain breaks: 3
          Unresolved chain link angles: 299
          Unresolved non-hydrogen bonds: 1467
          Unresolved non-hydrogen angles: 1992
          Unresolved non-hydrogen dihedrals: 764
          Unresolved non-hydrogen chiralities: 353
          Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 16, 'TYR:plan': 12, 'ASN:plan1': 7, 'TRP:plan': 2, 'HIS:plan': 8, 'PHE:plan': 14, 'GLU:plan': 20, 'ASP:plan': 17}
          Unresolved non-hydrogen planarities: 550
    Chain: "F"
      Number of atoms: 495
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 495
          Classifications: {'peptide': 165}
          Incomplete info: {'n_c_alpha_c_only': 165}
          Link IDs: {'PTRANS': 4, 'TRANS': 160}
          Unresolved chain link angles: 168
          Unresolved non-hydrogen bonds: 886
          Unresolved non-hydrogen angles: 1190
          Unresolved non-hydrogen dihedrals: 462
          Unresolved non-hydrogen chiralities: 211
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 8, 'HIS:plan': 5, 'PHE:plan': 11, 'GLU:plan': 19, 'ARG:plan': 12}
          Unresolved non-hydrogen planarities: 335
    Chain: "G"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 417
          Classifications: {'peptide': 139}
          Incomplete info: {'n_c_alpha_c_only': 139}
          Link IDs: {'PTRANS': 4, 'TRANS': 134}
          Chain breaks: 1
          Unresolved chain link angles: 142
          Unresolved non-hydrogen bonds: 658
          Unresolved non-hydrogen angles: 889
          Unresolved non-hydrogen dihedrals: 318
          Unresolved non-hydrogen chiralities: 164
          Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 230
    Chain: "C"
      Number of atoms: 1044
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 348, 1044
          Classifications: {'peptide': 348}
          Incomplete info: {'n_c_alpha_c_only': 348}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 333}
          Chain breaks: 1
          Unresolved chain link angles: 360
          Unresolved non-hydrogen bonds: 1764
          Unresolved non-hydrogen angles: 2409
          Unresolved non-hydrogen dihedrals: 949
          Unresolved non-hydrogen chiralities: 420
          Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 19, 'TYR:plan': 6, 'ASN:plan1': 14, 'TRP:plan': 13, 'HIS:plan': 13, 'PHE:plan': 15, 'GLU:plan': 15, 'ARG:plan': 13}
          Unresolved non-hydrogen planarities: 666
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.36, per 1000 atoms: 0.80
  Number of scatterers: 5426
  At special positions: 0
  Unit cell: (138.43, 91.56, 136.25, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     P       6     15.00
     O      26      8.00
     N    1798      7.00
     C    3596      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  - 3.50
        Amino acid           : False - 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: 1.67
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3516 Ramachandran restraints generated.
    1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  0

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      0 helices and 0 sheets defined
      0.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...

    No hydrogen bonds defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.00

  Time building geometry restraints manager: 1.54 seconds

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

  Histogram of bond lengths:
        1.15 -     1.27: 6
        1.27 -     1.39: 1767
        1.39 -     1.50: 2102
        1.50 -     1.62: 1530
        1.62 -     1.73: 10
  Bond restraints: 5415
  Sorted by residual:
  bond pdb=" C   VAL A  83 "
       pdb=" N   GLU A  84 "
    ideal  model  delta    sigma   weight residual
    1.334  1.733 -0.398 1.27e-02 6.20e+03 9.84e+02
  bond pdb=" C   GLU A 280 "
       pdb=" N   ILE A 281 "
    ideal  model  delta    sigma   weight residual
    1.335  1.155  0.181 1.05e-02 9.07e+03 2.96e+02
  bond pdb=" C   ILE B 184 "
       pdb=" N   ALA B 185 "
    ideal  model  delta    sigma   weight residual
    1.331  1.535 -0.204 1.29e-02 6.01e+03 2.50e+02
  bond pdb=" CA  ALA B 261 "
       pdb=" C   ALA B 261 "
    ideal  model  delta    sigma   weight residual
    1.524  1.707 -0.183 1.26e-02 6.30e+03 2.11e+02
  bond pdb=" C   TYR B 310 "
       pdb=" N   PRO B 311 "
    ideal  model  delta    sigma   weight residual
    1.330  1.501 -0.171 1.19e-02 7.06e+03 2.07e+02
  ... (remaining 5410 not shown)

  Histogram of bond angle deviations from ideal:
       50.01 -    69.36: 1
       69.36 -    88.71: 3
       88.71 -   108.05: 367
      108.05 -   127.40: 4986
      127.40 -   146.75: 81
  Bond angle restraints: 5438
  Sorted by residual:
  angle pdb=" CA  GLN B 267 "
        pdb=" C   GLN B 267 "
        pdb=" N   PRO B 268 "
      ideal   model   delta    sigma   weight residual
     118.87   93.23   25.64 9.00e-01 1.23e+00 8.11e+02
  angle pdb=" N   GLU A  39 "
        pdb=" CA  GLU A  39 "
        pdb=" C   GLU A  39 "
      ideal   model   delta    sigma   weight residual
     111.00   50.01   60.99 2.80e+00 1.28e-01 4.74e+02
  angle pdb=" CA  PHE D  83 "
        pdb=" C   PHE D  83 "
        pdb=" N   LEU D  84 "
      ideal   model   delta    sigma   weight residual
     118.38   90.25   28.13 1.30e+00 5.92e-01 4.68e+02
  angle pdb=" CA  LEU B 240 "
        pdb=" C   LEU B 240 "
        pdb=" N   VAL B 241 "
      ideal   model   delta    sigma   weight residual
     117.39   92.00   25.39 1.24e+00 6.50e-01 4.19e+02
  angle pdb=" CA  GLN A 366 "
        pdb=" C   GLN A 366 "
        pdb=" N   VAL A 367 "
      ideal   model   delta    sigma   weight residual
     116.01   85.37   30.64 1.51e+00 4.39e-01 4.12e+02
  ... (remaining 5433 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.28: 1758
       16.28 -    32.56: 58
       32.56 -    48.84: 17
       48.84 -    65.12: 4
       65.12 -    81.40: 4
  Dihedral angle restraints: 1841
    sinusoidal: 68
      harmonic: 1773
  Sorted by residual:
  dihedral pdb=" CA  LYS A  38 "
           pdb=" C   LYS A  38 "
           pdb=" N   GLU A  39 "
           pdb=" CA  GLU A  39 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -109.12  -70.88     0      5.00e+00 4.00e-02 2.01e+02
  dihedral pdb=" CA  PHE D  63 "
           pdb=" C   PHE D  63 "
           pdb=" N   TYR D  64 "
           pdb=" CA  TYR D  64 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -133.67  -46.33     0      5.00e+00 4.00e-02 8.59e+01
  dihedral pdb=" CA  ASP A  57 "
           pdb=" C   ASP A  57 "
           pdb=" N   LEU A  58 "
           pdb=" CA  LEU A  58 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -134.14  -45.86     0      5.00e+00 4.00e-02 8.41e+01
  ... (remaining 1838 not shown)

  Histogram of chiral volume deviations from ideal:
       0.008 -    0.041: 3
       0.041 -    0.074: 1
       0.074 -    0.107: 2
       0.107 -    0.140: 1
       0.140 -    0.173: 1
  Chirality restraints: 8
  Sorted by residual:
  chirality pdb=" C1' ATP A 501 "
            pdb=" C2' ATP A 501 "
            pdb=" N9  ATP A 501 "
            pdb=" O4' ATP A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.41    2.24    0.17 2.00e-01 2.50e+01 7.44e-01
  chirality pdb=" C2' ATP B 401 "
            pdb=" C1' ATP B 401 "
            pdb=" C3' ATP B 401 "
            pdb=" O2' ATP B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.54   -0.14 2.00e-01 2.50e+01 4.61e-01
  chirality pdb=" C1' ATP B 401 "
            pdb=" C2' ATP B 401 "
            pdb=" N9  ATP B 401 "
            pdb=" O4' ATP B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.41    2.50   -0.09 2.00e-01 2.50e+01 2.03e-01
  ... (remaining 5 not shown)

  Planarity restraints: 2
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' ATP A 501 "    0.023 2.00e-02 2.50e+03   1.59e-02 6.92e+00
        pdb=" C2  ATP A 501 "    0.001 2.00e-02 2.50e+03
        pdb=" C4  ATP A 501 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5  ATP A 501 "    0.000 2.00e-02 2.50e+03
        pdb=" C6  ATP A 501 "    0.002 2.00e-02 2.50e+03
        pdb=" C8  ATP A 501 "    0.015 2.00e-02 2.50e+03
        pdb=" N1  ATP A 501 "    0.000 2.00e-02 2.50e+03
        pdb=" N3  ATP A 501 "    0.001 2.00e-02 2.50e+03
        pdb=" N6  ATP A 501 "    0.003 2.00e-02 2.50e+03
        pdb=" N7  ATP A 501 "   -0.001 2.00e-02 2.50e+03
        pdb=" N9  ATP A 501 "   -0.045 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' ATP B 401 "    0.001 2.00e-02 2.50e+03   7.78e-04 1.66e-02
        pdb=" C2  ATP B 401 "   -0.000 2.00e-02 2.50e+03
        pdb=" C4  ATP B 401 "    0.002 2.00e-02 2.50e+03
        pdb=" C5  ATP B 401 "    0.001 2.00e-02 2.50e+03
        pdb=" C6  ATP B 401 "   -0.000 2.00e-02 2.50e+03
        pdb=" C8  ATP B 401 "   -0.000 2.00e-02 2.50e+03
        pdb=" N1  ATP B 401 "   -0.000 2.00e-02 2.50e+03
        pdb=" N3  ATP B 401 "   -0.001 2.00e-02 2.50e+03
        pdb=" N6  ATP B 401 "    0.000 2.00e-02 2.50e+03
        pdb=" N7  ATP B 401 "   -0.000 2.00e-02 2.50e+03
        pdb=" N9  ATP B 401 "   -0.002 2.00e-02 2.50e+03

  Histogram of nonbonded interaction distances:
        2.03 -     2.61: 44
        2.61 -     3.18: 2284
        3.18 -     3.75: 2819
        3.75 -     4.33: 5699
        4.33 -     4.90: 10226
  Nonbonded interactions: 21072
  Sorted by model distance:
  nonbonded pdb=" N   LEU B 240 "
            pdb=" N   VAL B 241 "
     model   vdw
     2.034 2.560
  nonbonded pdb=" N   PHE D  83 "
            pdb=" N   LEU D  84 "
     model   vdw
     2.040 2.560
  nonbonded pdb=" N   LEU A  58 "
            pdb=" N   ASP A  59 "
     model   vdw
     2.065 2.560
  nonbonded pdb=" N   SER C 196 "
            pdb=" N   GLU C 197 "
     model   vdw
     2.166 2.560
  nonbonded pdb=" C   LYS A  38 "
            pdb=" C   GLU A  39 "
     model   vdw
     2.190 2.800
  ... (remaining 21067 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             1.070
  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:          3.820
  Check model and map are aligned:         0.070
  Set scattering table:                    0.040
  Process input model:                     18.070
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.040
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3204
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      :  0.021   0.398   5415  Z= 1.606
  Angle     :  3.501  60.991   5438  Z= 2.353
  Chirality :  0.091   0.173      8
  Planarity :  0.011   0.016      2
  Dihedral  :  8.081  81.400   1841
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 2.17
  Ramachandran Plot:
    Outliers :  0.85 %
    Allowed  :  4.49 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.89 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.18), residues: 1758
  helix: -0.92 (0.18), residues: 641
  sheet: -0.01 (0.26), residues: 340
  loop : -1.34 (0.21), residues: 777


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

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

  3516 Ramachandran restraints generated.
    1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3516 Ramachandran restraints generated.
    1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.645 
Fit side-chains
TARDY: cannot create tardy model for: "MET A  52 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  89 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  93 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D   1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D  56 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E   9 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E  19 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B  85 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  91 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  94 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  96 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G  51 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C   1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it.
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0464
  time to fit residues: 4.6403
Evaluate side-chains
  41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 147 optimal weight:    5.9990
   chunk 132 optimal weight:    0.1980
   chunk 73 optimal weight:   40.0000
   chunk 45 optimal weight:    0.1980
   chunk 89 optimal weight:    4.9990
   chunk 70 optimal weight:   10.0000
   chunk 137 optimal weight:   20.0000
   chunk 53 optimal weight:   40.0000
   chunk 83 optimal weight:    0.0570
   chunk 102 optimal weight:    5.9990
   chunk 158 optimal weight:    0.7980
   overall best weight:    1.2500

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3515
moved from start:          0.2761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.037   5415  Z= 0.084
  Angle     :  0.445   7.990   5438  Z= 0.259
  Chirality :  0.035   0.054      8
  Planarity :  0.001   0.001      2
  Dihedral  :  5.084  79.122   1841
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 0.27
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.22 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.20), residues: 1758
  helix:  1.25 (0.21), residues: 634
  sheet:  0.58 (0.28), residues: 316
  loop : -0.47 (0.21), residues: 808


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

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

  3516 Ramachandran restraints generated.
    1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3516 Ramachandran restraints generated.
    1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.731 
Fit side-chains
TARDY: cannot create tardy model for: "MET A  52 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  89 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  93 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D   1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D  56 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E   9 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E  19 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B  85 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  91 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  94 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  96 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G  51 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C   1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it.
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0449
  time to fit residues: 4.7179
Evaluate side-chains
  41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 88 optimal weight:   30.0000
   chunk 49 optimal weight:    0.0770
   chunk 132 optimal weight:    0.3980
   chunk 108 optimal weight:    5.9990
   chunk 43 optimal weight:    0.1980
   chunk 159 optimal weight:   30.0000
   chunk 171 optimal weight:   40.0000
   chunk 141 optimal weight:   40.0000
   chunk 157 optimal weight:   40.0000
   chunk 54 optimal weight:   20.0000
   chunk 127 optimal weight:    4.9990
   overall best weight:    2.3342

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4607
moved from start:          1.0006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5415  Z= 0.130
  Angle     :  0.617   5.836   5438  Z= 0.373
  Chirality :  0.033   0.068      8
  Planarity :  0.001   0.001      2
  Dihedral  :  6.122  88.858   1841
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.32 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.20), residues: 1758
  helix:  1.38 (0.21), residues: 563
  sheet:  0.02 (0.31), residues: 262
  loop : -0.20 (0.21), residues: 933


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

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

  3516 Ramachandran restraints generated.
    1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3516 Ramachandran restraints generated.
    1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.798 
Fit side-chains
TARDY: cannot create tardy model for: "MET A  52 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  89 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  93 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D   1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D  56 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E   9 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E  19 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B  85 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  91 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  94 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  96 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G  51 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C   1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it.
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0453
  time to fit residues: 4.8297
Evaluate side-chains
  41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 157 optimal weight:   40.0000
   chunk 119 optimal weight:   40.0000
   chunk 82 optimal weight:   50.0000
   chunk 17 optimal weight:   20.0000
   chunk 75 optimal weight:    2.9990
   chunk 106 optimal weight:    0.3980
   chunk 159 optimal weight:   40.0000
   chunk 169 optimal weight:   30.0000
   chunk 83 optimal weight:    0.3980
   chunk 151 optimal weight:    0.0670
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.9720

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4568
moved from start:          1.0195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.015   5415  Z= 0.048
  Angle     :  0.267   3.264   5438  Z= 0.166
  Chirality :  0.017   0.031      8
  Planarity :  0.001   0.002      2
  Dihedral  :  4.472  89.403   1841
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 1.22
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  1.76 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.21), residues: 1758
  helix:  2.55 (0.22), residues: 597
  sheet:  0.31 (0.32), residues: 271
  loop :  0.07 (0.21), residues: 890


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

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

  3516 Ramachandran restraints generated.
    1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3516 Ramachandran restraints generated.
    1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.813 
Fit side-chains
TARDY: cannot create tardy model for: "MET A  52 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  89 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  93 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D   1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D  56 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E   9 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E  19 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B  85 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  91 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  94 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  96 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G  51 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C   1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it.
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0465
  time to fit residues: 4.9271
Evaluate side-chains
  41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 140 optimal weight:    0.0770
   chunk 96 optimal weight:    8.9990
   chunk 2 optimal weight:   20.0000
   chunk 125 optimal weight:    0.0970
   chunk 69 optimal weight:   20.0000
   chunk 144 optimal weight:   20.0000
   chunk 116 optimal weight:   30.0000
   chunk 0 optimal weight:   20.0000
   chunk 86 optimal weight:    5.9990
   chunk 151 optimal weight:    0.0020
   chunk 42 optimal weight:    8.9990
   overall best weight:    3.0348

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5101
moved from start:          1.4028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   5415  Z= 0.132
  Angle     :  0.522   4.800   5438  Z= 0.333
  Chirality :  0.031   0.055      8
  Planarity :  0.004   0.005      2
  Dihedral  :  5.919  85.626   1841
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.95 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.20), residues: 1758
  helix:  1.09 (0.22), residues: 529
  sheet:  0.77 (0.32), residues: 262
  loop : -0.06 (0.21), residues: 967


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

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

  3516 Ramachandran restraints generated.
    1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3516 Ramachandran restraints generated.
    1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.796 
Fit side-chains
TARDY: cannot create tardy model for: "MET A  52 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  89 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  93 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D   1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D  56 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E   9 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E  19 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B  85 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  91 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  94 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  96 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G  51 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C   1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it.
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0461
  time to fit residues: 4.8673
Evaluate side-chains
  41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 152 optimal weight:   30.0000
   chunk 33 optimal weight:    0.0370
   chunk 99 optimal weight:   30.0000
   chunk 41 optimal weight:    0.0040
   chunk 169 optimal weight:   50.0000
   chunk 140 optimal weight:   30.0000
   chunk 78 optimal weight:   50.0000
   chunk 14 optimal weight:    8.9990
   chunk 88 optimal weight:   20.0000
   chunk 163 optimal weight:   20.0000
   overall best weight:    6.6078

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5503
moved from start:          1.8296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5415  Z= 0.199
  Angle     :  0.686   7.930   5438  Z= 0.443
  Chirality :  0.033   0.069      8
  Planarity :  0.005   0.006      2
  Dihedral  :  7.274  82.520   1841
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.80 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.20), residues: 1758
  helix: -0.72 (0.23), residues: 447
  sheet: -0.19 (0.32), residues: 246
  loop : -0.53 (0.20), residues: 1065


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

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

  3516 Ramachandran restraints generated.
    1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3516 Ramachandran restraints generated.
    1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.818 
Fit side-chains
TARDY: cannot create tardy model for: "MET A  52 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  89 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  93 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D   1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D  56 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E   9 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E  19 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B  85 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  91 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  94 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  96 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G  51 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C   1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it.
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0479
  time to fit residues: 4.9938
Evaluate side-chains
  41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 19 optimal weight:   20.0000
   chunk 96 optimal weight:    0.0980
   chunk 123 optimal weight:   40.0000
   chunk 95 optimal weight:   20.0000
   chunk 142 optimal weight:   10.0000
   chunk 94 optimal weight:    0.0170
   chunk 168 optimal weight:   30.0000
   chunk 105 optimal weight:   20.0000
   chunk 102 optimal weight:   40.0000
   chunk 77 optimal weight:    0.8980
   chunk 104 optimal weight:   10.0000
   overall best weight:    4.2026

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5473
moved from start:          1.8661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   5415  Z= 0.113
  Angle     :  0.435   4.098   5438  Z= 0.279
  Chirality :  0.023   0.049      8
  Planarity :  0.002   0.003      2
  Dihedral  :  5.676  84.305   1841
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.69 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.20), residues: 1758
  helix: -0.43 (0.22), residues: 501
  sheet: -0.20 (0.34), residues: 228
  loop : -0.48 (0.20), residues: 1029


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

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

  3516 Ramachandran restraints generated.
    1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3516 Ramachandran restraints generated.
    1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.804 
Fit side-chains
TARDY: cannot create tardy model for: "MET A  52 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  89 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  93 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D   1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D  56 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E   9 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E  19 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B  85 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  91 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  94 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  96 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G  51 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C   1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it.
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0451
  time to fit residues: 4.7419
Evaluate side-chains
  41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 67 optimal weight:   50.0000
   chunk 100 optimal weight:   30.0000
   chunk 50 optimal weight:    9.9990
   chunk 33 optimal weight:    0.0020
   chunk 32 optimal weight:    0.0870
   chunk 107 optimal weight:   40.0000
   chunk 114 optimal weight:   20.0000
   chunk 83 optimal weight:    0.0670
   chunk 15 optimal weight:   20.0000
   chunk 132 optimal weight:   20.0000
   chunk 153 optimal weight:   40.0000
   overall best weight:    6.0310

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5691
moved from start:          2.0416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   5415  Z= 0.163
  Angle     :  0.583   5.242   5438  Z= 0.384
  Chirality :  0.023   0.040      8
  Planarity :  0.002   0.003      2
  Dihedral  :  6.879  86.506   1841
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 16.17
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.65 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.19), residues: 1758
  helix: -1.29 (0.22), residues: 442
  sheet: -0.43 (0.35), residues: 206
  loop : -1.03 (0.19), residues: 1110


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

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

  3516 Ramachandran restraints generated.
    1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3516 Ramachandran restraints generated.
    1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.767 
Fit side-chains
TARDY: cannot create tardy model for: "MET A  52 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  89 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  93 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D   1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D  56 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E   9 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E  19 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B  85 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  91 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  94 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  96 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G  51 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C   1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it.
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0446
  time to fit residues: 4.6626
Evaluate side-chains
  41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 161 optimal weight:   20.0000
   chunk 147 optimal weight:   30.0000
   chunk 157 optimal weight:   50.0000
   chunk 94 optimal weight:    0.0040
   chunk 68 optimal weight:   40.0000
   chunk 123 optimal weight:   40.0000
   chunk 48 optimal weight:   50.0000
   chunk 142 optimal weight:   10.0000
   chunk 148 optimal weight:    9.9990
   chunk 156 optimal weight:    8.9990
   chunk 103 optimal weight:    3.9990
   overall best weight:    6.6002

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5748
moved from start:          2.1471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5415  Z= 0.165
  Angle     :  0.559   6.527   5438  Z= 0.363
  Chirality :  0.024   0.050      8
  Planarity :  0.001   0.001      2
  Dihedral  :  6.368  81.539   1841
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 14.26
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.91 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.85 (0.19), residues: 1758
  helix: -1.35 (0.23), residues: 434
  sheet: -0.89 (0.38), residues: 184
  loop : -1.26 (0.18), residues: 1140


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

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

  3516 Ramachandran restraints generated.
    1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3516 Ramachandran restraints generated.
    1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.775 
Fit side-chains
TARDY: cannot create tardy model for: "MET A  52 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  89 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  93 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D   1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D  56 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E   9 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E  19 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B  85 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  91 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  94 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  96 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G  51 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C   1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it.
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0448
  time to fit residues: 4.6738
Evaluate side-chains
  41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 166 optimal weight:   40.0000
   chunk 101 optimal weight:   30.0000
   chunk 78 optimal weight:   20.0000
   chunk 115 optimal weight:   30.0000
   chunk 174 optimal weight:   30.0000
   chunk 160 optimal weight:    9.9990
   chunk 138 optimal weight:    0.0670
   chunk 14 optimal weight:   30.0000
   chunk 107 optimal weight:   50.0000
   chunk 85 optimal weight:   50.0000
   chunk 110 optimal weight:   50.0000
   overall best weight:   18.0132

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6082
moved from start:          2.3856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   5415  Z= 0.383
  Angle     :  1.131  20.326   5438  Z= 0.708
  Chirality :  0.024   0.040      8
  Planarity :  0.005   0.005      2
  Dihedral  :  9.904  88.634   1841
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 38.31
  Ramachandran Plot:
    Outliers :  0.57 %
    Allowed  : 17.18 %
    Favored  : 82.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.06 %
    Twisted Proline : 1.25 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.69 (0.18), residues: 1758
  helix: -3.56 (0.19), residues: 392
  sheet: -1.22 (0.49), residues: 112
  loop : -2.35 (0.17), residues: 1254


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

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

  3516 Ramachandran restraints generated.
    1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3516 Ramachandran restraints generated.
    1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.835 
Fit side-chains
TARDY: cannot create tardy model for: "MET A  52 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  89 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A  93 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D   1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D  56 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E   9 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E  19 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B  85 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  91 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  94 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F  96 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G  51 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C   1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it.
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0463
  time to fit residues: 4.7770
Evaluate side-chains
  41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 147 optimal weight:   20.0000
   chunk 42 optimal weight:   20.0000
   chunk 128 optimal weight:   40.0000
   chunk 20 optimal weight:    6.9990
   chunk 38 optimal weight:    0.0270
   chunk 139 optimal weight:    9.9990
   chunk 58 optimal weight:   50.0000
   chunk 142 optimal weight:   10.0000
   chunk 17 optimal weight:   30.0000
   chunk 25 optimal weight:   20.0000
   chunk 122 optimal weight:    0.3980
   overall best weight:    5.4846

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.046553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2542 r_free = 0.2542 target = 0.034502 restraints weight = 66087.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2533 r_free = 0.2533 target = 0.034257 restraints weight = 76800.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2526 r_free = 0.2526 target = 0.034082 restraints weight = 86697.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.2493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6335
moved from start:          2.3521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5415  Z= 0.143
  Angle     :  0.577  11.202   5438  Z= 0.361
  Chirality :  0.018   0.034      8
  Planarity :  0.001   0.001      2
  Dihedral  :  6.663  85.242   1841
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 16.71
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 11.55 %
    Favored  : 88.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.25 %
    Cis-general     : 0.06 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.19), residues: 1758
  helix: -2.56 (0.22), residues: 411
  sheet: -1.60 (0.42), residues: 158
  loop : -2.08 (0.18), residues: 1189

Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1080.67 seconds
wall clock time: 20 minutes 3.94 seconds (1203.94 seconds total)