Starting phenix.real_space_refine
on Mon May  4 10:13:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9s4q_54579/05_2026/9s4q_54579.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9s4q_54579/05_2026/9s4q_54579.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9s4q_54579/05_2026/9s4q_54579.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9s4q_54579/05_2026/9s4q_54579.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9s4q_54579/05_2026/9s4q_54579.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9s4q_54579/05_2026/9s4q_54579.cif"
  }
  resolution = 4.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    6116      2.51       5
     N    1647      2.21       5
     O    1890      1.98       5
     H    9782      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 19471
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "Nn"
      Number of atoms: 3233
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 3233
          Classifications: {'peptide': 198}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 195}
          Chain breaks: 1
    Chain: "Mt"
      Number of atoms: 4358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 4358
          Classifications: {'peptide': 263}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 256}
          Chain breaks: 2
    Chain: "Zw"
      Number of atoms: 1760
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 1760
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 1, 'TRANS': 104}
    Chain: "Kl"
      Number of atoms: 3301
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 3301
          Classifications: {'peptide': 199}
          Link IDs: {'PTRANS': 6, 'TRANS': 192}
    Chain: "Ds"
      Number of atoms: 2216
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 2216
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 6, 'TRANS': 131}
          Chain breaks: 1
    Chain: "24"
      Number of atoms: 1168
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 1168
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 2, 'TRANS': 68}
    Chain: "25"
      Number of atoms: 1499
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 1499
          Classifications: {'peptide': 98}
          Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 94}
    Chain: "Ns"
      Number of atoms: 1936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 1936
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 2, 'TRANS': 117}
  Time building chain proxies: 4.01, per 1000 atoms: 0.21
  Number of scatterers: 19471
  At special positions: 0
  Unit cell: (127.05, 181.5, 207.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      36     16.00
     O    1890      8.00
     N    1647      7.00
     C    6116      6.00
     H    9782      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.98
  Conformation dependent library (CDL) restraints added in 912.4 milliseconds
  

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2320

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 7 sheets defined
      71.7% alpha, 8.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'Nn' and resid 6 through 28
      removed outlier: 3.581A  pdb=" N   LYSNn  13 " --> pdb=" O   TYRNn   9 " (cutoff:3.500A)
    Processing helix  chain 'Nn' and resid 29 through 37
    Processing helix  chain 'Nn' and resid 37 through 43
      removed outlier: 3.964A  pdb=" N   SERNn  43 " --> pdb=" O   GLNNn  39 " (cutoff:3.500A)
    Processing helix  chain 'Nn' and resid 43 through 76
    Processing helix  chain 'Nn' and resid 77 through 98
      removed outlier: 3.721A  pdb=" N   ASPNn  98 " --> pdb=" O   GLUNn  94 " (cutoff:3.500A)
    Processing helix  chain 'Nn' and resid 100 through 104
    Processing helix  chain 'Nn' and resid 109 through 113
    Processing helix  chain 'Nn' and resid 115 through 175
      removed outlier: 3.557A  pdb=" N   VALNn 159 " --> pdb=" O   LEUNn 155 " (cutoff:3.500A)
    Processing helix  chain 'Nn' and resid 176 through 180
      removed outlier: 4.464A  pdb=" N   ASPNn 179 " --> pdb=" O   SERNn 176 " (cutoff:3.500A)
    Processing helix  chain 'Nn' and resid 185 through 199
      removed outlier: 3.830A  pdb=" N   SERNn 189 " --> pdb=" O   LEUNn 185 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ASPNn 192 " --> pdb=" O   GLNNn 188 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LEUNn 195 " --> pdb=" O   ASNNn 191 " (cutoff:3.500A)
    Processing helix  chain 'Mt' and resid 5 through 17
      removed outlier: 4.126A  pdb=" N   GLUMt  14 " --> pdb=" O   SERMt  10 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   HISMt  15 " --> pdb=" O   ILEMt  11 " (cutoff:3.500A)
    Processing helix  chain 'Mt' and resid 19 through 49
      removed outlier: 4.302A  pdb=" N   LEUMt  23 " --> pdb=" O   PROMt  19 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   VALMt  24 " --> pdb=" O   PROMt  20 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LYSMt  49 " --> pdb=" O   TYRMt  45 " (cutoff:3.500A)
    Processing helix  chain 'Mt' and resid 57 through 91
    Processing helix  chain 'Mt' and resid 96 through 101
      removed outlier: 3.603A  pdb=" N   ASPMt 100 " --> pdb=" O   GLUMt  96 " (cutoff:3.500A)
    Processing helix  chain 'Mt' and resid 106 through 110
      removed outlier: 3.815A  pdb=" N   LYSMt 110 " --> pdb=" O   GLUMt 107 " (cutoff:3.500A)
    Processing helix  chain 'Mt' and resid 116 through 169
      removed outlier: 3.568A  pdb=" N   LEUMt 120 " --> pdb=" O   ASPMt 116 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYSMt 150 " --> pdb=" O   LYSMt 146 " (cutoff:3.500A)
    Processing helix  chain 'Mt' and resid 174 through 185
    Processing helix  chain 'Mt' and resid 186 through 209
    Processing helix  chain 'Mt' and resid 210 through 219
      removed outlier: 3.631A  pdb=" N   LEUMt 218 " --> pdb=" O   VALMt 214 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   GLNMt 219 " --> pdb=" O   GLUMt 215 " (cutoff:3.500A)
    Processing helix  chain 'Mt' and resid 231 through 248
    Processing helix  chain 'Mt' and resid 281 through 289
    Processing helix  chain 'Zw' and resid 281 through 292
    Processing helix  chain 'Zw' and resid 297 through 299
      No H-bonds generated for 'chain 'Zw' and resid 297 through 299'
    Processing helix  chain 'Zw' and resid 352 through 364
    Processing helix  chain 'Zw' and resid 370 through 385
      removed outlier: 3.519A  pdb=" N   VALZw 374 " --> pdb=" O   GLNZw 370 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLUZw 385 " --> pdb=" O   GLUZw 381 " (cutoff:3.500A)
    Processing helix  chain 'Kl' and resid 720 through 732
    Processing helix  chain 'Kl' and resid 749 through 751
      No H-bonds generated for 'chain 'Kl' and resid 749 through 751'
    Processing helix  chain 'Kl' and resid 758 through 763
      removed outlier: 4.562A  pdb=" N   LYSKl 763 " --> pdb=" O   LEUKl 759 " (cutoff:3.500A)
    Processing helix  chain 'Kl' and resid 765 through 768
    Processing helix  chain 'Kl' and resid 782 through 794
    Processing helix  chain 'Kl' and resid 797 through 799
      No H-bonds generated for 'chain 'Kl' and resid 797 through 799'
    Processing helix  chain 'Kl' and resid 800 through 810
    Processing helix  chain 'Kl' and resid 813 through 815
      No H-bonds generated for 'chain 'Kl' and resid 813 through 815'
    Processing helix  chain 'Kl' and resid 816 through 824
      removed outlier: 4.861A  pdb=" N   LEUKl 822 " --> pdb=" O   TYRKl 818 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   LEUKl 824 " --> pdb=" O   LYSKl 820 " (cutoff:3.500A)
    Processing helix  chain 'Kl' and resid 859 through 868
      removed outlier: 3.939A  pdb=" N   ALAKl 863 " --> pdb=" O   LEUKl 859 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   GLNKl 864 " --> pdb=" O   VALKl 860 " (cutoff:3.500A)
    Processing helix  chain 'Kl' and resid 891 through 902
      removed outlier: 3.550A  pdb=" N   ARGKl 895 " --> pdb=" O   VALKl 891 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   GLYKl 902 " --> pdb=" O   HISKl 898 " (cutoff:3.500A)
    Processing helix  chain 'Ds' and resid 434 through 468
      removed outlier: 4.563A  pdb=" N   LYSDs 442 " --> pdb=" O   VALDs 438 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ASNDs 443 " --> pdb=" O   GLUDs 439 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   SERDs 445 " --> pdb=" O   THRDs 441 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   LYSDs 459 " --> pdb=" O   LYSDs 455 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLUDs 460 " --> pdb=" O   ASNDs 456 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   TRPDs 461 " --> pdb=" O   GLUDs 457 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ALADs 462 " --> pdb=" O   VALDs 458 " (cutoff:3.500A)
    Processing helix  chain 'Ds' and resid 470 through 482
    Processing helix  chain 'Ds' and resid 492 through 546
      removed outlier: 3.907A  pdb=" N   ILEDs 498 " --> pdb=" O   PRODs 494 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ALADs 499 " --> pdb=" O   ASPDs 495 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   LYSDs 504 " --> pdb=" O   ASPDs 500 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   LEUDs 505 " --> pdb=" O   VALDs 501 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   GLUDs 506 " --> pdb=" O   GLUDs 502 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LYSDs 544 " --> pdb=" O   GLUDs 540 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   SERDs 546 " --> pdb=" O   METDs 542 " (cutoff:3.500A)
    Processing helix  chain 'Ds' and resid 558 through 576
    Processing helix  chain '24' and resid 152 through 169
      removed outlier: 3.787A  pdb=" N   LEU24 160 " --> pdb=" O   ASN24 156 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLY24 169 " --> pdb=" O   TYR24 165 " (cutoff:3.500A)
    Processing helix  chain '24' and resid 199 through 213
    Processing helix  chain '25' and resid 125 through 132
      removed outlier: 3.867A  pdb=" N   GLN25 130 " --> pdb=" O   ARG25 126 " (cutoff:3.500A)
    Processing helix  chain '25' and resid 133 through 146
      removed outlier: 3.712A  pdb=" N   GLU25 137 " --> pdb=" O   ASN25 133 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   ALA25 139 " --> pdb=" O   ALA25 135 " (cutoff:3.500A)
    Processing helix  chain '25' and resid 189 through 204
      removed outlier: 3.509A  pdb=" N   LEU25 200 " --> pdb=" O   LEU25 196 " (cutoff:3.500A)
    Processing helix  chain '25' and resid 205 through 221
      removed outlier: 3.691A  pdb=" N   ASP25 215 " --> pdb=" O   VAL25 211 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU25 221 " --> pdb=" O   LEU25 217 " (cutoff:3.500A)
    Processing helix  chain 'Ns' and resid 98 through 160
      removed outlier: 4.198A  pdb=" N   GLNNs 102 " --> pdb=" O   ASPNs  98 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   GLNNs 108 " --> pdb=" O   ARGNs 104 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   GLUNs 111 " --> pdb=" O   TYRNs 107 " (cutoff:3.500A)
      Proline residue: Ns 125  - end of helix
    Processing helix  chain 'Ns' and resid 166 through 172
      removed outlier: 3.526A  pdb=" N   ALANs 169 " --> pdb=" O   THRNs 166 " (cutoff:3.500A)
    Processing helix  chain 'Ns' and resid 174 through 214
      removed outlier: 4.085A  pdb=" N   ASPNs 181 " --> pdb=" O   HISNs 177 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   ALANs 184 " --> pdb=" O   GLNNs 180 " (cutoff:3.500A)
      Proline residue: Ns 197  - end of helix
      removed outlier: 3.666A  pdb=" N   LYSNs 207 " --> pdb=" O   VALNs 203 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'Mt' and resid 51 through 52
    Processing sheet with id=AA2, first strand: chain 'Mt' and resid 277 through 278
      removed outlier: 5.626A  pdb=" N   PHEKl 735 " --> pdb=" O   ALAKl 746 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   ALAKl 746 " --> pdb=" O   PHEKl 735 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LYSKl 737 " --> pdb=" O   SERKl 744 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'Zw' and resid 301 through 307
      removed outlier: 5.885A  pdb=" N   ASNZw 303 " --> pdb=" O   GLUZw 316 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   GLUZw 316 " --> pdb=" O   ASNZw 303 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   TYRZw 322 " --> pdb=" O   ILEZw 317 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   SERZw 327 " --> pdb=" O   ASPZw 338 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ASPZw 338 " --> pdb=" O   SERZw 327 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ASNZw 348 " --> pdb=" O   ALAZw 345 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'Kl' and resid 828 through 832
      removed outlier: 3.762A  pdb=" N   THRKl 851 " --> pdb=" O   ASPKl 846 " (cutoff:3.500A)
      removed outlier: 5.711A  pdb=" N   SERKl 858 " --> pdb=" O   PROKl 874 " (cutoff:3.500A)
      removed outlier: 5.751A  pdb=" N   ILEKl 873 " --> pdb=" O   HISKl 913 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   GLUKl 915 " --> pdb=" O   ILEKl 873 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   METKl 875 " --> pdb=" O   GLUKl 915 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain '24' and resid 170 through 172
    Processing sheet with id=AA6, first strand: chain '25' and resid 148 through 151
    Processing sheet with id=AA7, first strand: chain '25' and resid 170 through 173
      removed outlier: 5.019A  pdb=" N   ASN25 183 " --> pdb=" O   GLU25 172 " (cutoff:3.500A)

    666 hydrogen bonds defined for protein.
    1950 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.97

  Time building geometry restraints manager: 2.74 seconds

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

  Histogram of bond lengths:
        0.82 -     1.02: 9775
        1.02 -     1.22: 8
        1.22 -     1.41: 3873
        1.41 -     1.61: 5883
        1.61 -     1.81: 65
  Bond restraints: 19604
  Sorted by residual:
  bond pdb=" C   LEUNs 143 "
       pdb=" O   LEUNs 143 "
    ideal  model  delta    sigma   weight residual
    1.236  1.205  0.031 1.32e-02 5.74e+03 5.36e+00
  bond pdb=" CA  ASNNn 191 "
       pdb=" C   ASNNn 191 "
    ideal  model  delta    sigma   weight residual
    1.522  1.495  0.028 1.40e-02 5.10e+03 3.92e+00
  bond pdb=" CA  LEUNs 140 "
       pdb=" C   LEUNs 140 "
    ideal  model  delta    sigma   weight residual
    1.525  1.501  0.024 1.37e-02 5.33e+03 2.99e+00
  bond pdb=" CA  ASPNs 144 "
       pdb=" C   ASPNs 144 "
    ideal  model  delta    sigma   weight residual
    1.524  1.502  0.021 1.29e-02 6.01e+03 2.75e+00
  bond pdb=" CA  TYRNs 139 "
       pdb=" C   TYRNs 139 "
    ideal  model  delta    sigma   weight residual
    1.524  1.504  0.020 1.26e-02 6.30e+03 2.52e+00
  ... (remaining 19599 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 34021
        1.20 -     2.41: 1421
        2.41 -     3.61: 86
        3.61 -     4.81: 23
        4.81 -     6.01: 4
  Bond angle restraints: 35555
  Sorted by residual:
  angle pdb=" N   ILEKl 819 "
        pdb=" CA  ILEKl 819 "
        pdb=" C   ILEKl 819 "
      ideal   model   delta    sigma   weight residual
     112.12  108.58    3.54 8.40e-01 1.42e+00 1.77e+01
  angle pdb=" N   ASPNs 144 "
        pdb=" CA  ASPNs 144 "
        pdb=" C   ASPNs 144 "
      ideal   model   delta    sigma   weight residual
     111.36  107.04    4.32 1.09e+00 8.42e-01 1.57e+01
  angle pdb=" C   TRPKl 812 "
        pdb=" N   ARGKl 813 "
        pdb=" CA  ARGKl 813 "
      ideal   model   delta    sigma   weight residual
     119.78  124.49   -4.71 1.24e+00 6.50e-01 1.44e+01
  angle pdb=" N   GLUNn 143 "
        pdb=" CA  GLUNn 143 "
        pdb=" C   GLUNn 143 "
      ideal   model   delta    sigma   weight residual
     111.28  107.90    3.38 1.09e+00 8.42e-01 9.59e+00
  angle pdb=" N   ASPZw 319 "
        pdb=" CA  ASPZw 319 "
        pdb=" CB  ASPZw 319 "
      ideal   model   delta    sigma   weight residual
     114.17  110.86    3.31 1.14e+00 7.69e-01 8.45e+00
  ... (remaining 35550 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.51: 8232
       17.51 -    35.02: 640
       35.02 -    52.53: 145
       52.53 -    70.04: 41
       70.04 -    87.55: 17
  Dihedral angle restraints: 9075
    sinusoidal: 5082
      harmonic: 3993
  Sorted by residual:
  dihedral pdb=" CA  PHEKl 807 "
           pdb=" C   PHEKl 807 "
           pdb=" N   ALAKl 808 "
           pdb=" CA  ALAKl 808 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.50   28.50     0      5.00e+00 4.00e-02 3.25e+01
  dihedral pdb=" CA  ASPKl 780 "
           pdb=" C   ASPKl 780 "
           pdb=" N   METKl 781 "
           pdb=" CA  METKl 781 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.28  -25.72     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" CA  GLN24 178 "
           pdb=" C   GLN24 178 "
           pdb=" N   VAL24 179 "
           pdb=" CA  VAL24 179 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.13  -19.87     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 9072 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1119
       0.032 -    0.064: 267
       0.064 -    0.097: 97
       0.097 -    0.129: 35
       0.129 -    0.161: 8
  Chirality restraints: 1526
  Sorted by residual:
  chirality pdb=" CA  ILE25 181 "
            pdb=" N   ILE25 181 "
            pdb=" C   ILE25 181 "
            pdb=" CB  ILE25 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.50e-01
  chirality pdb=" CA  ILEZw 323 "
            pdb=" N   ILEZw 323 "
            pdb=" C   ILEZw 323 "
            pdb=" CB  ILEZw 323 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.33e-01
  chirality pdb=" CA  PRODs 559 "
            pdb=" N   PRODs 559 "
            pdb=" C   PRODs 559 "
            pdb=" CB  PRODs 559 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.99e-01
  ... (remaining 1523 not shown)

  Planarity restraints: 2851
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLNNs 142 "   -0.035 2.00e-02 2.50e+03   3.74e-02 2.10e+01
        pdb=" CD  GLNNs 142 "    0.003 2.00e-02 2.50e+03
        pdb=" OE1 GLNNs 142 "    0.033 2.00e-02 2.50e+03
        pdb=" NE2 GLNNs 142 "    0.000 2.00e-02 2.50e+03
        pdb="HE21 GLNNs 142 "    0.054 2.00e-02 2.50e+03
        pdb="HE22 GLNNs 142 "   -0.056 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLNNs 156 "    0.008 2.00e-02 2.50e+03   1.55e-02 3.61e+00
        pdb=" CD  GLNNs 156 "   -0.033 2.00e-02 2.50e+03
        pdb=" OE1 GLNNs 156 "    0.014 2.00e-02 2.50e+03
        pdb=" NE2 GLNNs 156 "    0.009 2.00e-02 2.50e+03
        pdb="HE21 GLNNs 156 "    0.003 2.00e-02 2.50e+03
        pdb="HE22 GLNNs 156 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEUNs 143 "   -0.008 2.00e-02 2.50e+03   1.60e-02 2.57e+00
        pdb=" C   LEUNs 143 "    0.028 2.00e-02 2.50e+03
        pdb=" O   LEUNs 143 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ASPNs 144 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 2848 not shown)

  Histogram of nonbonded interaction distances:
        1.77 -     2.34: 5932
        2.34 -     2.90: 45970
        2.90 -     3.47: 48548
        3.47 -     4.03: 62072
        4.03 -     4.60: 96536
  Nonbonded interactions: 259058
  Sorted by model distance:
  nonbonded pdb=" O   ASN24 196 "
            pdb="HD21 ASN24 196 "
     model   vdw
     1.773 2.450
  nonbonded pdb=" HH2 TRPZw 288 "
            pdb=" HD2 PHEKl 735 "
     model   vdw
     1.782 2.100
  nonbonded pdb="HD22 ASNKl 761 "
            pdb=" HZ3 LYSKl 771 "
     model   vdw
     1.833 2.100
  nonbonded pdb=" HE2 PHEZw 372 "
            pdb=" HZ3 LYSKl 810 "
     model   vdw
     1.836 2.100
  nonbonded pdb=" HZ  PHEKl 853 "
            pdb=" HE2 TYRKl 885 "
     model   vdw
     1.844 2.100
  ... (remaining 259053 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.450
  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:             0.100
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     21.380
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.010
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7139
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      :  0.003   0.041   9822  Z= 0.171
  Angle     :  0.583   6.014  13234  Z= 0.358
  Chirality :  0.036   0.161   1526
  Planarity :  0.003   0.034   1698
  Dihedral  : 14.017  87.549   3786
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.62 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.36 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.25), residues: 1169
  helix:  0.94 (0.19), residues: 771
  sheet: -2.42 (0.44), residues: 118
  loop : -1.29 (0.39), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARGKl 911 
 TYR   0.016   0.001   TYRMt 202 
 PHE   0.022   0.002   PHEZw 372 
 TRP   0.013   0.001   TRPNs 110 
 HIS   0.005   0.001   HISDs 517 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9822)
  covalent geometry    : angle       0.58339 (13234)
  hydrogen bonds       : bond        0.15569 (  666)
  hydrogen bonds       : angle       6.86562 ( 1950)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  143 is missing expected H atoms. Skipping.
Evaluate side-chains
  356 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 355
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
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   revert: symmetry clash
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   revert: symmetry clash
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   revert: symmetry clash
   revert: symmetry clash
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   revert: symmetry clash
   revert: symmetry clash
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   revert: symmetry clash
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   revert: symmetry clash
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   revert: symmetry clash
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   revert: symmetry clash
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   revert: symmetry clash
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   revert: symmetry clash
   revert: symmetry clash
REVERT: Nn   31 ASP cc_start: 0.8380 (m-30) cc_final: 0.7955 (t70)
REVERT: Nn   77 ASN cc_start: 0.7834 (t0) cc_final: 0.7624 (t0)
REVERT: Nn   81 LYS cc_start: 0.8168 (mmtt) cc_final: 0.7942 (tppt)
REVERT: Nn  106 LYS cc_start: 0.9016 (mttt) cc_final: 0.8484 (mmmm)
REVERT: Nn  144 MET cc_start: 0.8969 (mtp) cc_final: 0.8418 (mmm)
REVERT: Nn  194 VAL cc_start: 0.9300 (t) cc_final: 0.8891 (m)
REVERT: Mt  111 ASP cc_start: 0.8793 (m-30) cc_final: 0.8257 (p0)
REVERT: Mt  197 SER cc_start: 0.8882 (m) cc_final: 0.8529 (p)
REVERT: Mt  215 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8247 (mm-30)
REVERT: Zw  307 PHE cc_start: 0.8021 (m-80) cc_final: 0.7776 (m-80)
REVERT: Zw  317 ILE cc_start: 0.8941 (mt) cc_final: 0.8691 (pt)
REVERT: Zw  318 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7818 (ttmt)
REVERT: Zw  323 ILE cc_start: 0.8185 (mt) cc_final: 0.7882 (mp)
REVERT: Kl  740 LYS cc_start: 0.8660 (mttt) cc_final: 0.8432 (mttp)
REVERT: Kl  754 ARG cc_start: 0.8183 (mpp80) cc_final: 0.7789 (mpp80)
REVERT: Kl  758 ASN cc_start: 0.9002 (t0) cc_final: 0.8768 (t0)
REVERT: Kl  773 MET cc_start: 0.6599 (ttt) cc_final: 0.6000 (tpp)
REVERT: Kl  779 ASP cc_start: 0.7238 (m-30) cc_final: 0.6470 (t0)
REVERT: Kl  788 MET cc_start: 0.9103 (ttt) cc_final: 0.8722 (tmm)
REVERT: Kl  806 PHE cc_start: 0.8818 (t80) cc_final: 0.8140 (t80)
REVERT: Kl  889 ARG cc_start: 0.8360 (ttt180) cc_final: 0.7481 (tmm160)
REVERT: Ds  451 VAL cc_start: 0.9555 (t) cc_final: 0.9286 (m)
REVERT: Ds  455 LYS cc_start: 0.8419 (mttt) cc_final: 0.8176 (pttm)
REVERT: Ds  475 GLN cc_start: 0.8636 (mt0) cc_final: 0.8294 (tm-30)
REVERT: Ds  560 GLN cc_start: 0.8005 (mt0) cc_final: 0.7547 (tt0)
REVERT: 24  165 TYR cc_start: 0.8984 (m-10) cc_final: 0.8543 (m-10)
REVERT: 24  172 LEU cc_start: 0.9234 (mt) cc_final: 0.8893 (mt)
REVERT: 24  179 VAL cc_start: 0.7872 (t) cc_final: 0.7611 (t)
REVERT: 24  181 ILE cc_start: 0.8469 (mp) cc_final: 0.7632 (tp)
REVERT: 24  190 ASP cc_start: 0.7534 (m-30) cc_final: 0.7019 (m-30)
REVERT: 24  200 ASP cc_start: 0.8778 (m-30) cc_final: 0.8424 (p0)
REVERT: 24  209 GLU cc_start: 0.8697 (mt-10) cc_final: 0.7704 (mm-30)
REVERT: 25  142 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7585 (mm-30)
REVERT: 25  146 GLN cc_start: 0.6697 (mt0) cc_final: 0.6321 (mt0)
REVERT: 25  151 PRO cc_start: 0.8829 (Cg_endo) cc_final: 0.8371 (Cg_exo)
REVERT: Ns  102 GLN cc_start: 0.8924 (mt0) cc_final: 0.8715 (mp10)
REVERT: Ns  130 GLU cc_start: 0.9005 (tt0) cc_final: 0.8765 (tp30)
REVERT: Ns  138 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8307 (tm-30)
REVERT: Ns  142 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8125 (tt0)
REVERT: Ns  150 LEU cc_start: 0.9432 (mt) cc_final: 0.9213 (mt)
REVERT: Ns  195 ASP cc_start: 0.7705 (m-30) cc_final: 0.7235 (m-30)
REVERT: Ns  198 LYS cc_start: 0.9046 (mttt) cc_final: 0.8658 (tptt)
REVERT: Ns  201 TYR cc_start: 0.8567 (t80) cc_final: 0.8186 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 356
  average time/residue: 0.2483
  time to fit residues: 118.2656
Evaluate side-chains
  270 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 269
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    0.0970
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
Nn  66 GLN
Kl 784 HIS
Ds 520 ASN
Ds 535 ASN
Ns 157 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.081523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.065851 restraints weight = 100614.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.069619 restraints weight = 51939.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.072052 restraints weight = 30927.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.073652 restraints weight = 20558.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.074738 restraints weight = 14997.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9822  Z= 0.168
  Angle     :  0.558   5.882  13234  Z= 0.318
  Chirality :  0.037   0.178   1526
  Planarity :  0.004   0.039   1698
  Dihedral  :  5.096  25.921   1269
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.79 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.25), residues: 1169
  helix:  1.23 (0.18), residues: 764
  sheet: -2.36 (0.43), residues: 123
  loop : -1.11 (0.38), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARGMt  89 
 TYR   0.016   0.002   TYRMt  86 
 PHE   0.015   0.001   PHEMt  80 
 TRP   0.012   0.002   TRP24 208 
 HIS   0.004   0.001   HISKl 878 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 9822)
  covalent geometry    : angle       0.55845 (13234)
  hydrogen bonds       : bond        0.04964 (  666)
  hydrogen bonds       : angle       5.33050 ( 1950)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  143 is missing expected H atoms. Skipping.
Evaluate side-chains
  319 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 319
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
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   revert: symmetry clash
   revert: symmetry clash
REVERT: Nn   13 LYS cc_start: 0.4113 (tttt) cc_final: 0.3204 (tttt)
REVERT: Nn   18 ARG cc_start: 0.7648 (ttp-170) cc_final: 0.7377 (ttp-170)
REVERT: Nn   31 ASP cc_start: 0.8601 (m-30) cc_final: 0.7917 (p0)
REVERT: Nn   72 ILE cc_start: 0.9092 (tp) cc_final: 0.8818 (tp)
REVERT: Nn   81 LYS cc_start: 0.9456 (mmtt) cc_final: 0.9020 (mmmt)
REVERT: Nn   94 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8050 (tp30)
REVERT: Nn  106 LYS cc_start: 0.9319 (mttt) cc_final: 0.8793 (mmmm)
REVERT: Nn  111 ASP cc_start: 0.8257 (t70) cc_final: 0.7866 (t0)
REVERT: Nn  128 MET cc_start: 0.9103 (mmp) cc_final: 0.8589 (mmm)
REVERT: Nn  140 LYS cc_start: 0.8892 (mttt) cc_final: 0.8646 (mtpt)
REVERT: Mt   16 LEU cc_start: 0.9228 (mt) cc_final: 0.8739 (mt)
REVERT: Mt   78 LYS cc_start: 0.8673 (tttt) cc_final: 0.8147 (tmtt)
REVERT: Mt  197 SER cc_start: 0.8832 (m) cc_final: 0.8508 (p)
REVERT: Mt  215 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8176 (mm-30)
REVERT: Mt  217 LEU cc_start: 0.8436 (tp) cc_final: 0.8235 (tt)
REVERT: Zw  317 ILE cc_start: 0.8807 (mt) cc_final: 0.8593 (mm)
REVERT: Zw  321 GLN cc_start: 0.7126 (tt0) cc_final: 0.6727 (tt0)
REVERT: Zw  324 ILE cc_start: 0.8786 (mt) cc_final: 0.8578 (mm)
REVERT: Zw  337 LYS cc_start: 0.8218 (tttt) cc_final: 0.7517 (ttpt)
REVERT: Kl  740 LYS cc_start: 0.8562 (mttt) cc_final: 0.8358 (mttp)
REVERT: Kl  758 ASN cc_start: 0.8808 (t0) cc_final: 0.8395 (t0)
REVERT: Kl  779 ASP cc_start: 0.7162 (m-30) cc_final: 0.6728 (t0)
REVERT: Kl  798 GLN cc_start: 0.7824 (tp40) cc_final: 0.7578 (tp40)
REVERT: Kl  844 ASP cc_start: 0.8848 (t0) cc_final: 0.8473 (t0)
REVERT: Kl  889 ARG cc_start: 0.8355 (ttt180) cc_final: 0.7894 (ttm-80)
REVERT: Ds  455 LYS cc_start: 0.8969 (mttt) cc_final: 0.8675 (mmtp)
REVERT: Ds  475 GLN cc_start: 0.8687 (mt0) cc_final: 0.8314 (tm-30)
REVERT: Ds  560 GLN cc_start: 0.7833 (mt0) cc_final: 0.7515 (tt0)
REVERT: Ds  566 LEU cc_start: 0.8984 (mm) cc_final: 0.8783 (mm)
REVERT: 24  165 TYR cc_start: 0.9114 (m-10) cc_final: 0.8808 (m-10)
REVERT: 24  172 LEU cc_start: 0.9203 (mt) cc_final: 0.8983 (pt)
REVERT: 24  178 GLN cc_start: 0.7284 (pt0) cc_final: 0.6648 (pt0)
REVERT: 24  179 VAL cc_start: 0.7886 (t) cc_final: 0.7550 (t)
REVERT: 24  181 ILE cc_start: 0.8056 (mp) cc_final: 0.7316 (tp)
REVERT: 24  190 ASP cc_start: 0.7447 (m-30) cc_final: 0.7047 (m-30)
REVERT: 24  200 ASP cc_start: 0.8776 (m-30) cc_final: 0.8415 (p0)
REVERT: 24  209 GLU cc_start: 0.8697 (mt-10) cc_final: 0.7682 (mm-30)
REVERT: 25  142 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7415 (mm-30)
REVERT: 25  144 LEU cc_start: 0.9490 (mt) cc_final: 0.9196 (mt)
REVERT: 25  147 LEU cc_start: 0.7844 (tp) cc_final: 0.7611 (tp)
REVERT: Ns  102 GLN cc_start: 0.9067 (mt0) cc_final: 0.8798 (mp10)
REVERT: Ns  104 ARG cc_start: 0.8562 (ttp-170) cc_final: 0.8088 (ttt180)
REVERT: Ns  106 MET cc_start: 0.9245 (mmp) cc_final: 0.8988 (mmm)
REVERT: Ns  116 LYS cc_start: 0.9246 (mttt) cc_final: 0.8837 (mtpt)
REVERT: Ns  127 LYS cc_start: 0.9471 (tptt) cc_final: 0.9270 (tttt)
REVERT: Ns  162 HIS cc_start: 0.8175 (m90) cc_final: 0.7936 (m-70)
REVERT: Ns  192 THR cc_start: 0.8306 (p) cc_final: 0.8047 (p)
REVERT: Ns  195 ASP cc_start: 0.7865 (m-30) cc_final: 0.7333 (m-30)
REVERT: Ns  198 LYS cc_start: 0.9067 (mttt) cc_final: 0.8298 (tptt)
REVERT: Ns  208 ARG cc_start: 0.8716 (mtt90) cc_final: 0.8305 (mmt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 319
  average time/residue: 0.2421
  time to fit residues: 103.7181
Evaluate side-chains
  275 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 275
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 74 optimal weight:    0.5980
   chunk 82 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 108 optimal weight:    3.9990
   chunk 64 optimal weight:    0.5980
   chunk 110 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** Nn 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Kl 784 HIS
24 196 ASN
Ns 157 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.081279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.065906 restraints weight = 99934.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.069586 restraints weight = 51532.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.071982 restraints weight = 30767.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.073536 restraints weight = 20456.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.074592 restraints weight = 14943.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.3041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9822  Z= 0.153
  Angle     :  0.525   5.361  13234  Z= 0.301
  Chirality :  0.037   0.187   1526
  Planarity :  0.003   0.037   1698
  Dihedral  :  4.994  24.778   1269
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.96 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.90 %
    Favored  : 98.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.25), residues: 1169
  helix:  1.49 (0.19), residues: 764
  sheet: -2.27 (0.44), residues: 125
  loop : -1.08 (0.38), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARGDs 469 
 TYR   0.010   0.001   TYRNn  40 
 PHE   0.016   0.001   PHEZw 372 
 TRP   0.012   0.002   TRPNs 110 
 HIS   0.005   0.001   HISDs 517 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 9822)
  covalent geometry    : angle       0.52544 (13234)
  hydrogen bonds       : bond        0.04717 (  666)
  hydrogen bonds       : angle       5.09539 ( 1950)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  143 is missing expected H atoms. Skipping.
Evaluate side-chains
  316 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 315
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Nn   13 LYS cc_start: 0.4166 (tttt) cc_final: 0.3213 (tttt)
REVERT: Nn   31 ASP cc_start: 0.8589 (m-30) cc_final: 0.7952 (p0)
REVERT: Nn   40 TYR cc_start: 0.5997 (m-80) cc_final: 0.5607 (m-80)
REVERT: Nn   55 ARG cc_start: 0.8223 (ttm110) cc_final: 0.7898 (ttp-110)
REVERT: Nn   81 LYS cc_start: 0.9506 (mmtt) cc_final: 0.9013 (mmmt)
REVERT: Nn   94 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8036 (tp30)
REVERT: Nn  106 LYS cc_start: 0.9329 (mttt) cc_final: 0.8809 (mmmm)
REVERT: Nn  111 ASP cc_start: 0.8173 (t70) cc_final: 0.7782 (t0)
REVERT: Nn  128 MET cc_start: 0.9086 (mmp) cc_final: 0.8559 (mmm)
REVERT: Nn  140 LYS cc_start: 0.8926 (mttt) cc_final: 0.8523 (mtpt)
REVERT: Nn  143 GLU cc_start: 0.8422 (mp0) cc_final: 0.8106 (mp0)
REVERT: Mt   16 LEU cc_start: 0.9251 (mt) cc_final: 0.8729 (mt)
REVERT: Mt   78 LYS cc_start: 0.8658 (tttt) cc_final: 0.8174 (tmtt)
REVERT: Mt  142 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8503 (tp30)
REVERT: Mt  197 SER cc_start: 0.8870 (m) cc_final: 0.8578 (p)
REVERT: Mt  215 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8137 (mm-30)
REVERT: Zw  317 ILE cc_start: 0.8752 (mt) cc_final: 0.8546 (mm)
REVERT: Zw  324 ILE cc_start: 0.8891 (mt) cc_final: 0.8480 (mm)
REVERT: Zw  326 ILE cc_start: 0.9485 (mp) cc_final: 0.9283 (mm)
REVERT: Zw  337 LYS cc_start: 0.8267 (tttt) cc_final: 0.7529 (ttpt)
REVERT: Kl  744 SER cc_start: 0.7987 (m) cc_final: 0.7474 (p)
REVERT: Kl  749 GLN cc_start: 0.8545 (mp10) cc_final: 0.8249 (mp10)
REVERT: Kl  758 ASN cc_start: 0.8780 (t0) cc_final: 0.8398 (t0)
REVERT: Kl  773 MET cc_start: 0.6284 (ttt) cc_final: 0.5758 (tpp)
REVERT: Kl  779 ASP cc_start: 0.7038 (m-30) cc_final: 0.6605 (t0)
REVERT: Kl  788 MET cc_start: 0.9182 (ttt) cc_final: 0.8692 (tmm)
REVERT: Kl  799 ASP cc_start: 0.8457 (m-30) cc_final: 0.7848 (t70)
REVERT: Kl  830 ILE cc_start: 0.9430 (mp) cc_final: 0.9046 (tp)
REVERT: Kl  844 ASP cc_start: 0.8759 (t0) cc_final: 0.8418 (t0)
REVERT: Ds  455 LYS cc_start: 0.9113 (mttt) cc_final: 0.8748 (mmtp)
REVERT: Ds  461 TRP cc_start: 0.8817 (m100) cc_final: 0.8579 (m100)
REVERT: Ds  475 GLN cc_start: 0.8758 (mt0) cc_final: 0.8358 (tm-30)
REVERT: Ds  558 ASN cc_start: 0.7649 (m-40) cc_final: 0.6882 (m-40)
REVERT: Ds  560 GLN cc_start: 0.7820 (mt0) cc_final: 0.7487 (tt0)
REVERT: Ds  566 LEU cc_start: 0.9105 (mm) cc_final: 0.8877 (mm)
REVERT: 24  165 TYR cc_start: 0.8887 (m-10) cc_final: 0.8683 (m-10)
REVERT: 24  178 GLN cc_start: 0.7273 (pt0) cc_final: 0.6618 (pt0)
REVERT: 24  200 ASP cc_start: 0.8782 (m-30) cc_final: 0.8468 (p0)
REVERT: 24  209 GLU cc_start: 0.8637 (mt-10) cc_final: 0.7712 (mm-30)
REVERT: 25  142 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7421 (mm-30)
REVERT: Ns  102 GLN cc_start: 0.9008 (mt0) cc_final: 0.8727 (mp10)
REVERT: Ns  104 ARG cc_start: 0.8487 (ttp-170) cc_final: 0.8131 (ttt180)
REVERT: Ns  106 MET cc_start: 0.9204 (mmp) cc_final: 0.8970 (mmm)
REVERT: Ns  116 LYS cc_start: 0.9220 (mttt) cc_final: 0.8863 (mtpt)
REVERT: Ns  162 HIS cc_start: 0.8157 (m90) cc_final: 0.7907 (m-70)
REVERT: Ns  195 ASP cc_start: 0.7973 (m-30) cc_final: 0.7459 (m-30)
REVERT: Ns  198 LYS cc_start: 0.8990 (mttt) cc_final: 0.8262 (tptt)
REVERT: Ns  201 TYR cc_start: 0.8882 (t80) cc_final: 0.8501 (t80)
REVERT: Ns  202 ASN cc_start: 0.9154 (m110) cc_final: 0.8806 (m110)
REVERT: Ns  208 ARG cc_start: 0.8717 (mtt90) cc_final: 0.8292 (mmt180)
  outliers start: 1
  outliers final: 0
  residues processed: 316
  average time/residue: 0.2475
  time to fit residues: 104.6485
Evaluate side-chains
  273 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 273
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   chunk 85 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 93 optimal weight:    3.9990
   chunk 98 optimal weight:    3.9990
   chunk 84 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** Nn 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Mt 102 ASN
Kl 784 HIS
Ds 520 ASN
Ns 157 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.080685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.065461 restraints weight = 100120.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.069121 restraints weight = 51663.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.071484 restraints weight = 30734.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.073028 restraints weight = 20434.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.074068 restraints weight = 14905.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.3429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9822  Z= 0.162
  Angle     :  0.520   5.735  13234  Z= 0.299
  Chirality :  0.036   0.160   1526
  Planarity :  0.003   0.036   1698
  Dihedral  :  4.904  25.035   1269
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.22 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.25), residues: 1169
  helix:  1.56 (0.18), residues: 764
  sheet: -2.23 (0.44), residues: 125
  loop : -1.05 (0.38), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARGNn  67 
 TYR   0.015   0.001   TYRMt  57 
 PHE   0.017   0.002   PHEZw 287 
 TRP   0.011   0.002   TRP24 208 
 HIS   0.005   0.001   HISKl 878 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9822)
  covalent geometry    : angle       0.52019 (13234)
  hydrogen bonds       : bond        0.04461 (  666)
  hydrogen bonds       : angle       5.01035 ( 1950)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  143 is missing expected H atoms. Skipping.
Evaluate side-chains
  301 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 301
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Nn   13 LYS cc_start: 0.4218 (tttt) cc_final: 0.3174 (tttt)
REVERT: Nn   18 ARG cc_start: 0.7161 (ttp-170) cc_final: 0.6930 (ttp80)
REVERT: Nn   31 ASP cc_start: 0.8591 (m-30) cc_final: 0.7943 (p0)
REVERT: Nn   55 ARG cc_start: 0.8210 (ttm110) cc_final: 0.7880 (ttp-110)
REVERT: Nn   94 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8085 (tp30)
REVERT: Nn  111 ASP cc_start: 0.8067 (t70) cc_final: 0.7785 (t0)
REVERT: Nn  128 MET cc_start: 0.9072 (mmp) cc_final: 0.8586 (mmm)
REVERT: Nn  140 LYS cc_start: 0.8871 (mttt) cc_final: 0.8638 (mtpt)
REVERT: Mt   16 LEU cc_start: 0.9193 (mt) cc_final: 0.8739 (mt)
REVERT: Mt   78 LYS cc_start: 0.8584 (tttt) cc_final: 0.8167 (tmtt)
REVERT: Mt  142 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8492 (mm-30)
REVERT: Mt  197 SER cc_start: 0.8908 (m) cc_final: 0.8558 (p)
REVERT: Mt  215 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7777 (mm-30)
REVERT: Zw  313 VAL cc_start: 0.8628 (m) cc_final: 0.8403 (m)
REVERT: Zw  317 ILE cc_start: 0.8737 (mt) cc_final: 0.8517 (mm)
REVERT: Zw  324 ILE cc_start: 0.8923 (mt) cc_final: 0.8502 (mm)
REVERT: Kl  744 SER cc_start: 0.8070 (m) cc_final: 0.7677 (p)
REVERT: Kl  749 GLN cc_start: 0.8603 (mp10) cc_final: 0.8375 (mp10)
REVERT: Kl  758 ASN cc_start: 0.8838 (t0) cc_final: 0.8472 (t0)
REVERT: Kl  773 MET cc_start: 0.6173 (ttt) cc_final: 0.5666 (tpp)
REVERT: Kl  779 ASP cc_start: 0.6984 (m-30) cc_final: 0.6605 (t0)
REVERT: Kl  788 MET cc_start: 0.9071 (ttt) cc_final: 0.8861 (tmm)
REVERT: Kl  792 ASN cc_start: 0.9142 (m-40) cc_final: 0.8898 (m110)
REVERT: Kl  799 ASP cc_start: 0.8398 (m-30) cc_final: 0.7677 (t70)
REVERT: Kl  830 ILE cc_start: 0.9383 (mp) cc_final: 0.8857 (tp)
REVERT: Kl  844 ASP cc_start: 0.8733 (t0) cc_final: 0.8434 (t0)
REVERT: Ds  455 LYS cc_start: 0.9078 (mttt) cc_final: 0.8862 (mmtp)
REVERT: Ds  461 TRP cc_start: 0.8815 (m100) cc_final: 0.8531 (m100)
REVERT: Ds  475 GLN cc_start: 0.8720 (mt0) cc_final: 0.8436 (tm-30)
REVERT: Ds  558 ASN cc_start: 0.7875 (m-40) cc_final: 0.7165 (m-40)
REVERT: Ds  560 GLN cc_start: 0.7832 (mt0) cc_final: 0.7488 (tt0)
REVERT: 24  179 VAL cc_start: 0.7212 (t) cc_final: 0.6889 (t)
REVERT: 24  200 ASP cc_start: 0.8798 (m-30) cc_final: 0.8461 (p0)
REVERT: 24  209 GLU cc_start: 0.8622 (mt-10) cc_final: 0.7680 (mm-30)
REVERT: 25  142 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7722 (mm-30)
REVERT: Ns  101 GLU cc_start: 0.8620 (tp30) cc_final: 0.8376 (tp30)
REVERT: Ns  102 GLN cc_start: 0.8951 (mt0) cc_final: 0.8636 (mp10)
REVERT: Ns  104 ARG cc_start: 0.8519 (ttp-170) cc_final: 0.8067 (ttt180)
REVERT: Ns  116 LYS cc_start: 0.9219 (mttt) cc_final: 0.8841 (mtpt)
REVERT: Ns  182 TYR cc_start: 0.8618 (t80) cc_final: 0.8405 (t80)
REVERT: Ns  190 TYR cc_start: 0.8692 (t80) cc_final: 0.8289 (t80)
REVERT: Ns  195 ASP cc_start: 0.8002 (m-30) cc_final: 0.7548 (m-30)
REVERT: Ns  198 LYS cc_start: 0.9021 (mttt) cc_final: 0.8280 (tptt)
REVERT: Ns  202 ASN cc_start: 0.9337 (m110) cc_final: 0.8889 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 301
  average time/residue: 0.2461
  time to fit residues: 100.0688
Evaluate side-chains
  269 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 269
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 55 optimal weight:    0.6980
   chunk 64 optimal weight:    0.0030
   chunk 3 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 110 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0370
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.4668

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

Flipped N/Q/H residues before XYZ refinement:
** Nn 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Kl 784 HIS
Ds 437 ASN
24 196 ASN
Ns 157 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.082605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.067030 restraints weight = 98744.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.070743 restraints weight = 50910.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.073190 restraints weight = 30473.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.074739 restraints weight = 20235.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.075855 restraints weight = 14851.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.3756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052   9822  Z= 0.115
  Angle     :  0.493   5.028  13234  Z= 0.274
  Chirality :  0.036   0.171   1526
  Planarity :  0.003   0.036   1698
  Dihedral  :  4.700  24.625   1269
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.88 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.25), residues: 1169
  helix:  1.77 (0.18), residues: 772
  sheet: -2.03 (0.43), residues: 129
  loop : -1.10 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARGMt  93 
 TYR   0.011   0.001   TYRZw 322 
 PHE   0.011   0.001   PHEMt  80 
 TRP   0.010   0.001   TRPNs 110 
 HIS   0.004   0.001   HISKl 784 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 9822)
  covalent geometry    : angle       0.49273 (13234)
  hydrogen bonds       : bond        0.04150 (  666)
  hydrogen bonds       : angle       4.71716 ( 1950)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  143 is missing expected H atoms. Skipping.
Evaluate side-chains
  304 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 304
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Nn    9 TYR cc_start: 0.8209 (t80) cc_final: 0.7982 (t80)
REVERT: Nn   13 LYS cc_start: 0.4124 (tttt) cc_final: 0.3241 (tttt)
REVERT: Nn   18 ARG cc_start: 0.7019 (ttp-170) cc_final: 0.6787 (ttp80)
REVERT: Nn   31 ASP cc_start: 0.8562 (m-30) cc_final: 0.7947 (p0)
REVERT: Nn   55 ARG cc_start: 0.8165 (ttm110) cc_final: 0.7822 (ttp-110)
REVERT: Nn   69 PHE cc_start: 0.9406 (t80) cc_final: 0.9143 (t80)
REVERT: Nn   74 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8247 (tm-30)
REVERT: Nn   80 GLN cc_start: 0.8540 (tt0) cc_final: 0.8062 (pp30)
REVERT: Nn   94 GLU cc_start: 0.8813 (mt-10) cc_final: 0.7950 (tp30)
REVERT: Nn  106 LYS cc_start: 0.9266 (mttt) cc_final: 0.8685 (mmmm)
REVERT: Nn  128 MET cc_start: 0.9092 (mmp) cc_final: 0.8732 (mmm)
REVERT: Nn  131 ILE cc_start: 0.9695 (mt) cc_final: 0.9446 (tp)
REVERT: Mt   16 LEU cc_start: 0.9146 (mt) cc_final: 0.8678 (mt)
REVERT: Mt   78 LYS cc_start: 0.8557 (tttt) cc_final: 0.8144 (tmtt)
REVERT: Mt  111 ASP cc_start: 0.8110 (p0) cc_final: 0.7894 (p0)
REVERT: Mt  142 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8483 (mm-30)
REVERT: Mt  197 SER cc_start: 0.8882 (m) cc_final: 0.8535 (p)
REVERT: Mt  215 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7737 (mm-30)
REVERT: Zw  317 ILE cc_start: 0.8668 (mt) cc_final: 0.8321 (mm)
REVERT: Zw  324 ILE cc_start: 0.8705 (mt) cc_final: 0.8439 (mm)
REVERT: Zw  337 LYS cc_start: 0.8120 (tttt) cc_final: 0.7448 (ttpt)
REVERT: Kl  724 LEU cc_start: 0.9078 (tp) cc_final: 0.8727 (tp)
REVERT: Kl  744 SER cc_start: 0.8040 (m) cc_final: 0.7542 (p)
REVERT: Kl  758 ASN cc_start: 0.8795 (t0) cc_final: 0.8384 (t0)
REVERT: Kl  779 ASP cc_start: 0.6900 (m-30) cc_final: 0.6608 (t0)
REVERT: Kl  781 MET cc_start: 0.8318 (tmm) cc_final: 0.7959 (tmm)
REVERT: Kl  784 HIS cc_start: 0.9082 (m-70) cc_final: 0.8860 (m90)
REVERT: Kl  799 ASP cc_start: 0.8554 (m-30) cc_final: 0.7959 (t70)
REVERT: Kl  830 ILE cc_start: 0.9318 (mp) cc_final: 0.8876 (tp)
REVERT: Kl  844 ASP cc_start: 0.8583 (t0) cc_final: 0.8266 (t0)
REVERT: Kl  906 SER cc_start: 0.9000 (m) cc_final: 0.8731 (p)
REVERT: Ds  455 LYS cc_start: 0.8989 (mttt) cc_final: 0.8788 (mmtp)
REVERT: Ds  475 GLN cc_start: 0.8719 (mt0) cc_final: 0.8431 (tm-30)
REVERT: Ds  558 ASN cc_start: 0.7653 (m-40) cc_final: 0.6877 (m-40)
REVERT: Ds  560 GLN cc_start: 0.7796 (mt0) cc_final: 0.7452 (tt0)
REVERT: 24  171 ILE cc_start: 0.8892 (mp) cc_final: 0.8483 (mm)
REVERT: 24  178 GLN cc_start: 0.6898 (pt0) cc_final: 0.6231 (pt0)
REVERT: 24  182 ASN cc_start: 0.8257 (t0) cc_final: 0.7702 (p0)
REVERT: 24  200 ASP cc_start: 0.8765 (m-30) cc_final: 0.8342 (p0)
REVERT: 24  209 GLU cc_start: 0.8585 (mt-10) cc_final: 0.7511 (mm-30)
REVERT: 25  142 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7690 (mm-30)
REVERT: 25  147 LEU cc_start: 0.7360 (tp) cc_final: 0.7150 (tp)
REVERT: Ns  102 GLN cc_start: 0.8964 (mt0) cc_final: 0.8649 (mp10)
REVERT: Ns  104 ARG cc_start: 0.8506 (ttp-170) cc_final: 0.8031 (ptt90)
REVERT: Ns  106 MET cc_start: 0.9219 (mmp) cc_final: 0.8998 (mmm)
REVERT: Ns  116 LYS cc_start: 0.9233 (mttt) cc_final: 0.8857 (mtpt)
REVERT: Ns  182 TYR cc_start: 0.8647 (t80) cc_final: 0.8387 (t80)
REVERT: Ns  195 ASP cc_start: 0.7960 (m-30) cc_final: 0.7458 (m-30)
REVERT: Ns  198 LYS cc_start: 0.9011 (mttt) cc_final: 0.8254 (tptt)
REVERT: Ns  202 ASN cc_start: 0.9338 (m110) cc_final: 0.8889 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 304
  average time/residue: 0.2417
  time to fit residues: 99.0216
Evaluate side-chains
  270 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 270
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 100 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 109 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
** Nn 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Zw 370 GLN
Ds 520 ASN
Ns 157 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.079673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.064382 restraints weight = 100972.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.068039 restraints weight = 52407.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.070411 restraints weight = 31324.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.071972 restraints weight = 20819.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.073014 restraints weight = 15136.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.4050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9822  Z= 0.186
  Angle     :  0.532   6.286  13234  Z= 0.307
  Chirality :  0.037   0.168   1526
  Planarity :  0.003   0.035   1698
  Dihedral  :  4.758  25.433   1269
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.99 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.25), residues: 1169
  helix:  1.74 (0.18), residues: 764
  sheet: -2.18 (0.44), residues: 125
  loop : -1.06 (0.38), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARGMt  93 
 TYR   0.014   0.002   TYR25 141 
 PHE   0.013   0.001   PHE25 209 
 TRP   0.017   0.002   TRPNs 110 
 HIS   0.005   0.001   HISKl 878 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 9822)
  covalent geometry    : angle       0.53178 (13234)
  hydrogen bonds       : bond        0.04305 (  666)
  hydrogen bonds       : angle       4.88333 ( 1950)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  143 is missing expected H atoms. Skipping.
Evaluate side-chains
  287 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 287
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Nn   31 ASP cc_start: 0.8598 (m-30) cc_final: 0.7938 (p0)
REVERT: Nn   55 ARG cc_start: 0.8187 (ttm110) cc_final: 0.7884 (ttp80)
REVERT: Nn   74 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8101 (mm-30)
REVERT: Nn   85 LEU cc_start: 0.9444 (tp) cc_final: 0.9217 (tp)
REVERT: Nn   94 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8024 (tp30)
REVERT: Nn  106 LYS cc_start: 0.9264 (mttt) cc_final: 0.8676 (mmmm)
REVERT: Nn  128 MET cc_start: 0.9093 (mmp) cc_final: 0.8521 (mmm)
REVERT: Mt   16 LEU cc_start: 0.9176 (mt) cc_final: 0.8719 (mt)
REVERT: Mt   78 LYS cc_start: 0.8862 (tttt) cc_final: 0.8408 (tmtt)
REVERT: Mt  142 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8651 (mm-30)
REVERT: Mt  215 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7927 (mm-30)
REVERT: Zw  317 ILE cc_start: 0.8804 (mt) cc_final: 0.8559 (mm)
REVERT: Zw  324 ILE cc_start: 0.8574 (mt) cc_final: 0.8243 (mm)
REVERT: Kl  724 LEU cc_start: 0.9058 (tp) cc_final: 0.8701 (tp)
REVERT: Kl  744 SER cc_start: 0.8216 (m) cc_final: 0.7838 (p)
REVERT: Kl  758 ASN cc_start: 0.8926 (t0) cc_final: 0.8631 (t0)
REVERT: Kl  779 ASP cc_start: 0.6891 (m-30) cc_final: 0.6566 (t0)
REVERT: Kl  781 MET cc_start: 0.8297 (tmm) cc_final: 0.7847 (tmm)
REVERT: Kl  784 HIS cc_start: 0.9084 (m-70) cc_final: 0.8875 (m90)
REVERT: Kl  788 MET cc_start: 0.9225 (ttt) cc_final: 0.8957 (tmm)
REVERT: Kl  790 LEU cc_start: 0.9377 (mt) cc_final: 0.9122 (mm)
REVERT: Kl  799 ASP cc_start: 0.8545 (m-30) cc_final: 0.7994 (t70)
REVERT: Kl  830 ILE cc_start: 0.9332 (mp) cc_final: 0.8626 (tp)
REVERT: Kl  844 ASP cc_start: 0.8664 (t0) cc_final: 0.8373 (t0)
REVERT: Ds  455 LYS cc_start: 0.9113 (mttt) cc_final: 0.8844 (mmtp)
REVERT: Ds  475 GLN cc_start: 0.8827 (mt0) cc_final: 0.8460 (tm-30)
REVERT: Ds  558 ASN cc_start: 0.7541 (m-40) cc_final: 0.6876 (m-40)
REVERT: Ds  560 GLN cc_start: 0.7877 (mt0) cc_final: 0.7504 (tt0)
REVERT: 24  200 ASP cc_start: 0.9001 (m-30) cc_final: 0.8593 (p0)
REVERT: 24  209 GLU cc_start: 0.8600 (mt-10) cc_final: 0.7617 (mm-30)
REVERT: 25  146 GLN cc_start: 0.7048 (mp10) cc_final: 0.6798 (mt0)
REVERT: Ns  102 GLN cc_start: 0.9036 (mt0) cc_final: 0.8625 (mp10)
REVERT: Ns  104 ARG cc_start: 0.8641 (ttp-170) cc_final: 0.8065 (ptt90)
REVERT: Ns  130 GLU cc_start: 0.8477 (tp30) cc_final: 0.7991 (tp30)
REVERT: Ns  190 TYR cc_start: 0.8841 (t80) cc_final: 0.8566 (t80)
REVERT: Ns  195 ASP cc_start: 0.8008 (m-30) cc_final: 0.7534 (m-30)
REVERT: Ns  198 LYS cc_start: 0.9037 (mttt) cc_final: 0.8447 (tptt)
REVERT: Ns  201 TYR cc_start: 0.8862 (t80) cc_final: 0.8314 (t80)
REVERT: Ns  215 GLU cc_start: 0.8163 (tt0) cc_final: 0.7834 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 287
  average time/residue: 0.2380
  time to fit residues: 92.8845
Evaluate side-chains
  259 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 103 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 112 optimal weight:    0.7980
   chunk 94 optimal weight:    0.0870
   chunk 78 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0370
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
** Nn 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
24 196 ASN
** Ns 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.081488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.066179 restraints weight = 99190.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.069859 restraints weight = 51329.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.072270 restraints weight = 30643.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.073845 restraints weight = 20311.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.074903 restraints weight = 14751.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.4280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9822  Z= 0.119
  Angle     :  0.496   5.357  13234  Z= 0.276
  Chirality :  0.037   0.172   1526
  Planarity :  0.003   0.040   1698
  Dihedral  :  4.573  24.325   1269
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.36 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.25), residues: 1169
  helix:  1.86 (0.18), residues: 775
  sheet: -1.94 (0.44), residues: 129
  loop : -1.02 (0.40), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARGKl 889 
 TYR   0.011   0.001   TYR25 141 
 PHE   0.016   0.001   PHEZw 287 
 TRP   0.026   0.002   TRPZw 288 
 HIS   0.003   0.001   HISDs 517 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 9822)
  covalent geometry    : angle       0.49640 (13234)
  hydrogen bonds       : bond        0.04032 (  666)
  hydrogen bonds       : angle       4.63302 ( 1950)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  143 is missing expected H atoms. Skipping.
Evaluate side-chains
  294 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 294
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Nn   31 ASP cc_start: 0.8573 (m-30) cc_final: 0.7957 (p0)
REVERT: Nn   55 ARG cc_start: 0.7995 (ttm110) cc_final: 0.7657 (ttp80)
REVERT: Nn   74 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8075 (mm-30)
REVERT: Nn   88 LEU cc_start: 0.8203 (tt) cc_final: 0.7599 (mt)
REVERT: Nn   94 GLU cc_start: 0.8815 (mt-10) cc_final: 0.7990 (tp30)
REVERT: Nn  106 LYS cc_start: 0.9252 (mttt) cc_final: 0.8659 (mmmm)
REVERT: Nn  111 ASP cc_start: 0.8524 (p0) cc_final: 0.8269 (p0)
REVERT: Nn  128 MET cc_start: 0.9045 (mmp) cc_final: 0.8438 (mmm)
REVERT: Nn  140 LYS cc_start: 0.8839 (mttt) cc_final: 0.8432 (tptt)
REVERT: Nn  144 MET cc_start: 0.9071 (mtp) cc_final: 0.8381 (mmm)
REVERT: Mt   16 LEU cc_start: 0.9147 (mt) cc_final: 0.8669 (mt)
REVERT: Mt   78 LYS cc_start: 0.8730 (tttt) cc_final: 0.8301 (tmtt)
REVERT: Mt  142 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8580 (mm-30)
REVERT: Mt  197 SER cc_start: 0.8847 (m) cc_final: 0.8520 (p)
REVERT: Mt  215 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7859 (mm-30)
REVERT: Zw  317 ILE cc_start: 0.8911 (mt) cc_final: 0.8516 (mm)
REVERT: Zw  324 ILE cc_start: 0.8514 (mt) cc_final: 0.8125 (mm)
REVERT: Zw  337 LYS cc_start: 0.8169 (tttt) cc_final: 0.7450 (ttpt)
REVERT: Zw  372 PHE cc_start: 0.8569 (t80) cc_final: 0.8090 (t80)
REVERT: Kl  724 LEU cc_start: 0.9153 (tp) cc_final: 0.8695 (tp)
REVERT: Kl  744 SER cc_start: 0.8055 (m) cc_final: 0.7701 (p)
REVERT: Kl  758 ASN cc_start: 0.8901 (t0) cc_final: 0.8505 (t0)
REVERT: Kl  779 ASP cc_start: 0.7031 (m-30) cc_final: 0.6752 (t0)
REVERT: Kl  781 MET cc_start: 0.8186 (tmm) cc_final: 0.7778 (tmm)
REVERT: Kl  784 HIS cc_start: 0.9059 (m-70) cc_final: 0.8828 (m90)
REVERT: Kl  790 LEU cc_start: 0.9292 (mt) cc_final: 0.9077 (mm)
REVERT: Kl  799 ASP cc_start: 0.8496 (m-30) cc_final: 0.7880 (t70)
REVERT: Kl  830 ILE cc_start: 0.9223 (mp) cc_final: 0.8622 (tp)
REVERT: Kl  833 THR cc_start: 0.8394 (p) cc_final: 0.8192 (p)
REVERT: Kl  844 ASP cc_start: 0.8543 (t0) cc_final: 0.8306 (t0)
REVERT: Kl  906 SER cc_start: 0.9020 (m) cc_final: 0.8760 (p)
REVERT: Ds  455 LYS cc_start: 0.9104 (mttt) cc_final: 0.8724 (mmtp)
REVERT: Ds  475 GLN cc_start: 0.8833 (mt0) cc_final: 0.8250 (tm-30)
REVERT: Ds  558 ASN cc_start: 0.7475 (m-40) cc_final: 0.6719 (m-40)
REVERT: Ds  560 GLN cc_start: 0.7845 (mt0) cc_final: 0.7487 (tt0)
REVERT: 24  182 ASN cc_start: 0.8238 (t0) cc_final: 0.7728 (p0)
REVERT: 24  200 ASP cc_start: 0.9031 (m-30) cc_final: 0.8531 (p0)
REVERT: 24  209 GLU cc_start: 0.8554 (mt-10) cc_final: 0.7469 (mm-30)
REVERT: 25  146 GLN cc_start: 0.6915 (mp10) cc_final: 0.6649 (mt0)
REVERT: Ns  101 GLU cc_start: 0.8962 (mp0) cc_final: 0.8529 (tp30)
REVERT: Ns  102 GLN cc_start: 0.8944 (mt0) cc_final: 0.8432 (mp10)
REVERT: Ns  104 ARG cc_start: 0.8606 (ttp-170) cc_final: 0.8076 (ttt180)
REVERT: Ns  157 GLN cc_start: 0.7535 (tp40) cc_final: 0.7332 (tp-100)
REVERT: Ns  182 TYR cc_start: 0.8664 (t80) cc_final: 0.8392 (t80)
REVERT: Ns  190 TYR cc_start: 0.8808 (t80) cc_final: 0.8549 (t80)
REVERT: Ns  195 ASP cc_start: 0.7832 (m-30) cc_final: 0.7355 (m-30)
REVERT: Ns  198 LYS cc_start: 0.9034 (mttt) cc_final: 0.8415 (tptt)
REVERT: Ns  201 TYR cc_start: 0.8861 (t80) cc_final: 0.8225 (t80)
REVERT: Ns  204 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8556 (tt0)
REVERT: Ns  215 GLU cc_start: 0.7855 (tt0) cc_final: 0.7503 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 294
  average time/residue: 0.2471
  time to fit residues: 98.8756
Evaluate side-chains
  262 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 72 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 80 optimal weight:    4.9990
   chunk 102 optimal weight:    0.5980
   chunk 85 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 76 optimal weight:    0.0980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** Nn 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Ns 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.081860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.066328 restraints weight = 99596.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.070099 restraints weight = 51456.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.072540 restraints weight = 30587.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.074160 restraints weight = 20230.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.075200 restraints weight = 14632.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.4484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   9822  Z= 0.116
  Angle     :  0.478   5.074  13234  Z= 0.267
  Chirality :  0.036   0.177   1526
  Planarity :  0.003   0.048   1698
  Dihedral  :  4.444  24.453   1269
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.88 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.26), residues: 1169
  helix:  2.04 (0.19), residues: 777
  sheet: -1.84 (0.44), residues: 130
  loop : -1.01 (0.41), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARGMt  93 
 TYR   0.009   0.001   TYRKl 845 
 PHE   0.013   0.001   PHEZw 372 
 TRP   0.021   0.002   TRPNs 110 
 HIS   0.003   0.001   HISDs 517 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 9822)
  covalent geometry    : angle       0.47773 (13234)
  hydrogen bonds       : bond        0.03900 (  666)
  hydrogen bonds       : angle       4.49445 ( 1950)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  143 is missing expected H atoms. Skipping.
Evaluate side-chains
  293 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 293
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Nn   31 ASP cc_start: 0.8750 (m-30) cc_final: 0.8093 (p0)
REVERT: Nn   74 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8378 (mm-30)
REVERT: Nn   94 GLU cc_start: 0.8823 (mt-10) cc_final: 0.7953 (tp30)
REVERT: Nn  106 LYS cc_start: 0.9206 (mttt) cc_final: 0.8511 (mmmm)
REVERT: Nn  111 ASP cc_start: 0.8518 (p0) cc_final: 0.8280 (p0)
REVERT: Nn  127 ARG cc_start: 0.9120 (ttm170) cc_final: 0.8760 (ttm170)
REVERT: Nn  128 MET cc_start: 0.9054 (mmp) cc_final: 0.8420 (mmm)
REVERT: Nn  140 LYS cc_start: 0.8877 (mttt) cc_final: 0.8431 (tptt)
REVERT: Nn  144 MET cc_start: 0.8995 (mtp) cc_final: 0.8426 (mmm)
REVERT: Mt   16 LEU cc_start: 0.9236 (mt) cc_final: 0.8821 (mt)
REVERT: Mt   78 LYS cc_start: 0.8722 (tttt) cc_final: 0.8302 (tmtt)
REVERT: Mt  197 SER cc_start: 0.8860 (m) cc_final: 0.8504 (p)
REVERT: Mt  215 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7846 (mm-30)
REVERT: Zw  317 ILE cc_start: 0.8887 (mt) cc_final: 0.8563 (mm)
REVERT: Zw  324 ILE cc_start: 0.8385 (mt) cc_final: 0.8063 (mm)
REVERT: Zw  372 PHE cc_start: 0.8684 (t80) cc_final: 0.8225 (t80)
REVERT: Kl  728 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8171 (mm-30)
REVERT: Kl  744 SER cc_start: 0.8106 (m) cc_final: 0.7687 (p)
REVERT: Kl  758 ASN cc_start: 0.8902 (t0) cc_final: 0.8484 (t0)
REVERT: Kl  790 LEU cc_start: 0.9267 (mt) cc_final: 0.9057 (mm)
REVERT: Kl  799 ASP cc_start: 0.8441 (m-30) cc_final: 0.7756 (t70)
REVERT: Kl  830 ILE cc_start: 0.9188 (mp) cc_final: 0.8774 (tp)
REVERT: Kl  844 ASP cc_start: 0.8418 (t0) cc_final: 0.8117 (t0)
REVERT: Kl  906 SER cc_start: 0.9027 (m) cc_final: 0.8769 (p)
REVERT: Ds  455 LYS cc_start: 0.9043 (mttt) cc_final: 0.8713 (mmtp)
REVERT: Ds  475 GLN cc_start: 0.8651 (mt0) cc_final: 0.8284 (tm-30)
REVERT: Ds  558 ASN cc_start: 0.7580 (m-40) cc_final: 0.6868 (m-40)
REVERT: Ds  560 GLN cc_start: 0.7889 (mt0) cc_final: 0.7590 (tt0)
REVERT: 24  168 LEU cc_start: 0.9278 (mt) cc_final: 0.9060 (mt)
REVERT: 24  182 ASN cc_start: 0.8282 (t0) cc_final: 0.7704 (p0)
REVERT: 24  200 ASP cc_start: 0.9061 (m-30) cc_final: 0.8501 (p0)
REVERT: 24  209 GLU cc_start: 0.8536 (mt-10) cc_final: 0.7575 (mm-30)
REVERT: Ns  101 GLU cc_start: 0.8967 (mp0) cc_final: 0.8437 (tp30)
REVERT: Ns  102 GLN cc_start: 0.8926 (mt0) cc_final: 0.8511 (mp10)
REVERT: Ns  104 ARG cc_start: 0.8621 (ttp-170) cc_final: 0.8017 (ttt180)
REVERT: Ns  106 MET cc_start: 0.9273 (mmp) cc_final: 0.8928 (mmm)
REVERT: Ns  109 GLU cc_start: 0.8439 (tm-30) cc_final: 0.7366 (tm-30)
REVERT: Ns  112 ASP cc_start: 0.8968 (t70) cc_final: 0.8447 (m-30)
REVERT: Ns  190 TYR cc_start: 0.8806 (t80) cc_final: 0.8537 (t80)
REVERT: Ns  195 ASP cc_start: 0.7844 (m-30) cc_final: 0.7349 (m-30)
REVERT: Ns  198 LYS cc_start: 0.8973 (mttt) cc_final: 0.8319 (tptt)
REVERT: Ns  201 TYR cc_start: 0.8828 (t80) cc_final: 0.8196 (t80)
REVERT: Ns  204 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8573 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 293
  average time/residue: 0.2538
  time to fit residues: 100.4266
Evaluate side-chains
  268 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 268
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 96 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0970
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0060
   chunk 55 optimal weight:    0.5980
   chunk 109 optimal weight:    8.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
** Nn 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
24 196 ASN
** Ns 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.082236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.066768 restraints weight = 98885.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.070486 restraints weight = 51158.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.072905 restraints weight = 30482.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.074500 restraints weight = 20223.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.075560 restraints weight = 14692.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.4679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9822  Z= 0.113
  Angle     :  0.489   5.356  13234  Z= 0.272
  Chirality :  0.037   0.167   1526
  Planarity :  0.003   0.068   1698
  Dihedral  :  4.395  24.398   1269
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.79 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.26), residues: 1169
  helix:  2.09 (0.19), residues: 776
  sheet: -1.61 (0.46), residues: 127
  loop : -1.02 (0.40), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.000   ARGMt  93 
 TYR   0.009   0.001   TYRMt  57 
 PHE   0.014   0.001   PHEMt 232 
 TRP   0.017   0.001   TRPNs 110 
 HIS   0.003   0.001   HISDs 517 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 9822)
  covalent geometry    : angle       0.48864 (13234)
  hydrogen bonds       : bond        0.03830 (  666)
  hydrogen bonds       : angle       4.47416 ( 1950)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  143 is missing expected H atoms. Skipping.
Evaluate side-chains
  283 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 283
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Nn   31 ASP cc_start: 0.8551 (m-30) cc_final: 0.8017 (p0)
REVERT: Nn   53 CYS cc_start: 0.9341 (t) cc_final: 0.9006 (t)
REVERT: Nn   55 ARG cc_start: 0.7947 (ttm110) cc_final: 0.7601 (ttp80)
REVERT: Nn   74 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8512 (mm-30)
REVERT: Nn   85 LEU cc_start: 0.9385 (tp) cc_final: 0.9175 (tp)
REVERT: Nn   94 GLU cc_start: 0.8813 (mt-10) cc_final: 0.7947 (tp30)
REVERT: Nn  106 LYS cc_start: 0.9201 (mttt) cc_final: 0.8498 (mmmm)
REVERT: Nn  111 ASP cc_start: 0.8527 (p0) cc_final: 0.8316 (p0)
REVERT: Nn  127 ARG cc_start: 0.9125 (ttm170) cc_final: 0.8734 (ttm170)
REVERT: Nn  128 MET cc_start: 0.9017 (mmp) cc_final: 0.8389 (mmm)
REVERT: Nn  140 LYS cc_start: 0.8846 (mttt) cc_final: 0.8441 (tptt)
REVERT: Nn  144 MET cc_start: 0.8983 (mtp) cc_final: 0.8522 (mmm)
REVERT: Nn  193 MET cc_start: 0.8873 (mmt) cc_final: 0.8616 (tpp)
REVERT: Mt   16 LEU cc_start: 0.9206 (mt) cc_final: 0.8789 (mt)
REVERT: Mt   78 LYS cc_start: 0.8719 (tttt) cc_final: 0.8289 (tmtt)
REVERT: Mt  197 SER cc_start: 0.8838 (m) cc_final: 0.8494 (p)
REVERT: Mt  215 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7672 (mm-30)
REVERT: Zw  314 GLN cc_start: 0.7737 (pt0) cc_final: 0.7474 (pt0)
REVERT: Zw  317 ILE cc_start: 0.8915 (mt) cc_final: 0.8608 (mm)
REVERT: Zw  324 ILE cc_start: 0.8305 (mt) cc_final: 0.7965 (mm)
REVERT: Kl  744 SER cc_start: 0.8016 (m) cc_final: 0.7623 (p)
REVERT: Kl  758 ASN cc_start: 0.8894 (t0) cc_final: 0.8465 (t0)
REVERT: Kl  790 LEU cc_start: 0.9283 (mt) cc_final: 0.9080 (mm)
REVERT: Kl  799 ASP cc_start: 0.8411 (m-30) cc_final: 0.7715 (t70)
REVERT: Kl  830 ILE cc_start: 0.9231 (mp) cc_final: 0.8830 (tp)
REVERT: Kl  844 ASP cc_start: 0.8396 (t0) cc_final: 0.8109 (t0)
REVERT: Kl  885 TYR cc_start: 0.9058 (t80) cc_final: 0.8832 (t80)
REVERT: Kl  906 SER cc_start: 0.9034 (m) cc_final: 0.8765 (p)
REVERT: Ds  455 LYS cc_start: 0.9046 (mttt) cc_final: 0.8811 (mmtt)
REVERT: Ds  475 GLN cc_start: 0.8708 (mt0) cc_final: 0.8267 (tm-30)
REVERT: Ds  558 ASN cc_start: 0.7970 (m-40) cc_final: 0.7214 (m-40)
REVERT: Ds  560 GLN cc_start: 0.7838 (mt0) cc_final: 0.7512 (tt0)
REVERT: 24  182 ASN cc_start: 0.8246 (t0) cc_final: 0.7715 (p0)
REVERT: 24  209 GLU cc_start: 0.8548 (mt-10) cc_final: 0.7563 (mm-30)
REVERT: 25  167 SER cc_start: 0.7190 (m) cc_final: 0.6477 (t)
REVERT: Ns  101 GLU cc_start: 0.8964 (mp0) cc_final: 0.8428 (tp30)
REVERT: Ns  102 GLN cc_start: 0.8918 (mt0) cc_final: 0.8447 (mp10)
REVERT: Ns  104 ARG cc_start: 0.8630 (ttp-170) cc_final: 0.8018 (ttt180)
REVERT: Ns  106 MET cc_start: 0.9258 (mmp) cc_final: 0.8843 (mmm)
REVERT: Ns  109 GLU cc_start: 0.8454 (tm-30) cc_final: 0.7926 (tt0)
REVERT: Ns  112 ASP cc_start: 0.8980 (t70) cc_final: 0.8457 (m-30)
REVERT: Ns  182 TYR cc_start: 0.8689 (t80) cc_final: 0.8389 (t80)
REVERT: Ns  190 TYR cc_start: 0.8697 (t80) cc_final: 0.8407 (t80)
REVERT: Ns  195 ASP cc_start: 0.7828 (m-30) cc_final: 0.7338 (m-30)
REVERT: Ns  198 LYS cc_start: 0.8942 (mttt) cc_final: 0.8365 (tptt)
REVERT: Ns  204 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8557 (tt0)
REVERT: Ns  208 ARG cc_start: 0.8958 (mmt180) cc_final: 0.8687 (mmt180)
  outliers start: 0
  outliers final: 0
  residues processed: 283
  average time/residue: 0.2391
  time to fit residues: 92.1993
Evaluate side-chains
  259 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 41 optimal weight:    2.9990
   chunk 107 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 60 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** Nn 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Mt 118 ASN
** Ns 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Ns 157 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.081295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.065809 restraints weight = 99207.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.069515 restraints weight = 51293.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.071917 restraints weight = 30627.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.073504 restraints weight = 20333.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.074548 restraints weight = 14789.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.4826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9822  Z= 0.136
  Angle     :  0.494   5.072  13234  Z= 0.280
  Chirality :  0.036   0.170   1526
  Planarity :  0.003   0.052   1698
  Dihedral  :  4.402  24.842   1269
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.05 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.45 (0.26), residues: 1169
  helix:  2.08 (0.19), residues: 777
  sheet: -1.66 (0.46), residues: 125
  loop : -1.05 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARGMt  93 
 TYR   0.010   0.001   TYRNn 170 
 PHE   0.015   0.001   PHEZw 372 
 TRP   0.024   0.002   TRPNs 110 
 HIS   0.004   0.001   HISDs 517 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9822)
  covalent geometry    : angle       0.49384 (13234)
  hydrogen bonds       : bond        0.03870 (  666)
  hydrogen bonds       : angle       4.54212 ( 1950)

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  143 is missing expected H atoms. Skipping.
Evaluate side-chains
  285 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 285
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: Nn   13 LYS cc_start: 0.5410 (tttt) cc_final: 0.4706 (ttmt)
REVERT: Nn   31 ASP cc_start: 0.8725 (m-30) cc_final: 0.8046 (p0)
REVERT: Nn   53 CYS cc_start: 0.9336 (t) cc_final: 0.9061 (t)
REVERT: Nn   74 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8323 (mm-30)
REVERT: Nn   94 GLU cc_start: 0.8821 (mt-10) cc_final: 0.7963 (tp30)
REVERT: Nn  106 LYS cc_start: 0.9142 (mttt) cc_final: 0.8385 (mmmm)
REVERT: Nn  111 ASP cc_start: 0.8558 (p0) cc_final: 0.8331 (p0)
REVERT: Nn  127 ARG cc_start: 0.9158 (ttm170) cc_final: 0.8755 (ttm170)
REVERT: Nn  128 MET cc_start: 0.9017 (mmp) cc_final: 0.8392 (mmm)
REVERT: Nn  140 LYS cc_start: 0.8824 (mttt) cc_final: 0.8475 (tptt)
REVERT: Nn  144 MET cc_start: 0.8999 (mtp) cc_final: 0.8472 (mmm)
REVERT: Nn  193 MET cc_start: 0.8931 (mmt) cc_final: 0.8679 (tpp)
REVERT: Mt   16 LEU cc_start: 0.9337 (mt) cc_final: 0.8864 (mt)
REVERT: Mt   78 LYS cc_start: 0.8833 (tttt) cc_final: 0.8377 (tmtt)
REVERT: Mt  215 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7696 (mm-30)
REVERT: Zw  301 ILE cc_start: 0.7131 (mt) cc_final: 0.6841 (mt)
REVERT: Zw  305 GLU cc_start: 0.8452 (tp30) cc_final: 0.8138 (tp30)
REVERT: Zw  314 GLN cc_start: 0.7697 (pt0) cc_final: 0.7457 (pm20)
REVERT: Zw  317 ILE cc_start: 0.8919 (mt) cc_final: 0.8717 (mm)
REVERT: Kl  728 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8481 (mm-30)
REVERT: Kl  744 SER cc_start: 0.8180 (m) cc_final: 0.7811 (p)
REVERT: Kl  758 ASN cc_start: 0.8967 (t0) cc_final: 0.8607 (t0)
REVERT: Kl  781 MET cc_start: 0.8237 (tmm) cc_final: 0.7940 (tmm)
REVERT: Kl  784 HIS cc_start: 0.9026 (m90) cc_final: 0.8718 (m90)
REVERT: Kl  799 ASP cc_start: 0.8455 (m-30) cc_final: 0.7747 (t70)
REVERT: Kl  844 ASP cc_start: 0.8431 (t0) cc_final: 0.8139 (t0)
REVERT: Kl  885 TYR cc_start: 0.9074 (t80) cc_final: 0.8798 (t80)
REVERT: Kl  906 SER cc_start: 0.9036 (m) cc_final: 0.8782 (p)
REVERT: Ds  455 LYS cc_start: 0.9014 (mttt) cc_final: 0.8685 (mmtt)
REVERT: Ds  475 GLN cc_start: 0.8690 (mt0) cc_final: 0.8281 (tm-30)
REVERT: Ds  558 ASN cc_start: 0.7667 (m-40) cc_final: 0.6948 (m-40)
REVERT: Ds  560 GLN cc_start: 0.7926 (mt0) cc_final: 0.7595 (tt0)
REVERT: 24  182 ASN cc_start: 0.8278 (t0) cc_final: 0.7703 (p0)
REVERT: 24  209 GLU cc_start: 0.8551 (mt-10) cc_final: 0.7568 (mm-30)
REVERT: 25  167 SER cc_start: 0.7216 (m) cc_final: 0.6491 (t)
REVERT: Ns  101 GLU cc_start: 0.8984 (mp0) cc_final: 0.8346 (tp30)
REVERT: Ns  102 GLN cc_start: 0.8927 (mt0) cc_final: 0.8333 (mp10)
REVERT: Ns  104 ARG cc_start: 0.8666 (ttp-170) cc_final: 0.8052 (ttt180)
REVERT: Ns  106 MET cc_start: 0.9280 (mmp) cc_final: 0.8872 (mmm)
REVERT: Ns  109 GLU cc_start: 0.8637 (tm-30) cc_final: 0.7784 (tm-30)
REVERT: Ns  112 ASP cc_start: 0.8997 (t70) cc_final: 0.8473 (m-30)
REVERT: Ns  127 LYS cc_start: 0.9470 (tptt) cc_final: 0.9231 (tttt)
REVERT: Ns  182 TYR cc_start: 0.8707 (t80) cc_final: 0.8400 (t80)
REVERT: Ns  190 TYR cc_start: 0.8714 (t80) cc_final: 0.8430 (t80)
REVERT: Ns  195 ASP cc_start: 0.7911 (m-30) cc_final: 0.7416 (m-30)
REVERT: Ns  198 LYS cc_start: 0.8940 (mttt) cc_final: 0.8365 (tptt)
REVERT: Ns  201 TYR cc_start: 0.8698 (t80) cc_final: 0.8187 (t80)
REVERT: Ns  204 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8550 (tt0)
REVERT: Ns  208 ARG cc_start: 0.8967 (mmt180) cc_final: 0.8727 (mmt180)
  outliers start: 0
  outliers final: 0
  residues processed: 285
  average time/residue: 0.2484
  time to fit residues: 96.3876
Evaluate side-chains
  261 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 82 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 83 optimal weight:    0.0980
   chunk 54 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** Nn 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Nn 142 ASN
24 196 ASN
** Ns 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Ns 157 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.081879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.066334 restraints weight = 99343.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.070058 restraints weight = 51308.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.072486 restraints weight = 30554.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.074088 restraints weight = 20282.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.075107 restraints weight = 14746.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.4973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9822  Z= 0.117
  Angle     :  0.488   6.103  13234  Z= 0.273
  Chirality :  0.037   0.175   1526
  Planarity :  0.003   0.058   1698
  Dihedral  :  4.295  24.519   1269
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.79 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.14 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.59 (0.26), residues: 1169
  helix:  2.16 (0.19), residues: 776
  sheet: -1.42 (0.47), residues: 127
  loop : -0.99 (0.40), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARGMt  93 
 TYR   0.009   0.001   TYRKl 845 
 PHE   0.016   0.001   PHEZw 372 
 TRP   0.018   0.002   TRPNs 110 
 HIS   0.003   0.001   HISDs 517 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 9822)
  covalent geometry    : angle       0.48837 (13234)
  hydrogen bonds       : bond        0.03746 (  666)
  hydrogen bonds       : angle       4.44302 ( 1950)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3531.56 seconds
wall clock time: 60 minutes 50.42 seconds (3650.42 seconds total)