Starting phenix.real_space_refine
on Sat May 10 09:35:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fzr_29638/05_2025/8fzr_29638.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fzr_29638/05_2025/8fzr_29638.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fzr_29638/05_2025/8fzr_29638.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fzr_29638/05_2025/8fzr_29638.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fzr_29638/05_2025/8fzr_29638.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fzr_29638/05_2025/8fzr_29638.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      76      5.49       5
     S      32      5.16       5
     C    3342      2.51       5
     N     966      2.21       5
     O    1294      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5711
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4071
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 503, 4071
          Classifications: {'peptide': 503}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 25, 'TRANS': 477}
    Chain: "R"
      Number of atoms: 1639
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1639
          Classifications: {'RNA': 77}
          Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 34, 'rna3p_pyr': 33}
          Link IDs: {'rna2p': 9, 'rna3p': 67}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    158  SG  CYS A  20      22.510  31.353  95.799  1.00  0.00           S
  ATOM    180  SG  CYS A  23      23.297  28.877  95.832  1.00  0.00           S
  ATOM    754  SG  CYS A  94      24.926  28.690  98.909  1.00  0.00           S
  ATOM    760  SG  CYS A  95      25.270  30.234  95.400  1.00  0.00           S

  Time building chain proxies: 4.47, per 1000 atoms: 0.78
  Number of scatterers: 5711
  At special positions: 0
  Unit cell: (66.3176, 78.534, 136.126, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      32     16.00
     P      76     15.00
     O    1294      8.00
     N     966      7.00
     C    3342      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.62
  Conformation dependent library (CDL) restraints added in 658.3 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 601 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A  23 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A  95 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A  20 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A  94 "
      Number of angles added : 6


  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  940

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 3 sheets defined
      40.4% alpha, 10.1% beta
      4 base pairs and 19 stacking pairs defined.
    Time for finding SS restraints: 1.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 20
    Processing helix  chain 'A' and resid 30 through 35
      removed outlier: 3.651A  pdb=" N   LEU A  34 " --> pdb=" O   ASN A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 45
      removed outlier: 3.988A  pdb=" N   ARG A  43 " --> pdb=" O   SER A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 77
      removed outlier: 4.139A  pdb=" N   ARG A  72 " --> pdb=" O   ALA A  68 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   MET A  73 " --> pdb=" O   THR A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 125
      removed outlier: 3.807A  pdb=" N   ILE A 117 " --> pdb=" O   LEU A 113 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   SER A 118 " --> pdb=" O   LYS A 114 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ARG A 119 " --> pdb=" O   LYS A 115 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   PHE A 120 " --> pdb=" O   CYS A 116 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ALA A 121 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   THR A 122 " --> pdb=" O   SER A 118 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ARG A 123 " --> pdb=" O   ARG A 119 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ILE A 124 " --> pdb=" O   PHE A 120 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   THR A 125 " --> pdb=" O   ALA A 121 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 113 through 125'
    Processing helix  chain 'A' and resid 140 through 145
      removed outlier: 3.992A  pdb=" N   ASN A 145 " --> pdb=" O   GLY A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 165
      No H-bonds generated for 'chain 'A' and resid 163 through 165'
    Processing helix  chain 'A' and resid 166 through 178
      removed outlier: 3.503A  pdb=" N   LYS A 172 " --> pdb=" O   HIS A 168 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   GLN A 174 " --> pdb=" O   PHE A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 194
      removed outlier: 3.610A  pdb=" N   LYS A 189 " --> pdb=" O   PRO A 185 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   PHE A 191 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   ASP A 194 " --> pdb=" O   ARG A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 204
    Processing helix  chain 'A' and resid 205 through 214
      removed outlier: 3.773A  pdb=" N   TRP A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 276
      removed outlier: 3.930A  pdb=" N   LEU A 272 " --> pdb=" O   SER A 268 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   SER A 273 " --> pdb=" O   LEU A 269 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   ALA A 274 " --> pdb=" O   GLY A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 284
      removed outlier: 3.590A  pdb=" N   ARG A 283 " --> pdb=" O   ALA A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 308
      removed outlier: 4.039A  pdb=" N   TYR A 303 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 326
    Processing helix  chain 'A' and resid 329 through 333
      removed outlier: 3.845A  pdb=" N   GLY A 332 " --> pdb=" O   ILE A 329 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LYS A 333 " --> pdb=" O   SER A 330 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 329 through 333'
    Processing helix  chain 'A' and resid 372 through 376
    Processing helix  chain 'A' and resid 382 through 396
      removed outlier: 3.836A  pdb=" N   SER A 386 " --> pdb=" O   CYS A 382 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ALA A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   LEU A 392 " --> pdb=" O   ASN A 388 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLU A 393 " --> pdb=" O   GLU A 389 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLU A 396 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
      removed outlier: 3.509A  pdb=" N   THR A 409 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ILE A 410 " --> pdb=" O   LEU A 407 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 406 through 410'
    Processing helix  chain 'A' and resid 413 through 418
      removed outlier: 3.671A  pdb=" N   ASN A 417 " --> pdb=" O   LYS A 414 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   GLY A 418 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 444
      removed outlier: 3.709A  pdb=" N   LEU A 437 " --> pdb=" O   PRO A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 450
      removed outlier: 4.245A  pdb=" N   ASP A 448 " --> pdb=" O   GLY A 444 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   LEU A 449 " --> pdb=" O   LYS A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 472
      removed outlier: 3.838A  pdb=" N   GLU A 472 " --> pdb=" O   PHE A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 485
      removed outlier: 3.715A  pdb=" N   VAL A 483 " --> pdb=" O   ARG A 479 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE A 484 " --> pdb=" O   ILE A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 493
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8
      removed outlier: 6.313A  pdb=" N   PHE A   5 " --> pdb=" O   VAL A 496 " (cutoff:3.500A)
      removed outlier: 7.455A  pdb=" N   LEU A 498 " --> pdb=" O   PHE A   5 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ILE A   7 " --> pdb=" O   LEU A 498 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 61
    Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 102
      removed outlier: 6.474A  pdb=" N   TYR A  98 " --> pdb=" O   TYR A 293 " (cutoff:3.500A)
      removed outlier: 5.416A  pdb=" N   TYR A 293 " --> pdb=" O   TYR A  98 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   ILE A 100 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   ILE A 253 " --> pdb=" O   TYR A 290 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   GLY A 292 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   SER A 255 " --> pdb=" O   GLY A 292 " (cutoff:3.500A)
      removed outlier: 8.267A  pdb=" N   TYR A 294 " --> pdb=" O   SER A 255 " (cutoff:3.500A)
      removed outlier: 13.408A  pdb=" N   TYR A 257 " --> pdb=" O   TYR A 294 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   VAL A 245 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   PHE A 258 " --> pdb=" O   ILE A 243 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   ILE A 243 " --> pdb=" O   PHE A 258 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   TRP A 260 " --> pdb=" O   ILE A 241 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   ILE A 241 " --> pdb=" O   TRP A 260 " (cutoff:3.500A)
      removed outlier: 4.932A  pdb=" N   LEU A 240 " --> pdb=" O   TYR A 236 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   TYR A 236 " --> pdb=" O   LEU A 240 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ALA A 242 " --> pdb=" O   TYR A 234 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ARG A 156 " --> pdb=" O   CYS A 233 " (cutoff:3.500A)

    93 hydrogen bonds defined for protein.
    219 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      9 hydrogen bonds
      18 hydrogen bond angles
      0 basepair planarities
      4 basepair parallelities
      19 stacking parallelities
  Total time for adding SS restraints: 1.49

  Time building geometry restraints manager: 1.80 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1507
        1.34 -     1.46: 1549
        1.46 -     1.57: 2749
        1.57 -     1.69: 152
        1.69 -     1.81: 49
  Bond restraints: 6006
  Sorted by residual:
  bond pdb=" N   GLU A 490 "
       pdb=" CA  GLU A 490 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.29e-02 6.01e+03 5.73e+00
  bond pdb=" N   THR A 491 "
       pdb=" CA  THR A 491 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.29e-02 6.01e+03 4.73e+00
  bond pdb=" N   PHE A 487 "
       pdb=" CA  PHE A 487 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.61e-02 3.86e+03 4.05e+00
  bond pdb=" N   GLY A 488 "
       pdb=" CA  GLY A 488 "
    ideal  model  delta    sigma   weight residual
    1.449  1.475 -0.026 1.45e-02 4.76e+03 3.24e+00
  bond pdb=" N   PHE A 489 "
       pdb=" CA  PHE A 489 "
    ideal  model  delta    sigma   weight residual
    1.457  1.475 -0.017 1.29e-02 6.01e+03 1.76e+00
  ... (remaining 6001 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 8372
        1.55 -     3.10: 100
        3.10 -     4.65: 20
        4.65 -     6.20: 4
        6.20 -     7.75: 1
  Bond angle restraints: 8497
  Sorted by residual:
  angle pdb=" N   PHE A 487 "
        pdb=" CA  PHE A 487 "
        pdb=" C   PHE A 487 "
      ideal   model   delta    sigma   weight residual
     109.11  115.29   -6.18 1.42e+00 4.96e-01 1.89e+01
  angle pdb=" C3'   C R  49 "
        pdb=" O3'   C R  49 "
        pdb=" P     G R  50 "
      ideal   model   delta    sigma   weight residual
     120.20  125.42   -5.22 1.50e+00 4.44e-01 1.21e+01
  angle pdb=" N   VAL A 177 "
        pdb=" CA  VAL A 177 "
        pdb=" C   VAL A 177 "
      ideal   model   delta    sigma   weight residual
     113.53  110.45    3.08 9.80e-01 1.04e+00 9.86e+00
  angle pdb=" O3'   C R  49 "
        pdb=" C3'   C R  49 "
        pdb=" C2'   C R  49 "
      ideal   model   delta    sigma   weight residual
     109.50  113.86   -4.36 1.50e+00 4.44e-01 8.47e+00
  angle pdb=" CA  PHE A 487 "
        pdb=" C   PHE A 487 "
        pdb=" O   PHE A 487 "
      ideal   model   delta    sigma   weight residual
     121.86  117.92    3.94 1.39e+00 5.18e-01 8.03e+00
  ... (remaining 8492 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.82: 3447
       34.82 -    69.63: 239
       69.63 -   104.45: 34
      104.45 -   139.26: 0
      139.26 -   174.08: 1
  Dihedral angle restraints: 3721
    sinusoidal: 2247
      harmonic: 1474
  Sorted by residual:
  dihedral pdb=" C4'   C R  49 "
           pdb=" C3'   C R  49 "
           pdb=" O3'   C R  49 "
           pdb=" P     G R  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     250.00   75.92  174.08     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" CA  TRP A 260 "
           pdb=" C   TRP A 260 "
           pdb=" N   ASP A 261 "
           pdb=" CA  ASP A 261 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.26   19.74     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" O4'   C R  49 "
           pdb=" C1'   C R  49 "
           pdb=" N1    C R  49 "
           pdb=" C2    C R  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -74.93  -53.07     1      1.70e+01 3.46e-03 1.33e+01
  ... (remaining 3718 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 787
       0.039 -    0.077: 137
       0.077 -    0.116: 48
       0.116 -    0.154: 4
       0.154 -    0.193: 1
  Chirality restraints: 977
  Sorted by residual:
  chirality pdb=" C3'   C R  49 "
            pdb=" C4'   C R  49 "
            pdb=" O3'   C R  49 "
            pdb=" C2'   C R  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.55   -0.19 2.00e-01 2.50e+01 9.29e-01
  chirality pdb=" CA  ILE A 259 "
            pdb=" N   ILE A 259 "
            pdb=" C   ILE A 259 "
            pdb=" CB  ILE A 259 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.85e-01
  chirality pdb=" CA  ILE A 253 "
            pdb=" N   ILE A 253 "
            pdb=" C   ILE A 253 "
            pdb=" CB  ILE A 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.13e-01
  ... (remaining 974 not shown)

  Planarity restraints: 803
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 486 "    0.011 2.00e-02 2.50e+03   2.19e-02 4.80e+00
        pdb=" C   LEU A 486 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   LEU A 486 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PHE A 487 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 487 "   -0.008 2.00e-02 2.50e+03   1.65e-02 2.72e+00
        pdb=" C   PHE A 487 "    0.029 2.00e-02 2.50e+03
        pdb=" O   PHE A 487 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLY A 488 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 249 "    0.020 5.00e-02 4.00e+02   3.07e-02 1.51e+00
        pdb=" N   PRO A 250 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 250 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 250 "    0.017 5.00e-02 4.00e+02
  ... (remaining 800 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1065
        2.77 -     3.30: 5148
        3.30 -     3.83: 9289
        3.83 -     4.37: 10496
        4.37 -     4.90: 16735
  Nonbonded interactions: 42733
  Sorted by model distance:
  nonbonded pdb=" N   ASP A  89 "
            pdb=" OD1 ASP A  89 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" O   ILE A 253 "
            pdb=" N   TYR A 290 "
     model   vdw
     2.252 3.120
  nonbonded pdb=" O2'   G R  15 "
            pdb=" OP1   G R  19 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   GLY A  77 "
            pdb=" OH  TYR A 293 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   ASP A  71 "
            pdb=" ND2 ASN A  75 "
     model   vdw
     2.290 3.120
  ... (remaining 42728 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:             1.450
  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:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.350
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2377
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   0.127   6010  Z= 0.136
  Angle     :  1.029  46.512   8503  Z= 0.317
  Chirality :  0.034   0.193    977
  Planarity :  0.004   0.031    803
  Dihedral  : 20.143 174.077   2781
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  1.00 %
    Allowed  :  4.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  6.97 %
    Allowed  : 10.56 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.87 (0.37), residues: 501
  helix: -0.88 (0.55), residues: 93
  sheet: -2.68 (0.69), residues: 45
  loop : -1.19 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 267 
 HIS   0.002   0.001   HIS A 226 
 PHE   0.008   0.001   PHE A 139 
 TYR   0.007   0.001   TYR A 173 
 ARG   0.001   0.000   ARG A 276 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.32909 (  102)
  hydrogen bonds       : angle      11.40266 (  237)
  metal coordination   : bond        0.08025 (    4)
  metal coordination   : angle      34.34967 (    6)
  covalent geometry    : bond        0.00198 ( 6006)
  covalent geometry    : angle       0.47673 ( 8497)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 81
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 PHE cc_start: 0.5898 (OUTLIER) cc_final: 0.5225 (p90)
REVERT: A  293 TYR cc_start: 0.4648 (OUTLIER) cc_final: 0.3981 (m-80)
REVERT: A  310 GLU cc_start: 0.3034 (OUTLIER) cc_final: 0.2770 (tp30)
REVERT: A  361 PHE cc_start: 0.4508 (OUTLIER) cc_final: 0.4079 (m-80)
  outliers start: 31
  outliers final: 8
  residues processed: 108
  average time/residue: 0.2041
  time to fit residues: 27.5392
Evaluate side-chains
  55 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  455 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   chunk 29 optimal weight:    0.7980
   chunk 44 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 51 optimal weight:   10.0000
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 168 HIS
A 174 GLN
A 183 ASN
** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 216 GLN
A 326 GLN
A 416 HIS
A 442 GLN
A 475 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4905 r_free = 0.4905 target = 0.149127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4661 r_free = 0.4661 target = 0.130729 restraints weight = 36099.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.132580 restraints weight = 28352.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4709 r_free = 0.4709 target = 0.133942 restraints weight = 23553.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.4519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6186
moved from start:          0.3093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6010  Z= 0.166
  Angle     :  0.710  10.845   8503  Z= 0.350
  Chirality :  0.040   0.202    977
  Planarity :  0.005   0.031    803
  Dihedral  : 23.045 176.022   1794
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  6.97 %
    Allowed  : 19.55 %
    Favored  : 73.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.38), residues: 501
  helix: -0.64 (0.55), residues: 87
  sheet: -2.79 (0.64), residues: 55
  loop : -0.94 (0.35), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 215 
 HIS   0.008   0.001   HIS A  64 
 PHE   0.020   0.002   PHE A 454 
 TYR   0.018   0.002   TYR A 162 
 ARG   0.004   0.001   ARG A  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06390 (  102)
  hydrogen bonds       : angle       7.58802 (  237)
  metal coordination   : bond        0.01257 (    4)
  metal coordination   : angle       6.33686 (    6)
  covalent geometry    : bond        0.00348 ( 6006)
  covalent geometry    : angle       0.68976 ( 8497)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 47
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.8482 (mmp) cc_final: 0.7795 (tpt)
REVERT: A   44 TYR cc_start: -0.3584 (OUTLIER) cc_final: -0.4446 (m-80)
REVERT: A   48 MET cc_start: 0.8939 (tpt) cc_final: 0.8629 (mmm)
REVERT: A  223 LYS cc_start: 0.8872 (tttp) cc_final: 0.8621 (tmtt)
REVERT: A  258 PHE cc_start: -0.0622 (OUTLIER) cc_final: -0.1201 (t80)
REVERT: A  293 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.6272 (m-80)
REVERT: A  310 GLU cc_start: 0.5774 (OUTLIER) cc_final: 0.4740 (tp30)
REVERT: A  361 PHE cc_start: 0.5673 (OUTLIER) cc_final: 0.4862 (m-80)
  outliers start: 31
  outliers final: 17
  residues processed: 75
  average time/residue: 0.2060
  time to fit residues: 19.5985
Evaluate side-chains
  64 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 42
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 TYR
Chi-restraints excluded: chain A residue   83 LYS
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  164 GLU
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  496 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 10 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    5.9990
   chunk 23 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
A 183 ASN
A 417 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4853 r_free = 0.4853 target = 0.137174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4622 r_free = 0.4622 target = 0.121304 restraints weight = 32298.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4645 r_free = 0.4645 target = 0.122928 restraints weight = 25333.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4661 r_free = 0.4661 target = 0.124068 restraints weight = 20955.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.4561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6066
moved from start:          0.3768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6010  Z= 0.125
  Angle     :  0.604   8.762   8503  Z= 0.305
  Chirality :  0.038   0.198    977
  Planarity :  0.005   0.061    803
  Dihedral  : 22.980 176.441   1790
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 20.45 %
    Favored  : 73.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.69 (0.37), residues: 501
  helix: -0.41 (0.54), residues: 91
  sheet: -2.98 (0.61), residues: 54
  loop : -1.02 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 209 
 HIS   0.006   0.001   HIS A  64 
 PHE   0.007   0.001   PHE A 456 
 TYR   0.014   0.001   TYR A 162 
 ARG   0.002   0.000   ARG A 485 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05368 (  102)
  hydrogen bonds       : angle       6.90826 (  237)
  metal coordination   : bond        0.00731 (    4)
  metal coordination   : angle       4.21542 (    6)
  covalent geometry    : bond        0.00261 ( 6006)
  covalent geometry    : angle       0.59366 ( 8497)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 45
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.8221 (mmp) cc_final: 0.7276 (tpt)
REVERT: A   44 TYR cc_start: -0.3192 (OUTLIER) cc_final: -0.4089 (m-80)
REVERT: A  153 PHE cc_start: 0.6660 (OUTLIER) cc_final: 0.4998 (p90)
REVERT: A  183 ASN cc_start: 0.7605 (OUTLIER) cc_final: 0.7266 (m110)
REVERT: A  186 LYS cc_start: 0.9193 (pttm) cc_final: 0.8571 (mmtt)
REVERT: A  223 LYS cc_start: 0.8885 (tttp) cc_final: 0.8643 (tmtt)
REVERT: A  258 PHE cc_start: -0.0481 (OUTLIER) cc_final: -0.1049 (t80)
REVERT: A  289 TYR cc_start: 0.6885 (t80) cc_final: 0.5822 (t80)
REVERT: A  293 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.6493 (m-80)
REVERT: A  310 GLU cc_start: 0.5771 (OUTLIER) cc_final: 0.4747 (tp30)
REVERT: A  361 PHE cc_start: 0.5484 (OUTLIER) cc_final: 0.4704 (m-80)
  outliers start: 27
  outliers final: 14
  residues processed: 68
  average time/residue: 0.1797
  time to fit residues: 16.2191
Evaluate side-chains
  63 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 42
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 TYR
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  139 PHE
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  164 GLU
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  183 ASN
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  496 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 46 optimal weight:   10.0000
   chunk 54 optimal weight:    9.9990
   chunk 1 optimal weight:    7.9990
   chunk 7 optimal weight:    1.9990
   chunk 42 optimal weight:    9.9990
   chunk 21 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 52 optimal weight:    6.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 302 ASN
A 316 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4881 r_free = 0.4881 target = 0.144891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4647 r_free = 0.4647 target = 0.126745 restraints weight = 36549.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.128552 restraints weight = 28563.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.129861 restraints weight = 23658.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.4507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6284
moved from start:          0.4444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6010  Z= 0.143
  Angle     :  0.646  13.139   8503  Z= 0.321
  Chirality :  0.038   0.201    977
  Planarity :  0.005   0.043    803
  Dihedral  : 23.134 175.741   1789
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 15.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  7.19 %
    Allowed  : 20.22 %
    Favored  : 72.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.38), residues: 501
  helix: -0.32 (0.53), residues: 91
  sheet: -2.27 (0.75), residues: 40
  loop : -0.90 (0.34), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 215 
 HIS   0.005   0.001   HIS A  64 
 PHE   0.011   0.002   PHE A  78 
 TYR   0.018   0.001   TYR A  44 
 ARG   0.008   0.001   ARG A 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05077 (  102)
  hydrogen bonds       : angle       6.92805 (  237)
  metal coordination   : bond        0.00662 (    4)
  metal coordination   : angle       3.64094 (    6)
  covalent geometry    : bond        0.00300 ( 6006)
  covalent geometry    : angle       0.63852 ( 8497)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 42
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.8448 (mmp) cc_final: 0.7712 (tpt)
REVERT: A   48 MET cc_start: 0.8032 (mmm) cc_final: 0.7369 (mmm)
REVERT: A  109 MET cc_start: 0.7204 (mtm) cc_final: 0.6865 (mpp)
REVERT: A  153 PHE cc_start: 0.6843 (OUTLIER) cc_final: 0.5436 (p90)
REVERT: A  183 ASN cc_start: 0.7508 (OUTLIER) cc_final: 0.6977 (m-40)
REVERT: A  186 LYS cc_start: 0.9221 (pttm) cc_final: 0.8645 (mmtt)
REVERT: A  223 LYS cc_start: 0.8896 (tttp) cc_final: 0.8666 (tmtt)
REVERT: A  258 PHE cc_start: -0.0282 (OUTLIER) cc_final: -0.0613 (t80)
REVERT: A  289 TYR cc_start: 0.7146 (t80) cc_final: 0.6142 (t80)
REVERT: A  293 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.6655 (m-80)
REVERT: A  310 GLU cc_start: 0.6159 (OUTLIER) cc_final: 0.5116 (tm-30)
REVERT: A  361 PHE cc_start: 0.5849 (OUTLIER) cc_final: 0.4939 (m-80)
  outliers start: 32
  outliers final: 20
  residues processed: 70
  average time/residue: 0.1780
  time to fit residues: 16.7959
Evaluate side-chains
  67 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 41
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LYS
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  139 PHE
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  183 ASN
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  268 SER
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  496 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 36 optimal weight:    8.9990
   chunk 17 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 4 optimal weight:    0.4980
   chunk 13 optimal weight:    7.9990
   chunk 40 optimal weight:    8.9990
   chunk 53 optimal weight:   20.0000
   chunk 41 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    3.4586

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 502 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4783 r_free = 0.4783 target = 0.135561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.117771 restraints weight = 37597.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.119572 restraints weight = 28876.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.120836 restraints weight = 23827.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.4358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6581
moved from start:          0.5594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6010  Z= 0.217
  Angle     :  0.732  11.366   8503  Z= 0.369
  Chirality :  0.041   0.207    977
  Planarity :  0.005   0.048    803
  Dihedral  : 23.742 176.924   1789
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 23.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.39 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  7.64 %
    Allowed  : 20.90 %
    Favored  : 71.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.38), residues: 501
  helix: -0.24 (0.56), residues: 81
  sheet: -2.16 (0.78), residues: 40
  loop : -1.08 (0.34), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 215 
 HIS   0.005   0.001   HIS A 226 
 PHE   0.020   0.002   PHE A  78 
 TYR   0.021   0.002   TYR A  44 
 ARG   0.004   0.001   ARG A 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05620 (  102)
  hydrogen bonds       : angle       7.41891 (  237)
  metal coordination   : bond        0.00998 (    4)
  metal coordination   : angle       4.96093 (    6)
  covalent geometry    : bond        0.00445 ( 6006)
  covalent geometry    : angle       0.72009 ( 8497)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 40
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.8777 (mmp) cc_final: 0.8106 (tpt)
REVERT: A   48 MET cc_start: 0.8306 (mmm) cc_final: 0.7784 (mmm)
REVERT: A  223 LYS cc_start: 0.8889 (tttp) cc_final: 0.8611 (tmtt)
REVERT: A  248 ILE cc_start: 0.9268 (mt) cc_final: 0.8896 (pt)
REVERT: A  258 PHE cc_start: 0.0747 (OUTLIER) cc_final: 0.0526 (t80)
REVERT: A  289 TYR cc_start: 0.7320 (t80) cc_final: 0.6312 (t80)
REVERT: A  310 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.5822 (tm-30)
REVERT: A  361 PHE cc_start: 0.5960 (OUTLIER) cc_final: 0.5205 (m-80)
  outliers start: 34
  outliers final: 26
  residues processed: 72
  average time/residue: 0.1581
  time to fit residues: 15.5289
Evaluate side-chains
  67 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 38
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ASP
Chi-restraints excluded: chain A residue   83 LYS
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  139 PHE
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  268 SER
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  307 TYR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  496 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 44 optimal weight:    0.1980
   chunk 25 optimal weight:    4.9990
   chunk 23 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 55 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9980
   chunk 42 optimal weight:    8.9990
   chunk 39 optimal weight:    2.9990
   chunk 47 optimal weight:   10.0000
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
A 178 HIS
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4861 r_free = 0.4861 target = 0.141987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4645 r_free = 0.4645 target = 0.124243 restraints weight = 36600.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4671 r_free = 0.4671 target = 0.126097 restraints weight = 28254.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.127434 restraints weight = 23180.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.4504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6289
moved from start:          0.5630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6010  Z= 0.114
  Angle     :  0.604  10.790   8503  Z= 0.307
  Chirality :  0.038   0.192    977
  Planarity :  0.004   0.034    803
  Dihedral  : 23.555 174.450   1789
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 14.43
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.59 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  6.29 %
    Allowed  : 21.80 %
    Favored  : 71.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.39), residues: 501
  helix: -0.42 (0.55), residues: 95
  sheet: -2.05 (0.79), residues: 40
  loop : -0.92 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 215 
 HIS   0.003   0.001   HIS A  64 
 PHE   0.008   0.001   PHE A  78 
 TYR   0.016   0.001   TYR A  44 
 ARG   0.002   0.000   ARG A 276 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04733 (  102)
  hydrogen bonds       : angle       6.72967 (  237)
  metal coordination   : bond        0.00470 (    4)
  metal coordination   : angle       3.09155 (    6)
  covalent geometry    : bond        0.00233 ( 6006)
  covalent geometry    : angle       0.59820 ( 8497)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 41
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 MET cc_start: 0.4890 (tpt) cc_final: 0.4161 (tpt)
REVERT: A   31 MET cc_start: 0.8587 (mmp) cc_final: 0.7584 (tpt)
REVERT: A   48 MET cc_start: 0.8273 (mmm) cc_final: 0.7631 (mmm)
REVERT: A  145 ASN cc_start: 0.9064 (OUTLIER) cc_final: 0.8757 (p0)
REVERT: A  147 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7383 (pm20)
REVERT: A  186 LYS cc_start: 0.9042 (pttm) cc_final: 0.8454 (mmtt)
REVERT: A  203 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7339 (tm)
REVERT: A  223 LYS cc_start: 0.8913 (tttp) cc_final: 0.8675 (tmtt)
REVERT: A  258 PHE cc_start: 0.0333 (OUTLIER) cc_final: 0.0099 (t80)
REVERT: A  289 TYR cc_start: 0.7261 (t80) cc_final: 0.6296 (t80)
REVERT: A  293 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.6667 (m-80)
REVERT: A  310 GLU cc_start: 0.6007 (OUTLIER) cc_final: 0.5155 (tm-30)
REVERT: A  361 PHE cc_start: 0.5862 (OUTLIER) cc_final: 0.5135 (m-10)
REVERT: A  397 LEU cc_start: 0.9318 (mt) cc_final: 0.8818 (tt)
  outliers start: 28
  outliers final: 13
  residues processed: 68
  average time/residue: 0.1723
  time to fit residues: 15.6698
Evaluate side-chains
  57 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 37
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LYS
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  139 PHE
Chi-restraints excluded: chain A residue  145 ASN
Chi-restraints excluded: chain A residue  147 GLU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  455 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 36 optimal weight:    0.0770
   chunk 40 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0980
   chunk 28 optimal weight:    0.4980
   chunk 4 optimal weight:   10.0000
   overall best weight:    0.5340

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

Flipped N/Q/H residues before XYZ refinement:
A 178 HIS
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 326 GLN ** 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 = 0.4885 r_free = 0.4885 target = 0.143873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4676 r_free = 0.4676 target = 0.126318 restraints weight = 36342.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4702 r_free = 0.4702 target = 0.128209 restraints weight = 27827.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4721 r_free = 0.4721 target = 0.129532 restraints weight = 22708.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.4539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6199
moved from start:          0.5969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6010  Z= 0.109
  Angle     :  0.615  11.604   8503  Z= 0.310
  Chirality :  0.038   0.195    977
  Planarity :  0.004   0.036    803
  Dihedral  : 23.368 174.577   1787
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.99 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  5.84 %
    Allowed  : 22.02 %
    Favored  : 72.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.38), residues: 501
  helix: -0.34 (0.54), residues: 102
  sheet: -2.00 (0.84), residues: 39
  loop : -0.88 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A  40 
 HIS   0.005   0.001   HIS A  64 
 PHE   0.011   0.001   PHE A  35 
 TYR   0.019   0.001   TYR A 411 
 ARG   0.002   0.000   ARG A 276 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04303 (  102)
  hydrogen bonds       : angle       6.47848 (  237)
  metal coordination   : bond        0.00463 (    4)
  metal coordination   : angle       2.75080 (    6)
  covalent geometry    : bond        0.00224 ( 6006)
  covalent geometry    : angle       0.61063 ( 8497)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 43
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.8663 (mmp) cc_final: 0.7962 (tpt)
REVERT: A   48 MET cc_start: 0.8245 (mmm) cc_final: 0.7695 (mmm)
REVERT: A   91 LEU cc_start: 0.7477 (tp) cc_final: 0.6866 (pt)
REVERT: A  147 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7404 (pm20)
REVERT: A  186 LYS cc_start: 0.8962 (pttm) cc_final: 0.8326 (mmtt)
REVERT: A  203 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7221 (tm)
REVERT: A  223 LYS cc_start: 0.8913 (tttp) cc_final: 0.8692 (tmtt)
REVERT: A  227 MET cc_start: 0.6655 (tmm) cc_final: 0.6308 (tmm)
REVERT: A  247 ASP cc_start: 0.7598 (t0) cc_final: 0.7153 (m-30)
REVERT: A  258 PHE cc_start: 0.0133 (OUTLIER) cc_final: -0.0143 (t80)
REVERT: A  289 TYR cc_start: 0.7313 (t80) cc_final: 0.6481 (t80)
REVERT: A  293 TYR cc_start: 0.8232 (OUTLIER) cc_final: 0.6710 (m-80)
REVERT: A  310 GLU cc_start: 0.5937 (OUTLIER) cc_final: 0.4846 (tm-30)
REVERT: A  361 PHE cc_start: 0.5791 (OUTLIER) cc_final: 0.5155 (m-10)
REVERT: A  397 LEU cc_start: 0.9274 (mt) cc_final: 0.8746 (tt)
  outliers start: 26
  outliers final: 16
  residues processed: 68
  average time/residue: 0.1584
  time to fit residues: 14.5087
Evaluate side-chains
  61 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 39
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LYS
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  139 PHE
Chi-restraints excluded: chain A residue  147 GLU
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  225 LYS
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  455 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 45 optimal weight:   30.0000
   chunk 38 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 46 optimal weight:    7.9990
   chunk 41 optimal weight:    5.9990
   chunk 31 optimal weight:    0.2980
   chunk 55 optimal weight:    8.9990
   chunk 23 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9980
   chunk 34 optimal weight:    6.9990
   overall best weight:    1.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 178 HIS
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 326 GLN ** 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 = 0.4829 r_free = 0.4829 target = 0.139366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.122008 restraints weight = 36158.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4640 r_free = 0.4640 target = 0.123816 restraints weight = 27786.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4658 r_free = 0.4658 target = 0.125095 restraints weight = 22879.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.4449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6414
moved from start:          0.6394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6010  Z= 0.139
  Angle     :  0.638  11.788   8503  Z= 0.320
  Chirality :  0.038   0.200    977
  Planarity :  0.004   0.032    803
  Dihedral  : 23.531 174.566   1787
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 16.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 21.80 %
    Favored  : 72.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.38), residues: 501
  helix: -0.39 (0.56), residues: 95
  sheet: -1.81 (0.86), residues: 39
  loop : -0.92 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 215 
 HIS   0.005   0.001   HIS A 226 
 PHE   0.014   0.001   PHE A  78 
 TYR   0.013   0.002   TYR A  86 
 ARG   0.002   0.000   ARG A  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04290 (  102)
  hydrogen bonds       : angle       6.61612 (  237)
  metal coordination   : bond        0.00584 (    4)
  metal coordination   : angle       3.12576 (    6)
  covalent geometry    : bond        0.00295 ( 6006)
  covalent geometry    : angle       0.63248 ( 8497)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 37
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.8648 (mmp) cc_final: 0.7873 (tpt)
REVERT: A   48 MET cc_start: 0.8514 (mmm) cc_final: 0.8003 (mmm)
REVERT: A  186 LYS cc_start: 0.8955 (pttm) cc_final: 0.8328 (mmtt)
REVERT: A  203 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7139 (tm)
REVERT: A  223 LYS cc_start: 0.8887 (tttp) cc_final: 0.8626 (tmtt)
REVERT: A  227 MET cc_start: 0.6943 (tmm) cc_final: 0.6488 (tmm)
REVERT: A  258 PHE cc_start: 0.0649 (OUTLIER) cc_final: 0.0421 (t80)
REVERT: A  289 TYR cc_start: 0.7388 (t80) cc_final: 0.6345 (t80)
REVERT: A  310 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5089 (tm-30)
REVERT: A  361 PHE cc_start: 0.5793 (OUTLIER) cc_final: 0.5057 (m-10)
REVERT: A  397 LEU cc_start: 0.9335 (mt) cc_final: 0.8923 (tt)
  outliers start: 25
  outliers final: 17
  residues processed: 61
  average time/residue: 0.1798
  time to fit residues: 14.5453
Evaluate side-chains
  58 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 37
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LYS
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  139 PHE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  486 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 39 optimal weight:    0.1980
   chunk 42 optimal weight:    0.4980
   chunk 29 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   chunk 16 optimal weight:    7.9990
   chunk 27 optimal weight:    0.2980
   chunk 41 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 178 HIS
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 326 GLN ** 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 = 0.4899 r_free = 0.4899 target = 0.144188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4691 r_free = 0.4691 target = 0.126815 restraints weight = 36294.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4719 r_free = 0.4719 target = 0.128709 restraints weight = 27568.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 75)----------------|
| r_work = 0.4736 r_free = 0.4736 target = 0.130124 restraints weight = 22503.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.4578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6207
moved from start:          0.6567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   6010  Z= 0.105
  Angle     :  0.616  12.040   8503  Z= 0.308
  Chirality :  0.038   0.192    977
  Planarity :  0.004   0.034    803
  Dihedral  : 23.354 173.611   1785
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.79 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 22.92 %
    Favored  : 71.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.38), residues: 501
  helix:  0.00 (0.59), residues: 93
  sheet: -1.69 (0.84), residues: 39
  loop : -0.93 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  40 
 HIS   0.005   0.001   HIS A 226 
 PHE   0.008   0.001   PHE A  78 
 TYR   0.010   0.001   TYR A 294 
 ARG   0.003   0.000   ARG A 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04121 (  102)
  hydrogen bonds       : angle       6.24317 (  237)
  metal coordination   : bond        0.00478 (    4)
  metal coordination   : angle       2.45957 (    6)
  covalent geometry    : bond        0.00224 ( 6006)
  covalent geometry    : angle       0.61317 ( 8497)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 39
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 MET cc_start: 0.4414 (tpt) cc_final: 0.3809 (tpt)
REVERT: A   31 MET cc_start: 0.8547 (mmp) cc_final: 0.7936 (tpt)
REVERT: A   48 MET cc_start: 0.8506 (mmm) cc_final: 0.8096 (mmm)
REVERT: A   91 LEU cc_start: 0.7368 (tp) cc_final: 0.6773 (pt)
REVERT: A  186 LYS cc_start: 0.8902 (pttm) cc_final: 0.8256 (mmtt)
REVERT: A  203 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7114 (tm)
REVERT: A  218 MET cc_start: 0.2346 (ptt) cc_final: 0.1871 (mtm)
REVERT: A  223 LYS cc_start: 0.8866 (tttp) cc_final: 0.8640 (tmtt)
REVERT: A  227 MET cc_start: 0.6667 (tmm) cc_final: 0.6181 (tmm)
REVERT: A  258 PHE cc_start: 0.0436 (OUTLIER) cc_final: 0.0099 (t80)
REVERT: A  289 TYR cc_start: 0.7389 (t80) cc_final: 0.6533 (t80)
REVERT: A  293 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.6915 (m-80)
REVERT: A  310 GLU cc_start: 0.5550 (OUTLIER) cc_final: 0.4489 (tm-30)
REVERT: A  361 PHE cc_start: 0.5701 (OUTLIER) cc_final: 0.5063 (m-10)
REVERT: A  397 LEU cc_start: 0.9288 (mt) cc_final: 0.8857 (tt)
  outliers start: 23
  outliers final: 14
  residues processed: 60
  average time/residue: 0.1722
  time to fit residues: 13.8974
Evaluate side-chains
  59 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 40
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LYS
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  139 PHE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  368 LYS
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  496 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 49 optimal weight:    0.5980
   chunk 14 optimal weight:    7.9990
   chunk 4 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   chunk 30 optimal weight:    0.3980
   chunk 5 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 54 optimal weight:   10.0000
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
A 178 HIS
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 326 GLN ** 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 = 0.4857 r_free = 0.4857 target = 0.141070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4642 r_free = 0.4642 target = 0.123548 restraints weight = 37015.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4670 r_free = 0.4670 target = 0.125505 restraints weight = 28069.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4687 r_free = 0.4687 target = 0.126881 restraints weight = 22797.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.4514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6251
moved from start:          0.6786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6010  Z= 0.120
  Angle     :  0.623  12.088   8503  Z= 0.309
  Chirality :  0.038   0.199    977
  Planarity :  0.004   0.034    803
  Dihedral  : 23.393 173.575   1785
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 22.92 %
    Favored  : 71.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.38), residues: 501
  helix: -0.27 (0.57), residues: 96
  sheet: -1.47 (0.85), residues: 39
  loop : -0.97 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  40 
 HIS   0.005   0.001   HIS A  64 
 PHE   0.012   0.001   PHE A  78 
 TYR   0.008   0.001   TYR A  86 
 ARG   0.002   0.000   ARG A 276 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03839 (  102)
  hydrogen bonds       : angle       6.33951 (  237)
  metal coordination   : bond        0.00515 (    4)
  metal coordination   : angle       2.75919 (    6)
  covalent geometry    : bond        0.00260 ( 6006)
  covalent geometry    : angle       0.61843 ( 8497)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 37
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.8529 (mmp) cc_final: 0.7907 (tpt)
REVERT: A   48 MET cc_start: 0.8541 (mmm) cc_final: 0.8176 (mmm)
REVERT: A   76 MET cc_start: 0.5693 (ttt) cc_final: 0.4440 (ptm)
REVERT: A   91 LEU cc_start: 0.7371 (tp) cc_final: 0.6807 (pt)
REVERT: A  186 LYS cc_start: 0.8926 (pttm) cc_final: 0.8301 (mmtt)
REVERT: A  203 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7014 (tm)
REVERT: A  223 LYS cc_start: 0.8854 (tttp) cc_final: 0.8623 (tmtt)
REVERT: A  227 MET cc_start: 0.6481 (tmm) cc_final: 0.6167 (tmm)
REVERT: A  258 PHE cc_start: 0.0296 (OUTLIER) cc_final: 0.0077 (t80)
REVERT: A  289 TYR cc_start: 0.7250 (t80) cc_final: 0.6334 (t80)
REVERT: A  293 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.6898 (m-80)
REVERT: A  310 GLU cc_start: 0.5707 (OUTLIER) cc_final: 0.4576 (tm-30)
REVERT: A  397 LEU cc_start: 0.9235 (mt) cc_final: 0.8720 (tt)
  outliers start: 24
  outliers final: 17
  residues processed: 59
  average time/residue: 0.1770
  time to fit residues: 13.9893
Evaluate side-chains
  58 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 37
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LYS
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  139 PHE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  225 LYS
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  496 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 54 optimal weight:    9.9990
   chunk 39 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0770
   chunk 49 optimal weight:    0.9990
   chunk 50 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 55 optimal weight:    7.9990
   chunk 10 optimal weight:    7.9990
   chunk 13 optimal weight:    0.0020
   chunk 22 optimal weight:    5.9990
   overall best weight:    0.7750

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

Flipped N/Q/H residues before XYZ refinement:
A 178 HIS
A 306 ASN
A 326 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4893 r_free = 0.4893 target = 0.143399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4678 r_free = 0.4678 target = 0.125941 restraints weight = 37014.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4708 r_free = 0.4708 target = 0.127893 restraints weight = 27957.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4726 r_free = 0.4726 target = 0.129239 restraints weight = 22764.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.4562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6233
moved from start:          0.6997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6010  Z= 0.103
  Angle     :  0.603  12.313   8503  Z= 0.300
  Chirality :  0.037   0.195    977
  Planarity :  0.004   0.035    803
  Dihedral  : 23.327 172.914   1785
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 23.15 %
    Favored  : 71.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.39), residues: 501
  helix: -0.11 (0.58), residues: 94
  sheet: -1.34 (0.84), residues: 39
  loop : -0.97 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  40 
 HIS   0.004   0.001   HIS A 226 
 PHE   0.010   0.001   PHE A  78 
 TYR   0.009   0.001   TYR A 294 
 ARG   0.002   0.000   ARG A 276 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03785 (  102)
  hydrogen bonds       : angle       6.11393 (  237)
  metal coordination   : bond        0.00465 (    4)
  metal coordination   : angle       2.54135 (    6)
  covalent geometry    : bond        0.00220 ( 6006)
  covalent geometry    : angle       0.59911 ( 8497)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2608.37 seconds
wall clock time: 46 minutes 9.46 seconds (2769.46 seconds total)