Starting phenix.real_space_refine
on Wed Feb  4 07:47:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nhd_49409/02_2026/9nhd_49409.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nhd_49409/02_2026/9nhd_49409.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nhd_49409/02_2026/9nhd_49409.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nhd_49409/02_2026/9nhd_49409.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nhd_49409/02_2026/9nhd_49409.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nhd_49409/02_2026/9nhd_49409.map"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.042
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
     P      48      5.49       5
     Mg      1      5.21       5
     S      39      5.16       5
     C    5712      2.51       5
     N    1582      2.21       5
     O    1853      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 61 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9235
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 736, 5941
          Classifications: {'peptide': 736}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 35, 'TRANS': 700}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 518
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 518
          Classifications: {'RNA': 24}
          Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 14, 'rna3p_pyr': 8}
          Link IDs: {'rna2p': 2, 'rna3p': 21}
    Chain: "C"
      Number of atoms: 501
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 501
          Classifications: {'RNA': 24}
          Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 2, 'rna3p': 21}
    Chain: "E"
      Number of atoms: 373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 373
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 3, 'TRANS': 41}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1901
          Classifications: {'peptide': 236}
          Link IDs: {'PTRANS': 13, 'TRANS': 222}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.86, per 1000 atoms: 0.20
  Number of scatterers: 9235
  At special positions: 0
  Unit cell: (105.56, 95.55, 108.29, 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)
     S      39     16.00
     P      48     15.00
     Mg      1     11.99
     O    1853      8.00
     N    1582      7.00
     C    5712      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 429.7 milliseconds
  

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1930

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 11 sheets defined
      40.0% alpha, 16.6% beta
      20 base pairs and 31 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 181 through 190
      removed outlier: 3.564A  pdb=" N   ARG A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 197
      removed outlier: 3.625A  pdb=" N   LEU A 196 " --> pdb=" O   HIS A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 262
    Processing helix  chain 'A' and resid 281 through 283
      No H-bonds generated for 'chain 'A' and resid 281 through 283'
    Processing helix  chain 'A' and resid 317 through 329
    Processing helix  chain 'A' and resid 333 through 342
      removed outlier: 3.536A  pdb=" N   VAL A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 388
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.966A  pdb=" N   ARG A 409 " --> pdb=" O   PRO A 405 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ALA A 410 " --> pdb=" O   ARG A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 421
      No H-bonds generated for 'chain 'A' and resid 419 through 421'
    Processing helix  chain 'A' and resid 431 through 434
      removed outlier: 4.052A  pdb=" N   ALA A 434 " --> pdb=" O   GLU A 431 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 431 through 434'
    Processing helix  chain 'A' and resid 435 through 447
      removed outlier: 3.654A  pdb=" N   MET A 439 " --> pdb=" O   ASN A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 467
    Processing helix  chain 'A' and resid 467 through 477
      removed outlier: 3.502A  pdb=" N   VAL A 471 " --> pdb=" O   THR A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 522
      removed outlier: 3.612A  pdb=" N   MET A 519 " --> pdb=" O   THR A 516 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ARG A 520 " --> pdb=" O   ARG A 517 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   SER A 521 " --> pdb=" O   ASP A 518 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LYS A 522 " --> pdb=" O   MET A 519 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 516 through 522'
    Processing helix  chain 'A' and resid 541 through 560
    Processing helix  chain 'A' and resid 575 through 590
    Processing helix  chain 'A' and resid 604 through 616
      removed outlier: 4.105A  pdb=" N   VAL A 616 " --> pdb=" O   LYS A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 650
      removed outlier: 3.505A  pdb=" N   LEU A 650 " --> pdb=" O   ILE A 646 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 729
    Processing helix  chain 'A' and resid 746 through 752
    Processing helix  chain 'A' and resid 754 through 767
    Processing helix  chain 'A' and resid 842 through 855
    Processing helix  chain 'A' and resid 867 through 880
    Processing helix  chain 'A' and resid 889 through 893
      removed outlier: 3.708A  pdb=" N   ASN A 893 " --> pdb=" O   TYR A 890 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 114 through 119
      removed outlier: 3.606A  pdb=" N   LYS E 118 " --> pdb=" O   ASP E 114 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 131 through 135
    Processing helix  chain 'E' and resid 137 through 145
      removed outlier: 4.221A  pdb=" N   LYS E 143 " --> pdb=" O   LYS E 139 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   THR E 144 " --> pdb=" O   GLU E 140 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 87 through 110
      removed outlier: 3.765A  pdb=" N   GLU F  93 " --> pdb=" O   MET F  89 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   ASP F  94 " --> pdb=" O   LYS F  90 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ASP F  99 " --> pdb=" O   ASN F  95 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLN F 101 " --> pdb=" O   LYS F  97 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 112 through 115
    Processing helix  chain 'F' and resid 166 through 178
    Processing helix  chain 'F' and resid 190 through 199
    Processing helix  chain 'F' and resid 218 through 233
      removed outlier: 3.740A  pdb=" N   ASP F 223 " --> pdb=" O   PRO F 219 " (cutoff:3.500A)
      removed outlier: 5.074A  pdb=" N   ALA F 224 " --> pdb=" O   GLU F 220 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 248 through 260
    Processing helix  chain 'F' and resid 271 through 277
      removed outlier: 4.064A  pdb=" N   THR F 275 " --> pdb=" O   SER F 271 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 290 through 296
      removed outlier: 3.652A  pdb=" N   GLU F 294 " --> pdb=" O   CYS F 290 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   SER F 295 " --> pdb=" O   GLU F 291 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 302 through 323
      removed outlier: 3.784A  pdb=" N   ARG F 317 " --> pdb=" O   THR F 313 " (cutoff:3.500A)
      Proline residue:  F 320  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 487 through 488
    Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 267
    Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 267
      removed outlier: 3.575A  pdb=" N   THR A 294 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ASN A 296 " --> pdb=" O   LEU A 303 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU A 303 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 5.416A  pdb=" N   LEU A 302 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLU A 161 " --> pdb=" O   LYS A 480 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   LYS A 480 " --> pdb=" O   GLU A 161 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 205 through 208
      removed outlier: 3.663A  pdb=" N   ASP A 174 " --> pdb=" O   LEU A 233 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   LEU A 233 " --> pdb=" O   ASP A 174 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 356
    Processing sheet with id=AA6, first strand: chain 'A' and resid 369 through 372
      removed outlier: 3.551A  pdb=" N   GLU A 375 " --> pdb=" O   MET A 372 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 399 through 402
    Processing sheet with id=AA8, first strand: chain 'A' and resid 491 through 492
      removed outlier: 3.570A  pdb=" N   ARG A 491 " --> pdb=" O   VAL A 802 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   THR A 801 " --> pdb=" O   VAL A 818 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   SER A 831 " --> pdb=" O   SER A 779 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   ILE A 735 " --> pdb=" O   ALA A 774 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   ILE A 776 " --> pdb=" O   ILE A 735 " (cutoff:3.500A)
      removed outlier: 5.828A  pdb=" N   ILE A 737 " --> pdb=" O   ILE A 776 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   VAL A 778 " --> pdb=" O   ILE A 737 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   ARG A 739 " --> pdb=" O   VAL A 778 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 497 through 500
      removed outlier: 3.553A  pdb=" N   GLN A 500 " --> pdb=" O   VAL A 504 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL A 504 " --> pdb=" O   GLN A 500 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 569 through 571
      removed outlier: 7.903A  pdb=" N   VAL A 569 " --> pdb=" O   TRP A 533 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL A 535 " --> pdb=" O   VAL A 569 " (cutoff:3.500A)
      removed outlier: 7.757A  pdb=" N   ILE A 571 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   THR A 537 " --> pdb=" O   ILE A 571 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   ILE A 595 " --> pdb=" O   GLN A 623 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   VAL A 625 " --> pdb=" O   ILE A 595 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   CYS A 597 " --> pdb=" O   VAL A 625 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 148 through 156
      removed outlier: 6.903A  pdb=" N   GLN F 142 " --> pdb=" O   LYS F 150 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   SER F 152 " --> pdb=" O   VAL F 140 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   VAL F 140 " --> pdb=" O   SER F 152 " (cutoff:3.500A)
      removed outlier: 4.622A  pdb=" N   HIS F 154 " --> pdb=" O   PHE F 138 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   PHE F 138 " --> pdb=" O   HIS F 154 " (cutoff:3.500A)
      removed outlier: 4.935A  pdb=" N   THR F 156 " --> pdb=" O   GLY F 136 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   GLY F 136 " --> pdb=" O   THR F 156 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   VAL F 120 " --> pdb=" O   THR F 141 " (cutoff:3.500A)
      removed outlier: 10.069A  pdb=" N   PHE F 216 " --> pdb=" O   ASP F 117 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   TYR F 119 " --> pdb=" O   PHE F 216 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   MET F 215 " --> pdb=" O   TYR F 246 " (cutoff:3.500A)

    323 hydrogen bonds defined for protein.
    921 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      48 hydrogen bonds
      96 hydrogen bond angles
      0 basepair planarities
      20 basepair parallelities
      31 stacking parallelities
  Total time for adding SS restraints: 1.53

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2583
        1.34 -     1.46: 1957
        1.46 -     1.58: 4826
        1.58 -     1.70: 94
        1.70 -     1.82: 61
  Bond restraints: 9521
  Sorted by residual:
  bond pdb=" CZ  ARG A 812 "
       pdb=" NH2 ARG A 812 "
    ideal  model  delta    sigma   weight residual
    1.330  1.282  0.048 1.30e-02 5.92e+03 1.35e+01
  bond pdb=" CA  PRO F 213 "
       pdb=" C   PRO F 213 "
    ideal  model  delta    sigma   weight residual
    1.514  1.533 -0.019 5.50e-03 3.31e+04 1.22e+01
  bond pdb=" CZ  ARG A 256 "
       pdb=" NH2 ARG A 256 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.037 1.30e-02 5.92e+03 8.13e+00
  bond pdb=" CZ  ARG A 491 "
       pdb=" NH2 ARG A 491 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.037 1.30e-02 5.92e+03 7.90e+00
  bond pdb=" CD2 HIS E 121 "
       pdb=" NE2 HIS E 121 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.36e+00
  ... (remaining 9516 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 12176
        2.33 -     4.65: 825
        4.65 -     6.98: 92
        6.98 -     9.31: 11
        9.31 -    11.63: 3
  Bond angle restraints: 13107
  Sorted by residual:
  angle pdb=" C3'   G B   5 "
        pdb=" O3'   G B   5 "
        pdb=" P     U B   6 "
      ideal   model   delta    sigma   weight residual
     120.20  108.57   11.63 1.50e+00 4.44e-01 6.02e+01
  angle pdb=" C3'   G B   3 "
        pdb=" O3'   G B   3 "
        pdb=" P     A B   4 "
      ideal   model   delta    sigma   weight residual
     120.20  111.18    9.02 1.50e+00 4.44e-01 3.62e+01
  angle pdb=" C3'   A B   4 "
        pdb=" O3'   A B   4 "
        pdb=" P     G B   5 "
      ideal   model   delta    sigma   weight residual
     120.20  112.12    8.08 1.50e+00 4.44e-01 2.90e+01
  angle pdb=" C   HIS A 712 "
        pdb=" N   MET A 713 "
        pdb=" CA  MET A 713 "
      ideal   model   delta    sigma   weight residual
     120.38  127.55   -7.17 1.37e+00 5.33e-01 2.74e+01
  angle pdb=" CA  ASP F 117 "
        pdb=" CB  ASP F 117 "
        pdb=" CG  ASP F 117 "
      ideal   model   delta    sigma   weight residual
     112.60  117.77   -5.17 1.00e+00 1.00e+00 2.68e+01
  ... (remaining 13102 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.86: 5498
       27.86 -    55.73: 256
       55.73 -    83.59: 71
       83.59 -   111.45: 5
      111.45 -   139.32: 1
  Dihedral angle restraints: 5831
    sinusoidal: 2843
      harmonic: 2988
  Sorted by residual:
  dihedral pdb=" CA  ILE F 198 "
           pdb=" C   ILE F 198 "
           pdb=" N   ILE F 199 "
           pdb=" CA  ILE F 199 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.17   27.83     0      5.00e+00 4.00e-02 3.10e+01
  dihedral pdb=" C5'   U B   6 "
           pdb=" C4'   U B   6 "
           pdb=" C3'   U B   6 "
           pdb=" O3'   U B   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00  112.03   34.97     1      8.00e+00 1.56e-02 2.71e+01
  dihedral pdb=" C3'   U B   6 "
           pdb=" C4'   U B   6 "
           pdb=" O4'   U B   6 "
           pdb=" C1'   U B   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -2.00   30.64  -32.64     1      8.00e+00 1.56e-02 2.37e+01
  ... (remaining 5828 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.105: 1359
       0.105 -    0.211: 135
       0.211 -    0.316: 15
       0.316 -    0.422: 4
       0.422 -    0.527: 2
  Chirality restraints: 1515
  Sorted by residual:
  chirality pdb=" P     U B   1 "
            pdb=" OP1   U B   1 "
            pdb=" OP2   U B   1 "
            pdb=" O5'   U B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    2.94   -0.53 2.00e-01 2.50e+01 6.94e+00
  chirality pdb=" P     G B   3 "
            pdb=" OP1   G B   3 "
            pdb=" OP2   G B   3 "
            pdb=" O5'   G B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.87   -0.46 2.00e-01 2.50e+01 5.27e+00
  chirality pdb=" P     A B   4 "
            pdb=" OP1   A B   4 "
            pdb=" OP2   A B   4 "
            pdb=" O5'   A B   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.80   -0.39 2.00e-01 2.50e+01 3.78e+00
  ... (remaining 1512 not shown)

  Planarity restraints: 1490
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C  18 "    0.144 2.00e-02 2.50e+03   6.32e-02 1.10e+02
        pdb=" N9    A C  18 "   -0.020 2.00e-02 2.50e+03
        pdb=" C8    A C  18 "   -0.091 2.00e-02 2.50e+03
        pdb=" N7    A C  18 "   -0.036 2.00e-02 2.50e+03
        pdb=" C5    A C  18 "    0.006 2.00e-02 2.50e+03
        pdb=" C6    A C  18 "    0.032 2.00e-02 2.50e+03
        pdb=" N6    A C  18 "    0.085 2.00e-02 2.50e+03
        pdb=" N1    A C  18 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A C  18 "   -0.045 2.00e-02 2.50e+03
        pdb=" N3    A C  18 "   -0.048 2.00e-02 2.50e+03
        pdb=" C4    A C  18 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 245 "    0.095 2.00e-02 2.50e+03   5.86e-02 6.88e+01
        pdb=" CG  TYR A 245 "    0.001 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 245 "   -0.064 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 245 "   -0.045 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 245 "   -0.030 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 245 "   -0.051 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 245 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 245 "    0.094 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 199 "    0.094 2.00e-02 2.50e+03   5.56e-02 6.19e+01
        pdb=" CG  TYR A 199 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 199 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 199 "   -0.049 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 199 "   -0.042 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 199 "   -0.031 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 199 "   -0.015 2.00e-02 2.50e+03
        pdb=" OH  TYR A 199 "    0.095 2.00e-02 2.50e+03
  ... (remaining 1487 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.51: 45
        2.51 -     3.11: 6753
        3.11 -     3.71: 14782
        3.71 -     4.30: 19700
        4.30 -     4.90: 31547
  Nonbonded interactions: 72827
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 612 "
            pdb=" OD2 ASP F 283 "
     model   vdw
     1.916 3.120
  nonbonded pdb=" O3'   G C  15 "
            pdb="MG    MG C 101 "
     model   vdw
     2.041 2.170
  nonbonded pdb=" OP1   U C  16 "
            pdb="MG    MG C 101 "
     model   vdw
     2.111 2.170
  nonbonded pdb=" OD1 ASP A 740 "
            pdb="MG    MG C 101 "
     model   vdw
     2.157 2.170
  nonbonded pdb=" OG1 THR A 516 "
            pdb=" OG  SER A 861 "
     model   vdw
     2.244 3.040
  ... (remaining 72822 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:             2.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.220
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048   9521  Z= 0.432
  Angle     :  1.199  11.634  13107  Z= 0.754
  Chirality :  0.068   0.527   1515
  Planarity :  0.010   0.108   1490
  Dihedral  : 16.584 139.317   3901
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.73 %
    Favored  : 97.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.21 (0.25), residues: 995
  helix: -0.27 (0.27), residues: 340
  sheet: -0.80 (0.39), residues: 169
  loop : -1.11 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 301 
 TYR   0.096   0.013   TYR A 271 
 PHE   0.071   0.008   PHE A 898 
 TRP   0.071   0.006   TRP A 477 
 HIS   0.010   0.002   HIS A 874 

Details of bonding type rmsd
  covalent geometry    : bond        0.00746 ( 9521)
  covalent geometry    : angle       1.19881 (13107)
  hydrogen bonds       : bond        0.20048 (  365)
  hydrogen bonds       : angle       7.07153 ( 1017)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 193
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 LYS cc_start: 0.9074 (ttpt) cc_final: 0.8791 (mttp)
REVERT: A  265 GLN cc_start: 0.7269 (tm-30) cc_final: 0.6960 (tm-30)
REVERT: A  267 MET cc_start: 0.8447 (mmm) cc_final: 0.7828 (mmm)
REVERT: A  381 GLU cc_start: 0.8429 (tt0) cc_final: 0.7735 (mt-10)
REVERT: A  412 LEU cc_start: 0.8027 (mm) cc_final: 0.7733 (mm)
REVERT: A  563 MET cc_start: 0.6960 (mtt) cc_final: 0.6703 (mtt)
REVERT: A  641 LYS cc_start: 0.7355 (mtpt) cc_final: 0.7147 (tppt)
REVERT: A  871 GLN cc_start: 0.7796 (mm110) cc_final: 0.7516 (mm110)
REVERT: A  897 TYR cc_start: 0.7623 (p90) cc_final: 0.7182 (p90)
REVERT: F  215 MET cc_start: 0.7039 (mpp) cc_final: 0.5993 (mpp)
REVERT: F  303 THR cc_start: 0.8681 (p) cc_final: 0.8406 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 194
  average time/residue: 0.0793
  time to fit residues: 21.7577
Evaluate side-chains
  149 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 249 GLN
A 297 GLN
A 388 ASN
** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 197 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.123408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.103107 restraints weight = 20740.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.106490 restraints weight = 11379.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.107216 restraints weight = 7025.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.107497 restraints weight = 5728.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.107596 restraints weight = 5292.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.1425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9521  Z= 0.166
  Angle     :  0.644   9.772  13107  Z= 0.338
  Chirality :  0.044   0.244   1515
  Planarity :  0.005   0.067   1490
  Dihedral  : 15.260 141.626   1846
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  3.71 %
    Favored  : 95.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.90 (0.27), residues: 995
  helix:  0.03 (0.27), residues: 358
  sheet: -0.70 (0.39), residues: 192
  loop : -0.95 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 865 
 TYR   0.025   0.002   TYR A 872 
 PHE   0.015   0.002   PHE A 464 
 TRP   0.009   0.002   TRP A 533 
 HIS   0.008   0.001   HIS E 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 9521)
  covalent geometry    : angle       0.64361 (13107)
  hydrogen bonds       : bond        0.05228 (  365)
  hydrogen bonds       : angle       5.25580 ( 1017)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 178
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 LYS cc_start: 0.9172 (ttpt) cc_final: 0.8870 (mttp)
REVERT: A  265 GLN cc_start: 0.7009 (tm-30) cc_final: 0.6626 (tm-30)
REVERT: A  267 MET cc_start: 0.8359 (mmm) cc_final: 0.7851 (mmm)
REVERT: A  337 PHE cc_start: 0.7964 (t80) cc_final: 0.7711 (t80)
REVERT: A  412 LEU cc_start: 0.7865 (mm) cc_final: 0.7628 (mm)
REVERT: A  641 LYS cc_start: 0.7377 (mtpt) cc_final: 0.7079 (tppt)
REVERT: F  101 GLN cc_start: 0.8053 (pm20) cc_final: 0.7817 (pm20)
REVERT: F  215 MET cc_start: 0.6810 (mpp) cc_final: 0.5855 (mpp)
REVERT: F  303 THR cc_start: 0.8689 (p) cc_final: 0.8365 (p)
  outliers start: 3
  outliers final: 0
  residues processed: 179
  average time/residue: 0.0674
  time to fit residues: 17.5373
Evaluate side-chains
  141 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    6.9990
   chunk 75 optimal weight:   10.0000
   chunk 60 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   chunk 4 optimal weight:    6.9990
   chunk 41 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 99 optimal weight:    0.0870
   chunk 61 optimal weight:    0.9990
   chunk 81 optimal weight:    9.9990
   chunk 91 optimal weight:    4.9990
   overall best weight:    2.8166

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

Flipped N/Q/H residues before XYZ refinement:
A 388 ASN
** A 863 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 = 0.3713 r_free = 0.3713 target = 0.118042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.098693 restraints weight = 21076.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.100944 restraints weight = 11624.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.102006 restraints weight = 7674.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.102410 restraints weight = 5751.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.102627 restraints weight = 5548.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   9521  Z= 0.260
  Angle     :  0.707  10.538  13107  Z= 0.371
  Chirality :  0.046   0.220   1515
  Planarity :  0.005   0.058   1490
  Dihedral  : 15.290 143.898   1846
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 15.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.84 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.80 %
    Favored  : 95.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.24 (0.26), residues: 995
  helix: -0.30 (0.26), residues: 359
  sheet: -1.21 (0.37), residues: 196
  loop : -0.92 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 606 
 TYR   0.025   0.002   TYR A 697 
 PHE   0.027   0.002   PHE F 267 
 TRP   0.045   0.003   TRP A 533 
 HIS   0.006   0.001   HIS A 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00584 ( 9521)
  covalent geometry    : angle       0.70688 (13107)
  hydrogen bonds       : bond        0.05581 (  365)
  hydrogen bonds       : angle       5.31142 ( 1017)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 166
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 THR cc_start: 0.7838 (m) cc_final: 0.7554 (p)
REVERT: A  265 GLN cc_start: 0.7224 (tm-30) cc_final: 0.6214 (tm-30)
REVERT: A  412 LEU cc_start: 0.7873 (mm) cc_final: 0.7556 (mm)
REVERT: A  455 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8103 (mm-30)
REVERT: A  541 GLN cc_start: 0.9247 (mp10) cc_final: 0.8763 (mp10)
REVERT: A  641 LYS cc_start: 0.7259 (mtpt) cc_final: 0.6839 (tppt)
REVERT: A  837 ASP cc_start: 0.8651 (t0) cc_final: 0.8395 (t0)
REVERT: A  872 TYR cc_start: 0.8231 (m-10) cc_final: 0.7925 (m-10)
REVERT: F  215 MET cc_start: 0.7003 (mpp) cc_final: 0.5999 (mpp)
REVERT: F  303 THR cc_start: 0.8827 (p) cc_final: 0.8527 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 166
  average time/residue: 0.0713
  time to fit residues: 17.3149
Evaluate side-chains
  130 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   chunk 42 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 95 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 98 optimal weight:    0.3980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
E 121 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.122721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.103061 restraints weight = 20918.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.105861 restraints weight = 11368.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.106772 restraints weight = 7350.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.107237 restraints weight = 5418.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.107537 restraints weight = 5172.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9521  Z= 0.127
  Angle     :  0.604   8.810  13107  Z= 0.313
  Chirality :  0.044   0.237   1515
  Planarity :  0.004   0.051   1490
  Dihedral  : 15.360 143.793   1846
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.18 %
    Favored  : 97.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.27), residues: 995
  helix: -0.00 (0.27), residues: 358
  sheet: -0.88 (0.38), residues: 196
  loop : -0.84 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 812 
 TYR   0.017   0.001   TYR A 603 
 PHE   0.019   0.001   PHE A 337 
 TRP   0.021   0.002   TRP A 533 
 HIS   0.005   0.001   HIS F 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9521)
  covalent geometry    : angle       0.60355 (13107)
  hydrogen bonds       : bond        0.04172 (  365)
  hydrogen bonds       : angle       4.89445 ( 1017)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 175
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 GLN cc_start: 0.7198 (tm-30) cc_final: 0.6737 (tm-30)
REVERT: A  455 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7997 (mm-30)
REVERT: A  518 ASP cc_start: 0.7886 (p0) cc_final: 0.7672 (p0)
REVERT: A  541 GLN cc_start: 0.9235 (mp10) cc_final: 0.8768 (mp10)
REVERT: A  563 MET cc_start: 0.6717 (mtt) cc_final: 0.6461 (mtt)
REVERT: A  636 MET cc_start: 0.6680 (ppp) cc_final: 0.5284 (mtt)
REVERT: A  871 GLN cc_start: 0.8012 (mm110) cc_final: 0.7770 (mm110)
REVERT: A  872 TYR cc_start: 0.8033 (m-10) cc_final: 0.7689 (m-10)
REVERT: F  101 GLN cc_start: 0.8089 (pm20) cc_final: 0.7869 (pm20)
REVERT: F  181 MET cc_start: 0.7820 (mmt) cc_final: 0.7491 (mmm)
REVERT: F  215 MET cc_start: 0.6949 (mpp) cc_final: 0.6047 (mpp)
REVERT: F  303 THR cc_start: 0.8651 (p) cc_final: 0.8323 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 175
  average time/residue: 0.0702
  time to fit residues: 17.2962
Evaluate side-chains
  144 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 77 optimal weight:    9.9990
   chunk 91 optimal weight:    7.9990
   chunk 66 optimal weight:    0.0030
   chunk 27 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.6990

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

Flipped N/Q/H residues before XYZ refinement:
E 121 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.123636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.103657 restraints weight = 20654.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.106752 restraints weight = 11007.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.107917 restraints weight = 6738.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.108360 restraints weight = 5292.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.108575 restraints weight = 4880.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.2512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9521  Z= 0.121
  Angle     :  0.584   7.793  13107  Z= 0.300
  Chirality :  0.043   0.217   1515
  Planarity :  0.004   0.047   1490
  Dihedral  : 15.318 143.944   1846
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.27), residues: 995
  helix:  0.15 (0.27), residues: 359
  sheet: -0.67 (0.39), residues: 196
  loop : -0.77 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 292 
 TYR   0.017   0.001   TYR A 207 
 PHE   0.015   0.001   PHE F 267 
 TRP   0.017   0.002   TRP A 533 
 HIS   0.003   0.001   HIS A 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 9521)
  covalent geometry    : angle       0.58394 (13107)
  hydrogen bonds       : bond        0.03909 (  365)
  hydrogen bonds       : angle       4.72847 ( 1017)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 GLN cc_start: 0.7166 (tm-30) cc_final: 0.6199 (tm-30)
REVERT: A  267 MET cc_start: 0.8229 (mmm) cc_final: 0.7301 (mmm)
REVERT: A  455 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8000 (mm-30)
REVERT: A  603 TYR cc_start: 0.6962 (m-10) cc_final: 0.6471 (m-10)
REVERT: A  636 MET cc_start: 0.6325 (ppp) cc_final: 0.5031 (mtt)
REVERT: A  695 GLN cc_start: 0.8128 (pt0) cc_final: 0.7792 (pm20)
REVERT: A  764 GLU cc_start: 0.8834 (pp20) cc_final: 0.8628 (pp20)
REVERT: A  871 GLN cc_start: 0.7857 (mm110) cc_final: 0.7610 (mm110)
REVERT: A  872 TYR cc_start: 0.7893 (m-10) cc_final: 0.7647 (m-10)
REVERT: F  101 GLN cc_start: 0.8246 (pm20) cc_final: 0.8025 (pm20)
REVERT: F  181 MET cc_start: 0.7928 (mmt) cc_final: 0.7642 (mmm)
REVERT: F  215 MET cc_start: 0.6932 (mpp) cc_final: 0.5919 (mpp)
REVERT: F  303 THR cc_start: 0.8637 (p) cc_final: 0.8331 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.0649
  time to fit residues: 16.6098
Evaluate side-chains
  138 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 76 optimal weight:    6.9990
   chunk 32 optimal weight:    0.5980
   chunk 100 optimal weight:    3.9990
   chunk 98 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   chunk 39 optimal weight:    4.9990
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 445 HIS
** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 121 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.118943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.099505 restraints weight = 21230.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.102327 restraints weight = 11304.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.103480 restraints weight = 7059.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.103832 restraints weight = 5561.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.103971 restraints weight = 5063.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.2822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9521  Z= 0.221
  Angle     :  0.672  11.973  13107  Z= 0.348
  Chirality :  0.045   0.216   1515
  Planarity :  0.005   0.044   1490
  Dihedral  : 15.297 144.985   1846
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.05 (0.27), residues: 995
  helix: -0.03 (0.27), residues: 358
  sheet: -1.14 (0.38), residues: 198
  loop : -0.90 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 292 
 TYR   0.014   0.002   TYR A 245 
 PHE   0.017   0.002   PHE A 787 
 TRP   0.021   0.002   TRP A 533 
 HIS   0.013   0.001   HIS A 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 9521)
  covalent geometry    : angle       0.67210 (13107)
  hydrogen bonds       : bond        0.04837 (  365)
  hydrogen bonds       : angle       5.00615 ( 1017)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 GLN cc_start: 0.7268 (tm-30) cc_final: 0.6230 (tm-30)
REVERT: A  381 GLU cc_start: 0.8388 (tt0) cc_final: 0.7928 (pt0)
REVERT: A  455 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8107 (mm-30)
REVERT: A  603 TYR cc_start: 0.7368 (m-10) cc_final: 0.6895 (m-10)
REVERT: A  764 GLU cc_start: 0.8914 (pp20) cc_final: 0.8688 (pp20)
REVERT: A  837 ASP cc_start: 0.8665 (t0) cc_final: 0.8407 (t0)
REVERT: A  871 GLN cc_start: 0.8173 (mm110) cc_final: 0.7881 (mm-40)
REVERT: A  872 TYR cc_start: 0.8111 (m-80) cc_final: 0.7748 (m-10)
REVERT: F  101 GLN cc_start: 0.8305 (pm20) cc_final: 0.8061 (pm20)
REVERT: F  181 MET cc_start: 0.8050 (mmt) cc_final: 0.7811 (mmm)
REVERT: F  215 MET cc_start: 0.7069 (mpp) cc_final: 0.6095 (mpp)
REVERT: F  303 THR cc_start: 0.8693 (p) cc_final: 0.8385 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.0708
  time to fit residues: 16.0586
Evaluate side-chains
  131 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 67 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 54 optimal weight:    0.3980
   chunk 89 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 81 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 445 HIS
A 500 GLN
A 712 HIS
** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 121 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.121365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.101858 restraints weight = 20877.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.104970 restraints weight = 10943.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.106104 restraints weight = 6565.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.106508 restraints weight = 5218.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.106722 restraints weight = 4747.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.2891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9521  Z= 0.136
  Angle     :  0.612   9.827  13107  Z= 0.315
  Chirality :  0.044   0.236   1515
  Planarity :  0.004   0.044   1490
  Dihedral  : 15.299 144.935   1846
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.27), residues: 995
  helix:  0.08 (0.27), residues: 359
  sheet: -1.03 (0.38), residues: 203
  loop : -0.82 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 292 
 TYR   0.009   0.001   TYR A 245 
 PHE   0.020   0.001   PHE A 337 
 TRP   0.019   0.002   TRP A 533 
 HIS   0.011   0.001   HIS A 445 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 9521)
  covalent geometry    : angle       0.61249 (13107)
  hydrogen bonds       : bond        0.04008 (  365)
  hydrogen bonds       : angle       4.78752 ( 1017)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 THR cc_start: 0.7209 (t) cc_final: 0.6775 (m)
REVERT: A  265 GLN cc_start: 0.7284 (tm-30) cc_final: 0.6292 (tm-30)
REVERT: A  381 GLU cc_start: 0.8346 (tt0) cc_final: 0.7931 (pt0)
REVERT: A  455 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8044 (mm-30)
REVERT: A  563 MET cc_start: 0.6972 (mtt) cc_final: 0.6514 (mtt)
REVERT: A  584 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7589 (mm-30)
REVERT: A  603 TYR cc_start: 0.7198 (m-10) cc_final: 0.6730 (m-10)
REVERT: A  636 MET cc_start: 0.6729 (ppp) cc_final: 0.5107 (mtt)
REVERT: A  695 GLN cc_start: 0.8148 (pt0) cc_final: 0.7865 (pm20)
REVERT: A  764 GLU cc_start: 0.8904 (pp20) cc_final: 0.8684 (pp20)
REVERT: A  872 TYR cc_start: 0.8022 (m-80) cc_final: 0.7721 (m-10)
REVERT: F  101 GLN cc_start: 0.8322 (pm20) cc_final: 0.8110 (pm20)
REVERT: F  215 MET cc_start: 0.6945 (mpp) cc_final: 0.5828 (mpp)
REVERT: F  303 THR cc_start: 0.8578 (p) cc_final: 0.8233 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.0671
  time to fit residues: 16.1425
Evaluate side-chains
  136 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 85 optimal weight:    5.9990
   chunk 101 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0370
   chunk 49 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 51 optimal weight:    0.2980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
A 425 GLN
A 500 GLN
E 121 HIS
F 227 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.123760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.104103 restraints weight = 20464.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.107148 restraints weight = 10875.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.108200 restraints weight = 6261.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.108354 restraints weight = 5468.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.108676 restraints weight = 5138.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.3023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9521  Z= 0.117
  Angle     :  0.598   8.724  13107  Z= 0.307
  Chirality :  0.043   0.214   1515
  Planarity :  0.004   0.043   1490
  Dihedral  : 15.273 144.983   1846
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.27), residues: 995
  helix:  0.14 (0.27), residues: 359
  sheet: -0.87 (0.37), residues: 208
  loop : -0.77 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 223 
 TYR   0.011   0.001   TYR A 245 
 PHE   0.022   0.001   PHE A 337 
 TRP   0.055   0.003   TRP A 533 
 HIS   0.004   0.001   HIS A 445 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 9521)
  covalent geometry    : angle       0.59793 (13107)
  hydrogen bonds       : bond        0.03826 (  365)
  hydrogen bonds       : angle       4.64072 ( 1017)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 GLN cc_start: 0.7255 (tm-30) cc_final: 0.6784 (tm-30)
REVERT: A  267 MET cc_start: 0.8194 (mmm) cc_final: 0.7736 (mmm)
REVERT: A  381 GLU cc_start: 0.8356 (tt0) cc_final: 0.7923 (pt0)
REVERT: A  455 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8004 (mm-30)
REVERT: A  563 MET cc_start: 0.6960 (mtt) cc_final: 0.6731 (mtt)
REVERT: A  603 TYR cc_start: 0.7023 (m-10) cc_final: 0.6684 (m-10)
REVERT: A  636 MET cc_start: 0.6133 (ppp) cc_final: 0.4859 (mtt)
REVERT: A  695 GLN cc_start: 0.8166 (pt0) cc_final: 0.7931 (pm20)
REVERT: A  872 TYR cc_start: 0.7907 (m-80) cc_final: 0.7629 (m-10)
REVERT: F  101 GLN cc_start: 0.8329 (pm20) cc_final: 0.8127 (pm20)
REVERT: F  167 MET cc_start: 0.8222 (tpt) cc_final: 0.7180 (tpt)
REVERT: F  215 MET cc_start: 0.6938 (mpp) cc_final: 0.5883 (mpp)
REVERT: F  303 THR cc_start: 0.8474 (p) cc_final: 0.8148 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.0687
  time to fit residues: 17.8317
Evaluate side-chains
  134 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 99 optimal weight:    0.0270
   chunk 33 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 86 optimal weight:    6.9990
   chunk 3 optimal weight:    0.1980
   chunk 28 optimal weight:    5.9990
   overall best weight:    0.8242

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

Flipped N/Q/H residues before XYZ refinement:
A 712 HIS
E 121 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.123265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.103912 restraints weight = 20347.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.107109 restraints weight = 10545.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.108139 restraints weight = 6008.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.108328 restraints weight = 5096.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.108518 restraints weight = 4842.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.3130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9521  Z= 0.124
  Angle     :  0.592   8.953  13107  Z= 0.305
  Chirality :  0.043   0.213   1515
  Planarity :  0.004   0.046   1490
  Dihedral  : 15.223 145.484   1846
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.27), residues: 995
  helix:  0.13 (0.27), residues: 359
  sheet: -0.85 (0.37), residues: 209
  loop : -0.77 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 223 
 TYR   0.010   0.001   TYR A 245 
 PHE   0.021   0.001   PHE A 337 
 TRP   0.025   0.002   TRP A 533 
 HIS   0.003   0.001   HIS A 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9521)
  covalent geometry    : angle       0.59200 (13107)
  hydrogen bonds       : bond        0.03802 (  365)
  hydrogen bonds       : angle       4.58966 ( 1017)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 GLN cc_start: 0.7356 (tm-30) cc_final: 0.6841 (tm-30)
REVERT: A  266 LEU cc_start: 0.8462 (pp) cc_final: 0.8072 (pp)
REVERT: A  267 MET cc_start: 0.8203 (mmm) cc_final: 0.7770 (mmm)
REVERT: A  381 GLU cc_start: 0.8363 (tt0) cc_final: 0.7997 (pt0)
REVERT: A  455 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7991 (mm-30)
REVERT: A  636 MET cc_start: 0.6330 (ppp) cc_final: 0.4933 (mtt)
REVERT: A  872 TYR cc_start: 0.7921 (m-80) cc_final: 0.7614 (m-10)
REVERT: F  101 GLN cc_start: 0.8315 (pm20) cc_final: 0.8098 (pm20)
REVERT: F  215 MET cc_start: 0.6972 (mpp) cc_final: 0.5852 (mpp)
REVERT: F  303 THR cc_start: 0.8538 (p) cc_final: 0.8206 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.0728
  time to fit residues: 17.3331
Evaluate side-chains
  138 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 82 optimal weight:    8.9990
   chunk 53 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   chunk 75 optimal weight:   10.0000
   chunk 98 optimal weight:    9.9990
   chunk 73 optimal weight:    6.9990
   chunk 94 optimal weight:    0.0770
   chunk 68 optimal weight:    4.9990
   chunk 20 optimal weight:    4.9990
   chunk 95 optimal weight:    0.7980
   overall best weight:    2.3342

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

Flipped N/Q/H residues before XYZ refinement:
A 388 ASN
E 121 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.118517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.099130 restraints weight = 21268.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.101989 restraints weight = 11407.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.103130 restraints weight = 7025.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.103456 restraints weight = 5557.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.103569 restraints weight = 5096.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.3334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9521  Z= 0.226
  Angle     :  0.692   7.396  13107  Z= 0.360
  Chirality :  0.046   0.213   1515
  Planarity :  0.005   0.043   1490
  Dihedral  : 15.286 146.453   1846
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 15.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.26 (0.26), residues: 995
  helix: -0.19 (0.27), residues: 357
  sheet: -1.32 (0.36), residues: 207
  loop : -0.98 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 562 
 TYR   0.026   0.002   TYR A 603 
 PHE   0.017   0.002   PHE A 787 
 TRP   0.032   0.002   TRP A 533 
 HIS   0.006   0.001   HIS A 445 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 ( 9521)
  covalent geometry    : angle       0.69193 (13107)
  hydrogen bonds       : bond        0.04830 (  365)
  hydrogen bonds       : angle       4.98236 ( 1017)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 GLN cc_start: 0.7300 (tm-30) cc_final: 0.6202 (tm-30)
REVERT: A  266 LEU cc_start: 0.8498 (pp) cc_final: 0.7932 (pp)
REVERT: A  381 GLU cc_start: 0.8417 (tt0) cc_final: 0.7915 (pt0)
REVERT: A  455 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8087 (mm-30)
REVERT: A  617 ASP cc_start: 0.8379 (m-30) cc_final: 0.8032 (m-30)
REVERT: A  636 MET cc_start: 0.6877 (ppp) cc_final: 0.5350 (mtt)
REVERT: A  764 GLU cc_start: 0.8841 (pp20) cc_final: 0.8636 (pp20)
REVERT: A  837 ASP cc_start: 0.8667 (t0) cc_final: 0.8386 (t0)
REVERT: A  872 TYR cc_start: 0.8113 (m-80) cc_final: 0.7742 (m-10)
REVERT: F  215 MET cc_start: 0.7074 (mpp) cc_final: 0.5819 (mpp)
REVERT: F  303 THR cc_start: 0.8699 (p) cc_final: 0.8388 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.0712
  time to fit residues: 16.4371
Evaluate side-chains
  128 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 94 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   chunk 78 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0670
   chunk 99 optimal weight:    0.0670
   chunk 52 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
E 121 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.124115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.104355 restraints weight = 20538.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.107209 restraints weight = 11144.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.108271 restraints weight = 7140.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.108610 restraints weight = 5634.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.109156 restraints weight = 5201.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.3353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9521  Z= 0.124
  Angle     :  0.626   8.623  13107  Z= 0.321
  Chirality :  0.044   0.211   1515
  Planarity :  0.004   0.044   1490
  Dihedral  : 15.284 146.157   1846
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.27), residues: 995
  helix:  0.01 (0.27), residues: 357
  sheet: -0.91 (0.37), residues: 206
  loop : -0.95 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 433 
 TYR   0.028   0.001   TYR A 603 
 PHE   0.025   0.001   PHE A 337 
 TRP   0.027   0.002   TRP A 533 
 HIS   0.005   0.001   HIS A 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9521)
  covalent geometry    : angle       0.62553 (13107)
  hydrogen bonds       : bond        0.03962 (  365)
  hydrogen bonds       : angle       4.71626 ( 1017)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1120.43 seconds
wall clock time: 20 minutes 16.25 seconds (1216.25 seconds total)