Starting phenix.real_space_refine
on Wed Mar 12 19:13:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dtt_47165/03_2025/9dtt_47165.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dtt_47165/03_2025/9dtt_47165.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dtt_47165/03_2025/9dtt_47165.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dtt_47165/03_2025/9dtt_47165.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dtt_47165/03_2025/9dtt_47165.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dtt_47165/03_2025/9dtt_47165.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.034
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P      66      5.49       5
     S      47      5.16       5
     C    4940      2.51       5
     N    1489      2.21       5
     O    1730      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8274
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 850, 6844
          Classifications: {'peptide': 850}
          Link IDs: {'PTRANS': 31, 'TRANS': 818}
          Chain breaks: 10
    Chain: "B"
      Number of atoms: 1428
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 67, 1428
          Classifications: {'RNA': 67}
          Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 30, 'rna3p_pyr': 26}
          Link IDs: {'rna2p': 11, 'rna3p': 55}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   3387  SG  CYS A 447      38.079  31.174  14.910  1.00 65.84           S
  ATOM   3409  SG  CYS A 450      35.736  32.847  18.002  1.00 59.79           S
  ATOM   5557  SG  CYS A 728      39.612  35.472  62.904  1.00 82.32           S
  ATOM   6542  SG  CYS A 847      42.380  37.452  64.857  1.00 89.41           S

  Time building chain proxies: 5.60, per 1000 atoms: 0.68
  Number of scatterers: 8274
  At special positions: 0
  Unit cell: (84.724, 102.674, 119.906, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      47     16.00
     P      66     15.00
     O    1730      8.00
     N    1489      7.00
     C    4940      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: 2.17
  Conformation dependent library (CDL) restraints added in 850.8 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1001 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 450 "
        pdb="ZN    ZN A1001 " - pdb=" NE2 HIS A 442 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 447 "
      pdb="  ZN A1002 "
        pdb="ZN    ZN A1002 " - pdb=" NE2 HIS A 714 "
        pdb="ZN    ZN A1002 " - pdb=" NE2 HIS A 712 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 847 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 728 "
      Number of angles added : 2


  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1566

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 7 sheets defined
      48.7% alpha, 8.9% beta
      16 base pairs and 30 stacking pairs defined.
    Time for finding SS restraints: 3.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 18
    Processing helix  chain 'A' and resid 21 through 30
      removed outlier: 4.012A  pdb=" N   LYS A  30 " --> pdb=" O   GLN A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 48
      removed outlier: 3.730A  pdb=" N   GLU A  43 " --> pdb=" O   THR A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 68
      removed outlier: 3.914A  pdb=" N   LYS A  61 " --> pdb=" O   ARG A  57 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ARG A  68 " --> pdb=" O   TRP A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 93
      removed outlier: 3.982A  pdb=" N   GLY A  93 " --> pdb=" O   TYR A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 135
      removed outlier: 3.534A  pdb=" N   THR A 135 " --> pdb=" O   VAL A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 169
      removed outlier: 3.779A  pdb=" N   GLU A 157 " --> pdb=" O   ASN A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 199
    Processing helix  chain 'A' and resid 228 through 242
    Processing helix  chain 'A' and resid 273 through 289
      removed outlier: 4.082A  pdb=" N   ILE A 277 " --> pdb=" O   ASN A 273 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   LYS A 279 " --> pdb=" O   ASP A 275 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   ARG A 280 " --> pdb=" O   ILE A 276 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLU A 287 " --> pdb=" O   LYS A 283 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   HIS A 288 " --> pdb=" O   ILE A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 328
      removed outlier: 3.864A  pdb=" N   LEU A 328 " --> pdb=" O   VAL A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 333
    Processing helix  chain 'A' and resid 335 through 343
      removed outlier: 3.540A  pdb=" N   THR A 339 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 358
    Processing helix  chain 'A' and resid 367 through 386
    Processing helix  chain 'A' and resid 395 through 402
      removed outlier: 4.099A  pdb=" N   PHE A 399 " --> pdb=" O   THR A 395 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   THR A 400 " --> pdb=" O   ARG A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 429
      removed outlier: 3.573A  pdb=" N   ALA A 425 " --> pdb=" O   SER A 421 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   VAL A 426 " --> pdb=" O   ALA A 422 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLU A 427 " --> pdb=" O   ARG A 423 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   SER A 429 " --> pdb=" O   ALA A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 442
      removed outlier: 4.338A  pdb=" N   GLU A 433 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   LYS A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   GLU A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 445
      No H-bonds generated for 'chain 'A' and resid 443 through 445'
    Processing helix  chain 'A' and resid 478 through 490
      removed outlier: 3.520A  pdb=" N   LEU A 484 " --> pdb=" O   GLY A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 496
      removed outlier: 3.647A  pdb=" N   HIS A 496 " --> pdb=" O   LEU A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 525
      removed outlier: 3.638A  pdb=" N   SER A 523 " --> pdb=" O   LEU A 519 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   LYS A 524 " --> pdb=" O   ARG A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 548
      removed outlier: 3.811A  pdb=" N   LEU A 547 " --> pdb=" O   THR A 543 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LYS A 548 " --> pdb=" O   LEU A 544 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 543 through 548'
    Processing helix  chain 'A' and resid 549 through 556
      removed outlier: 3.558A  pdb=" N   HIS A 556 " --> pdb=" O   VAL A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 558 through 572
    Processing helix  chain 'A' and resid 605 through 627
      removed outlier: 3.603A  pdb=" N   LEU A 609 " --> pdb=" O   GLY A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 657
      removed outlier: 6.547A  pdb=" N   ARG A 652 " --> pdb=" O   ALA A 648 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   GLU A 653 " --> pdb=" O   ARG A 649 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ARG A 657 " --> pdb=" O   GLU A 653 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 684
      removed outlier: 3.607A  pdb=" N   MET A 684 " --> pdb=" O   ALA A 680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 702 through 706
      removed outlier: 3.735A  pdb=" N   GLN A 705 " --> pdb=" O   ASP A 702 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   VAL A 706 " --> pdb=" O   TRP A 703 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 702 through 706'
    Processing helix  chain 'A' and resid 730 through 739
    Processing helix  chain 'A' and resid 748 through 766
    Processing helix  chain 'A' and resid 770 through 783
    Processing helix  chain 'A' and resid 801 through 805
      removed outlier: 3.790A  pdb=" N   MET A 804 " --> pdb=" O   HIS A 801 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   THR A 805 " --> pdb=" O   GLU A 802 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 801 through 805'
    Processing helix  chain 'A' and resid 808 through 818
    Processing helix  chain 'A' and resid 840 through 847
    Processing helix  chain 'A' and resid 853 through 862
    Processing helix  chain 'A' and resid 862 through 875
    Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36
      removed outlier: 3.533A  pdb=" N   GLU A  35 " --> pdb=" O   THR A 251 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 126
      removed outlier: 6.123A  pdb=" N   GLY A  75 " --> pdb=" O   VAL A  97 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLU A  99 " --> pdb=" O   GLY A  75 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   LEU A 103 " --> pdb=" O   ASP A  79 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   LEU A 143 " --> pdb=" O   CYS A 179 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N   LYS A 181 " --> pdb=" O   LEU A 143 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   CYS A 145 " --> pdb=" O   LYS A 181 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ILE A 180 " --> pdb=" O   TRP A 220 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 304 through 311
      removed outlier: 6.575A  pdb=" N   TYR A 305 " --> pdb=" O   SER A 594 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   SER A 594 " --> pdb=" O   TYR A 305 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   GLY A 307 " --> pdb=" O   ILE A 592 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   THR A 588 " --> pdb=" O   THR A 311 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 320 through 321
    Processing sheet with id=AA5, first strand: chain 'A' and resid 659 through 661
      removed outlier: 4.243A  pdb=" N   CYS A 665 " --> pdb=" O   ASP A 533 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ASP A 533 " --> pdb=" O   CYS A 665 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 535 through 536
      removed outlier: 4.235A  pdb=" N   VAL A 687 " --> pdb=" O   ALA A 536 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 712 through 717

    281 hydrogen bonds defined for protein.
    792 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      39 hydrogen bonds
      74 hydrogen bond angles
      0 basepair planarities
      16 basepair parallelities
      30 stacking parallelities
  Total time for adding SS restraints: 2.95

  Time building geometry restraints manager: 2.51 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2432
        1.34 -     1.46: 1812
        1.46 -     1.57: 4132
        1.57 -     1.69: 132
        1.69 -     1.81: 80
  Bond restraints: 8588
  Sorted by residual:
  bond pdb=" C3'   G B  40 "
       pdb=" O3'   G B  40 "
    ideal  model  delta    sigma   weight residual
    1.417  1.431 -0.014 1.50e-02 4.44e+03 8.78e-01
  bond pdb=" CE2 PHE A 178 "
       pdb=" CZ  PHE A 178 "
    ideal  model  delta    sigma   weight residual
    1.382  1.359  0.023 3.00e-02 1.11e+03 5.95e-01
  bond pdb=" CA  ARG A 404 "
       pdb=" C   ARG A 404 "
    ideal  model  delta    sigma   weight residual
    1.523  1.532 -0.009 1.34e-02 5.57e+03 4.48e-01
  bond pdb=" C   ASN A 227 "
       pdb=" N   ILE A 228 "
    ideal  model  delta    sigma   weight residual
    1.338  1.332  0.006 1.01e-02 9.80e+03 3.66e-01
  bond pdb=" O3'   U B  12 "
       pdb=" P     A B  13 "
    ideal  model  delta    sigma   weight residual
    1.607  1.616 -0.009 1.50e-02 4.44e+03 3.64e-01
  ... (remaining 8583 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.34: 11632
        1.34 -     2.68: 231
        2.68 -     4.02: 40
        4.02 -     5.36: 9
        5.36 -     6.71: 3
  Bond angle restraints: 11915
  Sorted by residual:
  angle pdb=" O3'   G B  40 "
        pdb=" C3'   G B  40 "
        pdb=" C2'   G B  40 "
      ideal   model   delta    sigma   weight residual
     113.70  118.03   -4.33 1.50e+00 4.44e-01 8.32e+00
  angle pdb=" C3'   G B  40 "
        pdb=" O3'   G B  40 "
        pdb=" P     A B  41 "
      ideal   model   delta    sigma   weight residual
     120.20  124.25   -4.05 1.50e+00 4.44e-01 7.28e+00
  angle pdb=" C   GLU A 357 "
        pdb=" N   LYS A 358 "
        pdb=" CA  LYS A 358 "
      ideal   model   delta    sigma   weight residual
     122.15  115.66    6.49 2.83e+00 1.25e-01 5.26e+00
  angle pdb=" C   ASP A 597 "
        pdb=" N   GLN A 598 "
        pdb=" CA  GLN A 598 "
      ideal   model   delta    sigma   weight residual
     121.54  125.82   -4.28 1.91e+00 2.74e-01 5.01e+00
  angle pdb=" C   ARG A 404 "
        pdb=" N   SER A 405 "
        pdb=" CA  SER A 405 "
      ideal   model   delta    sigma   weight residual
     121.54  125.67   -4.13 1.91e+00 2.74e-01 4.67e+00
  ... (remaining 11910 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.03: 4673
       23.03 -    46.05: 360
       46.05 -    69.08: 137
       69.08 -    92.11: 34
       92.11 -   115.13: 3
  Dihedral angle restraints: 5207
    sinusoidal: 2780
      harmonic: 2427
  Sorted by residual:
  dihedral pdb=" O4'   C B  30 "
           pdb=" C1'   C B  30 "
           pdb=" N1    C B  30 "
           pdb=" C2    C B  30 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -65.59  -62.41     1      1.70e+01 3.46e-03 1.78e+01
  dihedral pdb=" O4'   G B  32 "
           pdb=" C1'   G B  32 "
           pdb=" N9    G B  32 "
           pdb=" C4    G B  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -156.64   50.64     1      1.70e+01 3.46e-03 1.22e+01
  dihedral pdb=" CA  TRP A 700 "
           pdb=" C   TRP A 700 "
           pdb=" N   ASN A 701 "
           pdb=" CA  ASN A 701 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.08   16.92     0      5.00e+00 4.00e-02 1.15e+01
  ... (remaining 5204 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 947
       0.033 -    0.065: 288
       0.065 -    0.098: 73
       0.098 -    0.130: 23
       0.130 -    0.163: 4
  Chirality restraints: 1335
  Sorted by residual:
  chirality pdb=" C3'   G B  40 "
            pdb=" C4'   G B  40 "
            pdb=" O3'   G B  40 "
            pdb=" C2'   G B  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.31   -0.16 2.00e-01 2.50e+01 6.65e-01
  chirality pdb=" CA  ILE A 717 "
            pdb=" N   ILE A 717 "
            pdb=" C   ILE A 717 "
            pdb=" CB  ILE A 717 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.20e-01
  chirality pdb=" CA  ILE A 691 "
            pdb=" N   ILE A 691 "
            pdb=" C   ILE A 691 "
            pdb=" CB  ILE A 691 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.54e-01
  ... (remaining 1332 not shown)

  Planarity restraints: 1270
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B  13 "    0.022 2.00e-02 2.50e+03   1.02e-02 2.89e+00
        pdb=" N9    A B  13 "   -0.025 2.00e-02 2.50e+03
        pdb=" C8    A B  13 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    A B  13 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    A B  13 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    A B  13 "    0.002 2.00e-02 2.50e+03
        pdb=" N6    A B  13 "    0.005 2.00e-02 2.50e+03
        pdb=" N1    A B  13 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    A B  13 "    0.000 2.00e-02 2.50e+03
        pdb=" N3    A B  13 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    A B  13 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 220 "    0.010 2.00e-02 2.50e+03   1.02e-02 2.61e+00
        pdb=" CG  TRP A 220 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 220 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 220 "    0.011 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 220 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 220 "    0.006 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 220 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 220 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 220 "    0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 220 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 706 "    0.023 5.00e-02 4.00e+02   3.53e-02 2.00e+00
        pdb=" N   PRO A 707 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 707 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 707 "    0.019 5.00e-02 4.00e+02
  ... (remaining 1267 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 224
        2.69 -     3.24: 7683
        3.24 -     3.79: 13272
        3.79 -     4.35: 16762
        4.35 -     4.90: 26164
  Nonbonded interactions: 64105
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 602 "
            pdb=" OG1 THR A 606 "
     model   vdw
     2.136 3.040
  nonbonded pdb=" ND2 ASN A 273 "
            pdb=" OD1 ASP A 275 "
     model   vdw
     2.187 3.120
  nonbonded pdb=" O2'   G B  40 "
            pdb=" OP1   A B  41 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   ASN A 610 "
            pdb=" ND2 ASN A 614 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" O2'   G B  22 "
            pdb=" OP1   C B  24 "
     model   vdw
     2.286 3.040
  ... (remaining 64100 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:             2.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     27.050
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3964
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      :  0.002   0.028   8588  Z= 0.122
  Angle     :  0.486   6.705  11915  Z= 0.259
  Chirality :  0.036   0.163   1335
  Planarity :  0.003   0.035   1270
  Dihedral  : 18.762 115.133   3641
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.29), residues: 830
  helix:  0.83 (0.29), residues: 355
  sheet: -0.63 (0.62), residues: 70
  loop : -1.59 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 220 
 HIS   0.005   0.001   HIS A 768 
 PHE   0.012   0.001   PHE A 178 
 TYR   0.011   0.001   TYR A 452 
 ARG   0.003   0.000   ARG A 769 

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

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

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 ARG cc_start: 0.3731 (mpt90) cc_final: 0.1068 (ptp90)
REVERT: A  367 LYS cc_start: 0.5634 (mmtm) cc_final: 0.5224 (mmtm)
REVERT: A  534 ASP cc_start: 0.7143 (p0) cc_final: 0.6856 (p0)
REVERT: A  689 LYS cc_start: 0.7046 (pptt) cc_final: 0.6309 (tptt)
REVERT: A  770 ARG cc_start: 0.3436 (mtt90) cc_final: 0.2081 (ptp90)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.2940
  time to fit residues: 47.0393
Evaluate side-chains
  90 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    0.0050
   chunk 68 optimal weight:    0.7980
   chunk 38 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 71 optimal weight:    8.9990
   chunk 27 optimal weight:   10.0000
   chunk 43 optimal weight:    0.4980
   chunk 53 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    0.8596

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

Flipped N/Q/H residues before XYZ refinement:
A  52 HIS
A 213 ASN
A 581 GLN
** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 742 GLN
A 777 ASN
** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4923 r_free = 0.4923 target = 0.203500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4804 r_free = 0.4804 target = 0.192598 restraints weight = 30046.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.4828 r_free = 0.4828 target = 0.194690 restraints weight = 17518.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.4843 r_free = 0.4843 target = 0.196231 restraints weight = 11392.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.4833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3995
moved from start:          0.1370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   8588  Z= 0.140
  Angle     :  0.543   9.062  11915  Z= 0.279
  Chirality :  0.037   0.218   1335
  Planarity :  0.004   0.041   1270
  Dihedral  : 18.310 114.429   1942
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  7.85 %
    Favored  : 91.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.29), residues: 830
  helix:  0.69 (0.28), residues: 377
  sheet: -0.60 (0.61), residues: 72
  loop : -1.82 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 220 
 HIS   0.005   0.001   HIS A 712 
 PHE   0.011   0.002   PHE A 483 
 TYR   0.011   0.001   TYR A 476 
 ARG   0.003   0.000   ARG A 362 

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

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

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 ARG cc_start: 0.3821 (mpt90) cc_final: 0.1120 (ptp90)
REVERT: A  534 ASP cc_start: 0.7099 (p0) cc_final: 0.6853 (p0)
REVERT: A  668 LYS cc_start: 0.6507 (tttm) cc_final: 0.6227 (tttm)
REVERT: A  689 LYS cc_start: 0.7008 (pptt) cc_final: 0.6305 (tptt)
REVERT: A  824 MET cc_start: 0.4558 (mmm) cc_final: 0.3878 (mmm)
  outliers start: 6
  outliers final: 1
  residues processed: 98
  average time/residue: 0.2776
  time to fit residues: 35.5438
Evaluate side-chains
  84 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 20 optimal weight:   10.0000
   chunk 6 optimal weight:    7.9990
   chunk 44 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 32 optimal weight:   10.0000
   chunk 79 optimal weight:   10.0000
   chunk 86 optimal weight:    9.9990
   chunk 59 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 364 GLN
A 555 ASN
** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4851 r_free = 0.4851 target = 0.196755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4735 r_free = 0.4735 target = 0.185731 restraints weight = 30453.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4759 r_free = 0.4759 target = 0.187858 restraints weight = 17370.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.4774 r_free = 0.4774 target = 0.189402 restraints weight = 11021.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.4765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4314
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086   8588  Z= 0.262
  Angle     :  0.711   8.526  11915  Z= 0.372
  Chirality :  0.043   0.219   1335
  Planarity :  0.006   0.066   1270
  Dihedral  : 18.815 118.391   1942
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 16.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.07 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 10.55 %
    Favored  : 86.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.28), residues: 830
  helix: -0.05 (0.27), residues: 365
  sheet: -0.97 (0.59), residues: 72
  loop : -2.09 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 497 
 HIS   0.008   0.002   HIS A 712 
 PHE   0.017   0.003   PHE A 674 
 TYR   0.020   0.002   TYR A 476 
 ARG   0.008   0.001   ARG A 739 

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

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

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  245 MET cc_start: 0.0622 (ptt) cc_final: 0.0385 (ptt)
REVERT: A  246 ARG cc_start: 0.4404 (mpt90) cc_final: 0.1359 (ttp80)
REVERT: A  689 LYS cc_start: 0.7012 (pptt) cc_final: 0.6350 (tptt)
REVERT: A  770 ARG cc_start: 0.3501 (mtt90) cc_final: 0.2308 (ptp-170)
REVERT: A  824 MET cc_start: 0.4783 (mmm) cc_final: 0.3645 (mtp)
  outliers start: 20
  outliers final: 8
  residues processed: 110
  average time/residue: 0.3544
  time to fit residues: 51.2175
Evaluate side-chains
  87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 1.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  116 MET
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  643 VAL
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  813 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 85 optimal weight:    9.9990
   chunk 84 optimal weight:   10.0000
   chunk 63 optimal weight:    0.0020
   chunk 72 optimal weight:    8.9990
   chunk 14 optimal weight:    2.9990
   chunk 62 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9980
   chunk 30 optimal weight:    6.9990
   chunk 66 optimal weight:   10.0000
   chunk 46 optimal weight:    8.9990
   overall best weight:    3.9994

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4829 r_free = 0.4829 target = 0.194550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4706 r_free = 0.4706 target = 0.183397 restraints weight = 29918.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4731 r_free = 0.4731 target = 0.185528 restraints weight = 16879.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.4749 r_free = 0.4749 target = 0.187141 restraints weight = 10631.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.4743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4402
moved from start:          0.3454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.096   8588  Z= 0.282
  Angle     :  0.742   7.680  11915  Z= 0.387
  Chirality :  0.044   0.226   1335
  Planarity :  0.006   0.062   1270
  Dihedral  : 19.192 119.020   1942
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 18.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 15.56 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.02 (0.27), residues: 830
  helix: -0.52 (0.26), residues: 361
  sheet: -0.69 (0.75), residues: 52
  loop : -2.22 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 497 
 HIS   0.008   0.002   HIS A 634 
 PHE   0.018   0.003   PHE A 612 
 TYR   0.021   0.002   TYR A 476 
 ARG   0.008   0.001   ARG A 749 

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

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

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  245 MET cc_start: 0.0924 (ptt) cc_final: 0.0708 (ptt)
REVERT: A  246 ARG cc_start: 0.4804 (mpt90) cc_final: 0.1533 (ttp80)
REVERT: A  515 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6519 (mp)
REVERT: A  599 ARG cc_start: 0.4467 (tpm170) cc_final: 0.4209 (tpt170)
REVERT: A  689 LYS cc_start: 0.6959 (pptt) cc_final: 0.6439 (tptt)
REVERT: A  770 ARG cc_start: 0.3488 (mtt90) cc_final: 0.2519 (ptp-170)
REVERT: A  824 MET cc_start: 0.5112 (mmm) cc_final: 0.4229 (mtp)
  outliers start: 19
  outliers final: 10
  residues processed: 101
  average time/residue: 0.2598
  time to fit residues: 34.0312
Evaluate side-chains
  93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ASP
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  213 ASN
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  681 LEU
Chi-restraints excluded: chain A residue  772 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 70 optimal weight:    5.9990
   chunk 13 optimal weight:   10.0000
   chunk 38 optimal weight:    0.8980
   chunk 28 optimal weight:    0.1980
   chunk 44 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 364 GLN
** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 821 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4883 r_free = 0.4883 target = 0.199600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4766 r_free = 0.4766 target = 0.188542 restraints weight = 29862.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4791 r_free = 0.4791 target = 0.190770 restraints weight = 17131.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.4808 r_free = 0.4808 target = 0.192328 restraints weight = 10816.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.4797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4171
moved from start:          0.3301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8588  Z= 0.144
  Angle     :  0.573   7.698  11915  Z= 0.296
  Chirality :  0.038   0.223   1335
  Planarity :  0.004   0.050   1270
  Dihedral  : 18.738 116.255   1942
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 16.24 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.28), residues: 830
  helix: -0.11 (0.26), residues: 377
  sheet: -0.35 (0.69), residues: 62
  loop : -2.18 (0.28), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 220 
 HIS   0.003   0.001   HIS A 768 
 PHE   0.014   0.002   PHE A 708 
 TYR   0.011   0.001   TYR A 882 
 ARG   0.003   0.000   ARG A  38 

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

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

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 MET cc_start: 0.2409 (tpt) cc_final: 0.0156 (ptt)
REVERT: A  246 ARG cc_start: 0.4649 (mpt90) cc_final: 0.1420 (ptp90)
REVERT: A  668 LYS cc_start: 0.6778 (tttm) cc_final: 0.6520 (tttm)
REVERT: A  689 LYS cc_start: 0.6926 (pptt) cc_final: 0.6482 (tptt)
REVERT: A  770 ARG cc_start: 0.3438 (mtt90) cc_final: 0.2239 (ptp-170)
REVERT: A  824 MET cc_start: 0.5213 (mmm) cc_final: 0.3944 (mtp)
  outliers start: 13
  outliers final: 4
  residues processed: 105
  average time/residue: 0.2528
  time to fit residues: 35.0470
Evaluate side-chains
  91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 87
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  772 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 87 optimal weight:   10.0000
   chunk 25 optimal weight:    8.9990
   chunk 62 optimal weight:    9.9990
   chunk 50 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9990
   chunk 35 optimal weight:   10.0000
   chunk 6 optimal weight:    2.9990
   chunk 76 optimal weight:    7.9990
   chunk 5 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9990
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 712 HIS ** 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 = 0.4863 r_free = 0.4863 target = 0.198453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4743 r_free = 0.4743 target = 0.187673 restraints weight = 29445.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4770 r_free = 0.4770 target = 0.189863 restraints weight = 17312.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.4787 r_free = 0.4787 target = 0.191337 restraints weight = 10953.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.4782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4204
moved from start:          0.3502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8588  Z= 0.158
  Angle     :  0.585   7.018  11915  Z= 0.302
  Chirality :  0.039   0.217   1335
  Planarity :  0.004   0.055   1270
  Dihedral  : 18.591 115.039   1942
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.78 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.28), residues: 830
  helix: -0.06 (0.26), residues: 377
  sheet: -0.62 (0.63), residues: 72
  loop : -2.14 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 803 
 HIS   0.004   0.001   HIS A 768 
 PHE   0.033   0.002   PHE A 708 
 TYR   0.010   0.001   TYR A 186 
 ARG   0.004   0.000   ARG A 739 

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

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

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.826 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 MET cc_start: 0.2209 (tpt) cc_final: 0.0078 (ptt)
REVERT: A  246 ARG cc_start: 0.4741 (mpt90) cc_final: 0.1481 (ptp90)
REVERT: A  367 LYS cc_start: 0.5573 (mmtm) cc_final: 0.3435 (tptp)
REVERT: A  668 LYS cc_start: 0.7010 (tttm) cc_final: 0.6635 (tttm)
REVERT: A  689 LYS cc_start: 0.6991 (pptt) cc_final: 0.6551 (tptt)
REVERT: A  797 ILE cc_start: 0.5139 (OUTLIER) cc_final: 0.4790 (mm)
REVERT: A  824 MET cc_start: 0.5126 (mmm) cc_final: 0.3917 (mtp)
  outliers start: 18
  outliers final: 11
  residues processed: 103
  average time/residue: 0.2618
  time to fit residues: 35.9366
Evaluate side-chains
  96 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  116 MET
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  213 ASN
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  455 MET
Chi-restraints excluded: chain A residue  483 PHE
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  797 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 55 optimal weight:    8.9990
   chunk 20 optimal weight:    0.4980
   chunk 6 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   chunk 45 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 34 optimal weight:    6.9990
   overall best weight:    3.2988

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 768 HIS ** 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 = 0.4820 r_free = 0.4820 target = 0.194352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4701 r_free = 0.4701 target = 0.183984 restraints weight = 29519.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4726 r_free = 0.4726 target = 0.186033 restraints weight = 17158.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.4743 r_free = 0.4743 target = 0.187410 restraints weight = 10882.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.4737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4357
moved from start:          0.4096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   8588  Z= 0.256
  Angle     :  0.723   8.943  11915  Z= 0.377
  Chirality :  0.043   0.220   1335
  Planarity :  0.006   0.060   1270
  Dihedral  : 18.934 117.578   1942
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 18.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.55 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 18.13 %
    Favored  : 79.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.04 (0.27), residues: 830
  helix: -0.43 (0.26), residues: 370
  sheet: -1.14 (0.64), residues: 64
  loop : -2.33 (0.28), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 382 
 HIS   0.006   0.002   HIS A 634 
 PHE   0.030   0.003   PHE A 708 
 TYR   0.017   0.002   TYR A 476 
 ARG   0.006   0.001   ARG A 212 

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

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

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.3785 (mmp) cc_final: 0.3092 (mtt)
REVERT: A  359 VAL cc_start: 0.4259 (OUTLIER) cc_final: 0.3915 (t)
REVERT: A  689 LYS cc_start: 0.7049 (pptt) cc_final: 0.6720 (tptt)
REVERT: A  770 ARG cc_start: 0.3313 (mtt90) cc_final: 0.2352 (ptp-170)
REVERT: A  824 MET cc_start: 0.5121 (mmm) cc_final: 0.4040 (mtp)
  outliers start: 19
  outliers final: 11
  residues processed: 100
  average time/residue: 0.2448
  time to fit residues: 32.9068
Evaluate side-chains
  90 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  213 ASN
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  577 VAL
Chi-restraints excluded: chain A residue  612 PHE
Chi-restraints excluded: chain A residue  717 ILE
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  797 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 86 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 85 optimal weight:    9.9990
   chunk 79 optimal weight:    7.9990
   chunk 87 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 56 optimal weight:    0.7980
   chunk 67 optimal weight:    6.9990
   overall best weight:    4.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
A 364 GLN
A 556 HIS
** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4799 r_free = 0.4799 target = 0.191992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4678 r_free = 0.4678 target = 0.181478 restraints weight = 29561.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4705 r_free = 0.4705 target = 0.183590 restraints weight = 17355.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.4722 r_free = 0.4722 target = 0.185031 restraints weight = 11030.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.4716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4493
moved from start:          0.4933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076   8588  Z= 0.314
  Angle     :  0.815   8.222  11915  Z= 0.428
  Chirality :  0.047   0.224   1335
  Planarity :  0.006   0.056   1270
  Dihedral  : 19.464 119.447   1942
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 20.65
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.55 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 19.35 %
    Favored  : 77.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.54 (0.26), residues: 830
  helix: -0.92 (0.25), residues: 367
  sheet: -1.42 (0.65), residues: 54
  loop : -2.49 (0.27), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 382 
 HIS   0.009   0.002   HIS A 216 
 PHE   0.035   0.003   PHE A 708 
 TYR   0.021   0.002   TYR A 476 
 ARG   0.007   0.001   ARG A 749 

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

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

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.3688 (mmp) cc_final: 0.3406 (mtp)
REVERT: A  359 VAL cc_start: 0.4585 (OUTLIER) cc_final: 0.4190 (t)
REVERT: A  689 LYS cc_start: 0.7047 (pptt) cc_final: 0.6745 (tptt)
REVERT: A  718 MET cc_start: 0.6434 (ptp) cc_final: 0.6094 (ptp)
REVERT: A  770 ARG cc_start: 0.3396 (mtt90) cc_final: 0.2613 (ptp-170)
REVERT: A  867 ILE cc_start: 0.2581 (mt) cc_final: 0.2190 (mt)
  outliers start: 22
  outliers final: 13
  residues processed: 98
  average time/residue: 0.2238
  time to fit residues: 30.4785
Evaluate side-chains
  92 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ASP
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  175 ASN
Chi-restraints excluded: chain A residue  213 ASN
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain A residue  577 VAL
Chi-restraints excluded: chain A residue  612 PHE
Chi-restraints excluded: chain A residue  746 TRP
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  797 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 64 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 7 optimal weight:    7.9990
   chunk 30 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 49 optimal weight:    0.1980
   chunk 74 optimal weight:    8.9990
   chunk 88 optimal weight:   10.0000
   overall best weight:    2.8388

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
A 556 HIS
** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4826 r_free = 0.4826 target = 0.193476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4701 r_free = 0.4701 target = 0.183010 restraints weight = 30006.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4730 r_free = 0.4730 target = 0.185194 restraints weight = 17559.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4747 r_free = 0.4747 target = 0.186584 restraints weight = 11065.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.4739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4419
moved from start:          0.4964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8588  Z= 0.233
  Angle     :  0.704   7.314  11915  Z= 0.369
  Chirality :  0.042   0.224   1335
  Planarity :  0.006   0.070   1270
  Dihedral  : 19.448 118.788   1942
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 18.42
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.07 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 20.43 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.36 (0.27), residues: 830
  helix: -0.75 (0.25), residues: 373
  sheet: -1.40 (0.66), residues: 54
  loop : -2.41 (0.28), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 382 
 HIS   0.006   0.001   HIS A 768 
 PHE   0.019   0.002   PHE A 708 
 TYR   0.016   0.002   TYR A 476 
 ARG   0.006   0.001   ARG A 621 

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

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

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  689 LYS cc_start: 0.6980 (pptt) cc_final: 0.6740 (tptt)
REVERT: A  770 ARG cc_start: 0.3382 (mtt90) cc_final: 0.2428 (ptp-170)
  outliers start: 17
  outliers final: 14
  residues processed: 92
  average time/residue: 0.2330
  time to fit residues: 29.5000
Evaluate side-chains
  91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ASP
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  175 ASN
Chi-restraints excluded: chain A residue  213 ASN
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  483 PHE
Chi-restraints excluded: chain A residue  577 VAL
Chi-restraints excluded: chain A residue  612 PHE
Chi-restraints excluded: chain A residue  615 MET
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  797 ILE
Chi-restraints excluded: chain A residue  824 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 44 optimal weight:    8.9990
   chunk 2 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A  96 ASN
A 213 ASN
A 364 GLN
A 705 GLN
** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4866 r_free = 0.4866 target = 0.197374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4746 r_free = 0.4746 target = 0.187040 restraints weight = 30122.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4775 r_free = 0.4775 target = 0.189245 restraints weight = 17713.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4792 r_free = 0.4792 target = 0.190647 restraints weight = 11162.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.4783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4261
moved from start:          0.4834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8588  Z= 0.159
  Angle     :  0.635  10.406  11915  Z= 0.327
  Chirality :  0.039   0.222   1335
  Planarity :  0.005   0.059   1270
  Dihedral  : 19.199 116.186   1942
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.78 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 20.57 %
    Favored  : 77.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.28), residues: 830
  helix: -0.36 (0.26), residues: 375
  sheet: -1.39 (0.63), residues: 63
  loop : -2.25 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 382 
 HIS   0.004   0.001   HIS A 768 
 PHE   0.016   0.002   PHE A 674 
 TYR   0.011   0.001   TYR A 607 
 ARG   0.004   0.000   ARG A 769 

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

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

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1660 Ramachandran restraints generated.
    830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  367 LYS cc_start: 0.5274 (mmtm) cc_final: 0.4660 (mptt)
REVERT: A  477 MET cc_start: 0.6329 (pmm) cc_final: 0.4463 (tpp)
REVERT: A  615 MET cc_start: 0.5942 (OUTLIER) cc_final: 0.5691 (ptp)
REVERT: A  689 LYS cc_start: 0.7139 (pptt) cc_final: 0.6802 (tptt)
REVERT: A  770 ARG cc_start: 0.3255 (mtt90) cc_final: 0.2090 (ptp-170)
REVERT: A  824 MET cc_start: 0.5379 (OUTLIER) cc_final: 0.4123 (mtp)
  outliers start: 13
  outliers final: 8
  residues processed: 95
  average time/residue: 0.2405
  time to fit residues: 31.1257
Evaluate side-chains
  91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  213 ASN
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  580 VAL
Chi-restraints excluded: chain A residue  612 PHE
Chi-restraints excluded: chain A residue  615 MET
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  824 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 39 optimal weight:    9.9990
   chunk 25 optimal weight:    0.9980
   chunk 85 optimal weight:   10.0000
   chunk 72 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 62 optimal weight:    9.9990
   chunk 43 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0670
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.8120

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 768 HIS ** 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 = 0.4873 r_free = 0.4873 target = 0.198137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4754 r_free = 0.4754 target = 0.187737 restraints weight = 30245.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4782 r_free = 0.4782 target = 0.189924 restraints weight = 17620.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.4799 r_free = 0.4799 target = 0.191350 restraints weight = 11186.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.4791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4222
moved from start:          0.4872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8588  Z= 0.158
  Angle     :  0.622   9.908  11915  Z= 0.319
  Chirality :  0.038   0.217   1335
  Planarity :  0.005   0.061   1270
  Dihedral  : 18.979 114.589   1942
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.75 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 20.84 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.28), residues: 830
  helix: -0.18 (0.26), residues: 377
  sheet: -1.42 (0.65), residues: 65
  loop : -2.17 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 382 
 HIS   0.004   0.001   HIS A 216 
 PHE   0.011   0.001   PHE A 674 
 TYR   0.019   0.001   TYR A 882 
 ARG   0.009   0.000   ARG A 657 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3214.28 seconds
wall clock time: 57 minutes 31.96 seconds (3451.96 seconds total)