Starting phenix.real_space_refine
on Fri Nov 15 04:03:10 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dtt_47165/11_2024/9dtt_47165.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dtt_47165/11_2024/9dtt_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dtt_47165/11_2024/9dtt_47165.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dtt_47165/11_2024/9dtt_47165.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dtt_47165/11_2024/9dtt_47165.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dtt_47165/11_2024/9dtt_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-5513/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: 5.88, per 1000 atoms: 0.71
  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: 2.38
  Conformation dependent library (CDL) restraints added in 820.4 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: 3.20
  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: 2.99

  Time building geometry restraints manager: 2.71 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:             2.460
  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:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     26.700
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.760
-------------------------------------------------------------------------------
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  : 0.892 
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: 0.2932
  time to fit residues: 47.1042
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  : 1.115 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3994
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  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 ARG cc_start: 0.3769 (mpt90) cc_final: 0.1077 (ptp90)
REVERT: A  534 ASP cc_start: 0.7102 (p0) cc_final: 0.6852 (p0)
REVERT: A  668 LYS cc_start: 0.6413 (tttm) cc_final: 0.6168 (tttm)
REVERT: A  689 LYS cc_start: 0.6997 (pptt) cc_final: 0.6308 (tptt)
REVERT: A  824 MET cc_start: 0.4554 (mmm) cc_final: 0.3877 (mmm)
  outliers start: 6
  outliers final: 1
  residues processed: 98
  average time/residue: 0.2739
  time to fit residues: 35.1002
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  : 0.852 
-------------------------------------------------------------------------------
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 45 optimal weight:   10.0000
   chunk 25 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 89 optimal weight:   20.0000
   chunk 73 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   chunk 66 optimal weight:    0.0870
   chunk 81 optimal weight:    2.9990
   overall best weight:    2.4166

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

Flipped N/Q/H residues before XYZ refinement:
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: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4146
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   8588  Z= 0.190
  Angle     :  0.590   8.548  11915  Z= 0.306
  Chirality :  0.039   0.216   1335
  Planarity :  0.005   0.051   1270
  Dihedral  : 18.389 115.794   1942
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 10.28 %
    Favored  : 87.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.16 (0.28), residues: 830
  helix:  0.39 (0.27), residues: 375
  sheet: -0.71 (0.61), residues: 70
  loop : -1.99 (0.29), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 803 
 HIS   0.006   0.001   HIS A 712 
 PHE   0.019   0.002   PHE A 674 
 TYR   0.013   0.002   TYR A 476 
 ARG   0.005   0.000   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
  108 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 GLN cc_start: 0.5627 (mm110) cc_final: 0.5338 (tm-30)
REVERT: A  245 MET cc_start: 0.0334 (ptt) cc_final: 0.0099 (ptt)
REVERT: A  246 ARG cc_start: 0.4012 (mpt90) cc_final: 0.1188 (ptp90)
REVERT: A  668 LYS cc_start: 0.6765 (tttm) cc_final: 0.6422 (tttm)
REVERT: A  689 LYS cc_start: 0.7021 (pptt) cc_final: 0.6353 (tptt)
REVERT: A  770 ARG cc_start: 0.3390 (mtt90) cc_final: 0.2128 (ptp-170)
REVERT: A  825 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6562 (mm-30)
  outliers start: 13
  outliers final: 6
  residues processed: 102
  average time/residue: 0.2623
  time to fit residues: 35.0707
Evaluate side-chains
  87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
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  772 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 42 optimal weight:    5.9990
   chunk 9 optimal weight:    0.2980
   chunk 39 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 83 optimal weight:    6.9990
   chunk 87 optimal weight:    9.9990
   chunk 43 optimal weight:    6.9990
   chunk 78 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 73 optimal weight:   10.0000
   overall best weight:    3.4588

-------------------------------------------------------------------------------
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 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4312
moved from start:          0.2930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.092   8588  Z= 0.254
  Angle     :  0.696   8.622  11915  Z= 0.363
  Chirality :  0.043   0.224   1335
  Planarity :  0.005   0.071   1270
  Dihedral  : 18.835 118.805   1942
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 16.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.07 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 12.86 %
    Favored  : 84.84 %
  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: -1.62 (0.28), residues: 830
  helix: -0.16 (0.27), residues: 364
  sheet: -0.89 (0.61), residues: 72
  loop : -2.01 (0.29), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 419 
 HIS   0.007   0.002   HIS A 634 
 PHE   0.016   0.003   PHE A 243 
 TYR   0.019   0.002   TYR A 476 
 ARG   0.008   0.001   ARG A 621 

*********************** 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
  105 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  245 MET cc_start: 0.0332 (ptt) cc_final: 0.0122 (ptt)
REVERT: A  246 ARG cc_start: 0.4245 (mpt90) cc_final: 0.1175 (ttp80)
REVERT: A  689 LYS cc_start: 0.6955 (pptt) cc_final: 0.6362 (tptt)
REVERT: A  770 ARG cc_start: 0.3369 (mtt90) cc_final: 0.2438 (ptp-170)
REVERT: A  824 MET cc_start: 0.3836 (mmm) cc_final: 0.2968 (mtp)
  outliers start: 17
  outliers final: 11
  residues processed: 100
  average time/residue: 0.2612
  time to fit residues: 34.4769
Evaluate side-chains
  91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
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  190 VAL
Chi-restraints excluded: chain A residue  213 ASN
Chi-restraints excluded: chain A residue  252 TYR
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  797 ILE
Chi-restraints excluded: chain A residue  813 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 1 optimal weight:    9.9990
   chunk 65 optimal weight:    7.9990
   chunk 36 optimal weight:    0.8980
   chunk 75 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0970
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
A 364 GLN
** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4176
moved from start:          0.2931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   8588  Z= 0.155
  Angle     :  0.580   7.248  11915  Z= 0.300
  Chirality :  0.038   0.223   1335
  Planarity :  0.004   0.051   1270
  Dihedral  : 18.625 117.072   1942
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.07 %
    Favored  : 83.76 %
  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: -1.40 (0.28), residues: 830
  helix:  0.07 (0.27), residues: 372
  sheet: -0.40 (0.68), residues: 62
  loop : -2.03 (0.28), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 700 
 HIS   0.004   0.001   HIS A 216 
 PHE   0.014   0.002   PHE A 708 
 TYR   0.011   0.002   TYR A 476 
 ARG   0.003   0.000   ARG A 749 

*********************** 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: 16
    poor density    : 93
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 MET cc_start: 0.1991 (tpt) cc_final: -0.0273 (ptt)
REVERT: A  245 MET cc_start: 0.0394 (ptt) cc_final: 0.0181 (ptt)
REVERT: A  246 ARG cc_start: 0.4266 (mpt90) cc_final: 0.1192 (ttp80)
REVERT: A  668 LYS cc_start: 0.6723 (tttm) cc_final: 0.6466 (tttm)
REVERT: A  689 LYS cc_start: 0.6864 (pptt) cc_final: 0.6356 (tptt)
REVERT: A  824 MET cc_start: 0.3999 (mmm) cc_final: 0.2960 (mtp)
  outliers start: 16
  outliers final: 9
  residues processed: 104
  average time/residue: 0.2909
  time to fit residues: 39.8703
Evaluate side-chains
  92 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  252 TYR
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  483 PHE
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  797 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 79 optimal weight:    9.9990
   chunk 17 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 88 optimal weight:    9.9990
   chunk 73 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:   10.0000
   chunk 29 optimal weight:    0.1980
   chunk 46 optimal weight:    8.9990
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4091
moved from start:          0.3095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8588  Z= 0.141
  Angle     :  0.561   8.256  11915  Z= 0.290
  Chirality :  0.038   0.218   1335
  Planarity :  0.004   0.053   1270
  Dihedral  : 18.469 114.510   1942
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 16.51 %
    Favored  : 82.14 %
  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: -1.29 (0.28), residues: 830
  helix:  0.17 (0.27), residues: 371
  sheet: -0.49 (0.63), residues: 72
  loop : -1.98 (0.28), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 382 
 HIS   0.003   0.001   HIS A 768 
 PHE   0.035   0.002   PHE A 708 
 TYR   0.010   0.001   TYR A 607 
 ARG   0.007   0.000   ARG A 621 

*********************** 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
  97 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.797 
Fit side-chains
   revert: symmetry clash
REVERT: A  238 MET cc_start: 0.2014 (tpt) cc_final: 0.0002 (ptt)
REVERT: A  245 MET cc_start: 0.0313 (ptt) cc_final: 0.0107 (ptt)
REVERT: A  246 ARG cc_start: 0.4298 (mpt90) cc_final: 0.1262 (ptp90)
REVERT: A  668 LYS cc_start: 0.6594 (tttm) cc_final: 0.6371 (tttm)
REVERT: A  689 LYS cc_start: 0.6937 (pptt) cc_final: 0.6371 (tptt)
REVERT: A  770 ARG cc_start: 0.3290 (mtt90) cc_final: 0.2026 (ptp-170)
REVERT: A  824 MET cc_start: 0.4032 (mmm) cc_final: 0.3040 (mtp)
  outliers start: 10
  outliers final: 5
  residues processed: 92
  average time/residue: 0.2728
  time to fit residues: 32.7823
Evaluate side-chains
  84 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  373 LEU
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 9 optimal weight:    0.7980
   chunk 50 optimal weight:   20.0000
   chunk 64 optimal weight:    0.8980
   chunk 49 optimal weight:    8.9990
   chunk 74 optimal weight:    3.9990
   chunk 87 optimal weight:    9.9990
   chunk 54 optimal weight:    0.0970
   chunk 53 optimal weight:    1.9990
   chunk 40 optimal weight:    8.9990
   chunk 35 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4091
moved from start:          0.3306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8588  Z= 0.141
  Angle     :  0.558   6.705  11915  Z= 0.286
  Chirality :  0.038   0.214   1335
  Planarity :  0.004   0.047   1270
  Dihedral  : 18.411 113.360   1942
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 16.37 %
    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: -1.22 (0.28), residues: 830
  helix:  0.35 (0.27), residues: 371
  sheet: -0.92 (0.61), residues: 72
  loop : -1.99 (0.28), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP A 813 
 HIS   0.003   0.001   HIS A 768 
 PHE   0.033   0.002   PHE A 708 
 TYR   0.018   0.001   TYR A 882 
 ARG   0.008   0.000   ARG A 739 

*********************** 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
  92 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.845 
Fit side-chains
   revert: symmetry clash
REVERT: A  238 MET cc_start: 0.1989 (tpt) cc_final: 0.0015 (ptt)
REVERT: A  245 MET cc_start: 0.0322 (ptt) cc_final: 0.0110 (ptt)
REVERT: A  246 ARG cc_start: 0.4280 (mpt90) cc_final: 0.1249 (ptp90)
REVERT: A  327 LEU cc_start: 0.1645 (OUTLIER) cc_final: 0.1222 (pp)
REVERT: A  621 ARG cc_start: 0.3813 (ttt180) cc_final: 0.3471 (tmt170)
REVERT: A  668 LYS cc_start: 0.6588 (tttm) cc_final: 0.6377 (tttm)
REVERT: A  689 LYS cc_start: 0.6899 (pptt) cc_final: 0.6439 (tptt)
REVERT: A  770 ARG cc_start: 0.3208 (mtt90) cc_final: 0.1950 (ptp-170)
REVERT: A  824 MET cc_start: 0.3994 (mmm) cc_final: 0.3068 (mtp)
  outliers start: 12
  outliers final: 8
  residues processed: 88
  average time/residue: 0.2453
  time to fit residues: 29.1127
Evaluate side-chains
  83 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  190 VAL
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  373 LEU
Chi-restraints excluded: chain A residue  518 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 26 optimal weight:    0.0980
   chunk 17 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 59 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0470
   chunk 8 optimal weight:   10.0000
   chunk 68 optimal weight:    6.9990
   chunk 79 optimal weight:    6.9990
   chunk 84 optimal weight:    0.0970
   chunk 76 optimal weight:    5.9990
   overall best weight:    0.6278

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4029
moved from start:          0.3484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8588  Z= 0.134
  Angle     :  0.547   6.431  11915  Z= 0.280
  Chirality :  0.037   0.228   1335
  Planarity :  0.004   0.049   1270
  Dihedral  : 18.234 111.106   1942
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 17.19 %
    Favored  : 81.60 %
  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: -1.05 (0.28), residues: 830
  helix:  0.51 (0.27), residues: 373
  sheet: -0.96 (0.57), residues: 82
  loop : -1.91 (0.29), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 813 
 HIS   0.003   0.001   HIS A 712 
 PHE   0.020   0.001   PHE A 708 
 TYR   0.011   0.001   TYR A 607 
 ARG   0.008   0.000   ARG A 739 

*********************** 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
  88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
REVERT: A  238 MET cc_start: 0.2197 (tpt) cc_final: 0.0223 (ptt)
REVERT: A  245 MET cc_start: 0.0452 (ptt) cc_final: 0.0144 (ptt)
REVERT: A  246 ARG cc_start: 0.4291 (mpt90) cc_final: 0.1245 (ptp90)
REVERT: A  327 LEU cc_start: 0.1776 (OUTLIER) cc_final: 0.1358 (pp)
REVERT: A  689 LYS cc_start: 0.6953 (pptt) cc_final: 0.6482 (tptt)
REVERT: A  770 ARG cc_start: 0.3301 (mtt90) cc_final: 0.1763 (ptp-170)
REVERT: A  824 MET cc_start: 0.4038 (mmm) cc_final: 0.3211 (mtp)
REVERT: A  882 TYR cc_start: 0.3674 (m-80) cc_final: 0.3320 (m-80)
REVERT: A  883 MET cc_start: 0.6965 (mtp) cc_final: 0.6621 (mtp)
  outliers start: 9
  outliers final: 6
  residues processed: 84
  average time/residue: 0.2838
  time to fit residues: 32.0352
Evaluate side-chains
  83 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 1.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  518 ILE
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 81 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0970
   chunk 25 optimal weight:    0.3980
   chunk 73 optimal weight:    0.8980
   chunk 77 optimal weight:    0.4980
   chunk 53 optimal weight:    6.9990
   chunk 86 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9990
   overall best weight:    0.5780

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4007
moved from start:          0.3650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8588  Z= 0.129
  Angle     :  0.546   7.364  11915  Z= 0.277
  Chirality :  0.036   0.201   1335
  Planarity :  0.004   0.056   1270
  Dihedral  : 18.084 108.830   1942
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 16.91 %
    Favored  : 81.60 %
  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: -0.94 (0.29), residues: 830
  helix:  0.60 (0.28), residues: 375
  sheet: -0.82 (0.59), residues: 82
  loop : -1.87 (0.29), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 813 
 HIS   0.003   0.001   HIS A 712 
 PHE   0.009   0.001   PHE A 708 
 TYR   0.012   0.001   TYR A 607 
 ARG   0.007   0.000   ARG A 599 

*********************** 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
  93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
REVERT: A  238 MET cc_start: 0.2179 (tpt) cc_final: 0.0238 (ptt)
REVERT: A  245 MET cc_start: 0.0501 (ptt) cc_final: 0.0189 (ptt)
REVERT: A  246 ARG cc_start: 0.4287 (mpt90) cc_final: 0.1260 (ptp90)
REVERT: A  689 LYS cc_start: 0.7021 (pptt) cc_final: 0.6478 (tptt)
REVERT: A  770 ARG cc_start: 0.3347 (mtt90) cc_final: 0.1898 (ptp-170)
REVERT: A  824 MET cc_start: 0.4019 (mmm) cc_final: 0.3335 (mtp)
REVERT: A  883 MET cc_start: 0.7117 (mtp) cc_final: 0.6829 (mtp)
  outliers start: 11
  outliers final: 8
  residues processed: 89
  average time/residue: 0.2362
  time to fit residues: 28.5676
Evaluate side-chains
  85 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain A residue  612 PHE
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  797 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   chunk 90 optimal weight:    9.9990
   chunk 83 optimal weight:    1.9990
   chunk 72 optimal weight:    8.9990
   chunk 7 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9990
   chunk 44 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   overall best weight:    1.9188

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4172
moved from start:          0.3853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8588  Z= 0.179
  Angle     :  0.624  10.140  11915  Z= 0.319
  Chirality :  0.039   0.202   1335
  Planarity :  0.005   0.054   1270
  Dihedral  : 18.213 110.816   1942
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 17.59 %
    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: -1.02 (0.29), residues: 830
  helix:  0.54 (0.28), residues: 365
  sheet: -0.59 (0.63), residues: 72
  loop : -1.92 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP A 382 
 HIS   0.006   0.001   HIS A 712 
 PHE   0.014   0.002   PHE A 708 
 TYR   0.021   0.002   TYR A 882 
 ARG   0.008   0.001   ARG A 599 

********************** 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
  88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.883 
Fit side-chains
REVERT: A  245 MET cc_start: 0.0485 (ptt) cc_final: 0.0251 (ptt)
REVERT: A  246 ARG cc_start: 0.4337 (mpt90) cc_final: 0.1272 (ptp90)
REVERT: A  327 LEU cc_start: 0.1707 (OUTLIER) cc_final: 0.1115 (pp)
REVERT: A  477 MET cc_start: 0.6543 (pmm) cc_final: 0.5911 (pmm)
REVERT: A  689 LYS cc_start: 0.7052 (pptt) cc_final: 0.6537 (tptt)
REVERT: A  770 ARG cc_start: 0.3304 (mtt90) cc_final: 0.2095 (ptp90)
REVERT: A  824 MET cc_start: 0.4020 (mmm) cc_final: 0.3209 (mtp)
REVERT: A  867 ILE cc_start: 0.2635 (mt) cc_final: 0.2362 (mt)
  outliers start: 12
  outliers final: 11
  residues processed: 86
  average time/residue: 0.2264
  time to fit residues: 27.2101
Evaluate side-chains
  86 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  213 ASN
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  518 ILE
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain A residue  612 PHE
Chi-restraints excluded: chain A residue  634 HIS
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  797 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   chunk 20 optimal weight:    7.9990
   chunk 72 optimal weight:    0.9990
   chunk 30 optimal weight:    5.9990
   chunk 74 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   chunk 63 optimal weight:   10.0000
   chunk 4 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    3.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4871 r_free = 0.4871 target = 0.198747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4756 r_free = 0.4756 target = 0.188311 restraints weight = 29584.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4783 r_free = 0.4783 target = 0.190472 restraints weight = 17371.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.4799 r_free = 0.4799 target = 0.191887 restraints weight = 11011.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.4790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4164
moved from start:          0.3863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.115   8588  Z= 0.280
  Angle     :  0.947  59.197  11915  Z= 0.553
  Chirality :  0.044   0.687   1335
  Planarity :  0.006   0.098   1270
  Dihedral  : 18.215 110.729   1942
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 17.73 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.13 %
  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: -1.06 (0.29), residues: 830
  helix:  0.51 (0.27), residues: 365
  sheet: -0.62 (0.63), residues: 72
  loop : -1.95 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 382 
 HIS   0.006   0.001   HIS A 712 
 PHE   0.011   0.002   PHE A 674 
 TYR   0.012   0.002   TYR A 186 
 ARG   0.007   0.000   ARG A 599 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1951.23 seconds
wall clock time: 36 minutes 29.94 seconds (2189.94 seconds total)