Starting phenix.real_space_refine
on Tue Apr 29 00:52:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dtt_47165/04_2025/9dtt_47165.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dtt_47165/04_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_47165/04_2025/9dtt_47165.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dtt_47165/04_2025/9dtt_47165.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dtt_47165/04_2025/9dtt_47165.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dtt_47165/04_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-5669/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: 5.97, per 1000 atoms: 0.72
  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: 2.29
  Conformation dependent library (CDL) restraints added in 816.1 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: 2.88
  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: 2.87

  Time building geometry restraints manager: 2.66 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:             3.340
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     26.890
  Find NCS groups from input model:        0.080
  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:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.810
-------------------------------------------------------------------------------
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   8595  Z= 0.096
  Angle     :  0.488   6.705  11917  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13976 (  320)
  hydrogen bonds       : angle       6.60387 (  866)
  metal coordination   : bond        0.00623 (    7)
  metal coordination   : angle       3.00807 (    2)
  covalent geometry    : bond        0.00189 ( 8588)
  covalent geometry    : angle       0.48642 (11915)

*********************** 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  : 0.625 
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: 0.2728
  time to fit residues: 43.4121
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  : 0.745 
-------------------------------------------------------------------------------
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   8595  Z= 0.104
  Angle     :  0.549   9.062  11917  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04342 (  320)
  hydrogen bonds       : angle       4.89223 (  866)
  metal coordination   : bond        0.01261 (    7)
  metal coordination   : angle       6.23100 (    2)
  covalent geometry    : bond        0.00222 ( 8588)
  covalent geometry    : angle       0.54337 (11915)

*********************** 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  : 1.088 
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: 0.3000
  time to fit residues: 38.7851
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  : 0.927 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 56 optimal weight:    4.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4838 r_free = 0.4838 target = 0.195535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4720 r_free = 0.4720 target = 0.184370 restraints weight = 30365.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4744 r_free = 0.4744 target = 0.186565 restraints weight = 17228.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.4760 r_free = 0.4760 target = 0.188164 restraints weight = 10877.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.4753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4381
moved from start:          0.2745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.113   8595  Z= 0.229
  Angle     :  0.774  11.466  11917  Z= 0.403
  Chirality :  0.045   0.221   1335
  Planarity :  0.006   0.060   1270
  Dihedral  : 18.971 119.058   1942
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 18.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 11.37 %
    Favored  : 85.79 %
  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: -1.75 (0.28), residues: 830
  helix: -0.24 (0.26), residues: 364
  sheet: -1.02 (0.59), residues: 72
  loop : -2.10 (0.29), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 497 
 HIS   0.010   0.003   HIS A 712 
 PHE   0.024   0.003   PHE A 674 
 TYR   0.022   0.003   TYR A 476 
 ARG   0.008   0.001   ARG A 739 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06166 (  320)
  hydrogen bonds       : angle       5.55858 (  866)
  metal coordination   : bond        0.01286 (    7)
  metal coordination   : angle       8.25082 (    2)
  covalent geometry    : bond        0.00498 ( 8588)
  covalent geometry    : angle       0.76694 (11915)

*********************** 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
  114 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 1.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  245 MET cc_start: 0.0610 (ptt) cc_final: 0.0399 (ptt)
REVERT: A  246 ARG cc_start: 0.4385 (mpt90) cc_final: 0.1304 (ttp80)
REVERT: A  534 ASP cc_start: 0.7436 (p0) cc_final: 0.7232 (p0)
REVERT: A  689 LYS cc_start: 0.7026 (pptt) cc_final: 0.6307 (tptt)
REVERT: A  770 ARG cc_start: 0.3585 (mtt90) cc_final: 0.2346 (ptp-170)
REVERT: A  824 MET cc_start: 0.4803 (mmm) cc_final: 0.3631 (mtp)
  outliers start: 21
  outliers final: 8
  residues processed: 108
  average time/residue: 0.3140
  time to fit residues: 45.9195
Evaluate side-chains
  89 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
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:    0.0770
   chunk 72 optimal weight:    0.5980
   chunk 14 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 30 optimal weight:   10.0000
   chunk 66 optimal weight:    9.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    2.3344

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4860 r_free = 0.4860 target = 0.197485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4738 r_free = 0.4738 target = 0.186031 restraints weight = 29983.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4764 r_free = 0.4764 target = 0.188214 restraints weight = 17001.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.4780 r_free = 0.4780 target = 0.189823 restraints weight = 10804.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.4771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4289
moved from start:          0.2913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8595  Z= 0.141
  Angle     :  0.637   9.431  11917  Z= 0.328
  Chirality :  0.040   0.224   1335
  Planarity :  0.005   0.060   1270
  Dihedral  : 18.798 118.246   1942
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 15.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.07 %
    Favored  : 83.90 %
  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: -1.61 (0.28), residues: 830
  helix: -0.08 (0.27), residues: 363
  sheet: -0.81 (0.61), residues: 72
  loop : -2.09 (0.28), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 700 
 HIS   0.006   0.001   HIS A 768 
 PHE   0.016   0.002   PHE A 708 
 TYR   0.014   0.002   TYR A 476 
 ARG   0.005   0.000   ARG A 621 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05032 (  320)
  hydrogen bonds       : angle       5.06677 (  866)
  metal coordination   : bond        0.01248 (    7)
  metal coordination   : angle       6.73440 (    2)
  covalent geometry    : bond        0.00306 ( 8588)
  covalent geometry    : angle       0.63102 (11915)

*********************** 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
  108 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  245 MET cc_start: 0.0778 (ptt) cc_final: 0.0536 (ptt)
REVERT: A  246 ARG cc_start: 0.4588 (mpt90) cc_final: 0.1410 (ttp80)
REVERT: A  515 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6522 (mp)
REVERT: A  599 ARG cc_start: 0.4543 (tpm170) cc_final: 0.4243 (tpt170)
REVERT: A  689 LYS cc_start: 0.6983 (pptt) cc_final: 0.6336 (tptt)
REVERT: A  770 ARG cc_start: 0.3505 (mtt90) cc_final: 0.2482 (ptp-170)
REVERT: A  824 MET cc_start: 0.5022 (mmm) cc_final: 0.4105 (mtp)
REVERT: A  838 TYR cc_start: 0.5021 (m-80) cc_final: 0.4783 (m-80)
  outliers start: 15
  outliers final: 9
  residues processed: 102
  average time/residue: 0.2604
  time to fit residues: 34.5360
Evaluate side-chains
  94 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
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  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  515 LEU
Chi-restraints excluded: chain A residue  518 ILE
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:    7.9990
   chunk 57 optimal weight:    3.9990
   chunk 27 optimal weight:    8.9990
   chunk 70 optimal weight:    3.9990
   chunk 13 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 67 optimal weight:    8.9990
   chunk 3 optimal weight:    0.4980
   overall best weight:    2.6988

-------------------------------------------------------------------------------
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**
** A 821 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 = 0.4846 r_free = 0.4846 target = 0.196086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4724 r_free = 0.4724 target = 0.184906 restraints weight = 29738.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4750 r_free = 0.4750 target = 0.187084 restraints weight = 16915.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.4767 r_free = 0.4767 target = 0.188606 restraints weight = 10709.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.4762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4325
moved from start:          0.3261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   8595  Z= 0.155
  Angle     :  0.654   9.455  11917  Z= 0.337
  Chirality :  0.040   0.222   1335
  Planarity :  0.005   0.057   1270
  Dihedral  : 18.874 117.840   1942
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 16.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 16.51 %
    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: -1.73 (0.28), residues: 830
  helix: -0.21 (0.27), residues: 370
  sheet: -0.98 (0.61), residues: 74
  loop : -2.13 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 700 
 HIS   0.006   0.001   HIS A 216 
 PHE   0.016   0.002   PHE A 674 
 TYR   0.015   0.002   TYR A 476 
 ARG   0.005   0.000   ARG A 621 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05139 (  320)
  hydrogen bonds       : angle       5.08412 (  866)
  metal coordination   : bond        0.01279 (    7)
  metal coordination   : angle       6.76022 (    2)
  covalent geometry    : bond        0.00344 ( 8588)
  covalent geometry    : angle       0.64831 (11915)

*********************** 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
  104 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.748 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.4725 (mmm) cc_final: 0.3745 (mtt)
REVERT: A  238 MET cc_start: 0.1741 (tpt) cc_final: -0.0471 (ptt)
REVERT: A  245 MET cc_start: 0.0857 (ptt) cc_final: 0.0636 (ptt)
REVERT: A  246 ARG cc_start: 0.4701 (mpt90) cc_final: 0.1450 (ttp80)
REVERT: A  367 LYS cc_start: 0.5668 (OUTLIER) cc_final: 0.3926 (tptp)
REVERT: A  515 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6467 (mp)
REVERT: A  689 LYS cc_start: 0.6930 (pptt) cc_final: 0.6397 (tptt)
REVERT: A  770 ARG cc_start: 0.3470 (mtt90) cc_final: 0.2497 (ptp-170)
REVERT: A  797 ILE cc_start: 0.5352 (OUTLIER) cc_final: 0.4975 (mm)
REVERT: A  824 MET cc_start: 0.5152 (mmm) cc_final: 0.4141 (mtp)
REVERT: A  838 TYR cc_start: 0.5051 (m-80) cc_final: 0.4796 (m-80)
  outliers start: 20
  outliers final: 8
  residues processed: 100
  average time/residue: 0.2708
  time to fit residues: 36.2738
Evaluate side-chains
  88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
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  252 TYR
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  367 LYS
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  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 87 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 62 optimal weight:    7.9990
   chunk 50 optimal weight:   20.0000
   chunk 58 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 76 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 75 optimal weight:    7.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A 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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4871 r_free = 0.4871 target = 0.199081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4751 r_free = 0.4751 target = 0.188112 restraints weight = 29778.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4778 r_free = 0.4778 target = 0.190318 restraints weight = 17189.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.4795 r_free = 0.4795 target = 0.191859 restraints weight = 10861.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.4785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4155
moved from start:          0.3274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8595  Z= 0.109
  Angle     :  0.569   7.272  11917  Z= 0.295
  Chirality :  0.038   0.222   1335
  Planarity :  0.004   0.049   1270
  Dihedral  : 18.652 116.344   1942
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.59 %
    Favored  : 80.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.51 (0.28), residues: 830
  helix:  0.03 (0.27), residues: 371
  sheet: -0.58 (0.65), residues: 62
  loop : -2.12 (0.28), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 803 
 HIS   0.004   0.001   HIS A 216 
 PHE   0.012   0.002   PHE A 708 
 TYR   0.010   0.001   TYR A 531 
 ARG   0.004   0.000   ARG A 212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04406 (  320)
  hydrogen bonds       : angle       4.77528 (  866)
  metal coordination   : bond        0.01367 (    7)
  metal coordination   : angle       4.69971 (    2)
  covalent geometry    : bond        0.00233 ( 8588)
  covalent geometry    : angle       0.56590 (11915)

*********************** 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: 16
    poor density    : 94
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.4818 (mmm) cc_final: 0.4012 (mtt)
REVERT: A  238 MET cc_start: 0.2337 (tpt) cc_final: 0.0151 (ptt)
REVERT: A  245 MET cc_start: 0.0905 (ptt) cc_final: 0.0698 (ptt)
REVERT: A  246 ARG cc_start: 0.4727 (mpt90) cc_final: 0.1508 (ptp90)
REVERT: A  668 LYS cc_start: 0.6796 (tttm) cc_final: 0.6523 (tttm)
REVERT: A  689 LYS cc_start: 0.6858 (pptt) cc_final: 0.6395 (tptt)
REVERT: A  770 ARG cc_start: 0.3355 (mtt90) cc_final: 0.2288 (ptp-170)
REVERT: A  824 MET cc_start: 0.5219 (mmm) cc_final: 0.4076 (mtp)
  outliers start: 16
  outliers final: 9
  residues processed: 103
  average time/residue: 0.2474
  time to fit residues: 33.7994
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  : 0.815 
-------------------------------------------------------------------------------
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  359 VAL
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   chunk 48 optimal weight:    8.9990
   chunk 45 optimal weight:    0.0570
   chunk 15 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   chunk 34 optimal weight:    5.9990
   overall best weight:    1.2106

-------------------------------------------------------------------------------
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 = 0.4872 r_free = 0.4872 target = 0.198959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4752 r_free = 0.4752 target = 0.188353 restraints weight = 29742.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4778 r_free = 0.4778 target = 0.190462 restraints weight = 17323.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.4795 r_free = 0.4795 target = 0.191914 restraints weight = 10959.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.4787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4154
moved from start:          0.3483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8595  Z= 0.112
  Angle     :  0.583   6.933  11917  Z= 0.301
  Chirality :  0.038   0.218   1335
  Planarity :  0.004   0.046   1270
  Dihedral  : 18.549 114.949   1942
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 16.91 %
    Favored  : 80.51 %
  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: -1.51 (0.28), residues: 830
  helix:  0.09 (0.27), residues: 370
  sheet: -1.19 (0.60), residues: 72
  loop : -2.07 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 382 
 HIS   0.004   0.001   HIS A 768 
 PHE   0.016   0.002   PHE A 708 
 TYR   0.016   0.001   TYR A 882 
 ARG   0.003   0.000   ARG A 621 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04350 (  320)
  hydrogen bonds       : angle       4.78630 (  866)
  metal coordination   : bond        0.01342 (    7)
  metal coordination   : angle       4.63237 (    2)
  covalent geometry    : bond        0.00243 ( 8588)
  covalent geometry    : angle       0.57960 (11915)

*********************** 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
  102 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 MET cc_start: 0.2407 (tpt) cc_final: 0.0224 (ptt)
REVERT: A  245 MET cc_start: 0.1048 (ptt) cc_final: 0.0799 (ptt)
REVERT: A  246 ARG cc_start: 0.4845 (mpt90) cc_final: 0.1616 (ptp90)
REVERT: A  367 LYS cc_start: 0.5379 (OUTLIER) cc_final: 0.4129 (tptp)
REVERT: A  668 LYS cc_start: 0.6792 (tttm) cc_final: 0.6501 (tttm)
REVERT: A  689 LYS cc_start: 0.6897 (pptt) cc_final: 0.6489 (tptt)
REVERT: A  824 MET cc_start: 0.5133 (OUTLIER) cc_final: 0.4089 (mtp)
  outliers start: 19
  outliers final: 13
  residues processed: 98
  average time/residue: 0.2523
  time to fit residues: 32.7911
Evaluate side-chains
  94 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
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  252 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  367 LYS
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  609 LEU
Chi-restraints excluded: chain A residue  612 PHE
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  824 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 57 optimal weight:   10.0000
   chunk 86 optimal weight:    9.9990
   chunk 24 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 21 optimal weight:    5.9990
   chunk 85 optimal weight:   10.0000
   chunk 79 optimal weight:    4.9990
   chunk 87 optimal weight:    9.9990
   chunk 20 optimal weight:    7.9990
   chunk 56 optimal weight:    1.9990
   chunk 67 optimal weight:   20.0000
   overall best weight:    2.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4833 r_free = 0.4833 target = 0.195257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4710 r_free = 0.4710 target = 0.184613 restraints weight = 29753.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4738 r_free = 0.4738 target = 0.186844 restraints weight = 16864.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.4756 r_free = 0.4756 target = 0.188377 restraints weight = 10549.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.4748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4345
moved from start:          0.3972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   8595  Z= 0.169
  Angle     :  0.699   9.457  11917  Z= 0.361
  Chirality :  0.042   0.218   1335
  Planarity :  0.006   0.058   1270
  Dihedral  : 18.800 116.808   1942
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 17.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 17.46 %
    Favored  : 79.57 %
  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: -1.85 (0.28), residues: 830
  helix: -0.26 (0.27), residues: 369
  sheet: -1.22 (0.63), residues: 64
  loop : -2.20 (0.29), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 382 
 HIS   0.006   0.001   HIS A 634 
 PHE   0.018   0.003   PHE A 708 
 TYR   0.014   0.002   TYR A 186 
 ARG   0.007   0.001   ARG A 599 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05272 (  320)
  hydrogen bonds       : angle       5.18943 (  866)
  metal coordination   : bond        0.01274 (    7)
  metal coordination   : angle       5.66164 (    2)
  covalent geometry    : bond        0.00373 ( 8588)
  covalent geometry    : angle       0.69525 (11915)

*********************** 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  : 0.943 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.4110 (mmp) cc_final: 0.3150 (mtt)
REVERT: A  245 MET cc_start: 0.1097 (ptt) cc_final: 0.0880 (ptt)
REVERT: A  246 ARG cc_start: 0.4899 (mpt90) cc_final: 0.1647 (ttp80)
REVERT: A  327 LEU cc_start: 0.1365 (OUTLIER) cc_final: 0.0737 (pp)
REVERT: A  367 LYS cc_start: 0.5731 (OUTLIER) cc_final: 0.3923 (tptp)
REVERT: A  599 ARG cc_start: 0.5642 (OUTLIER) cc_final: 0.5346 (tmm-80)
REVERT: A  668 LYS cc_start: 0.7164 (tttm) cc_final: 0.6652 (tttm)
REVERT: A  689 LYS cc_start: 0.7079 (pptt) cc_final: 0.6684 (tptt)
REVERT: A  770 ARG cc_start: 0.3419 (mtt90) cc_final: 0.2227 (ptp-170)
REVERT: A  824 MET cc_start: 0.5150 (mmm) cc_final: 0.4066 (mtp)
  outliers start: 22
  outliers final: 15
  residues processed: 99
  average time/residue: 0.2444
  time to fit residues: 32.6575
Evaluate side-chains
  93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
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  335 VAL
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  577 VAL
Chi-restraints excluded: chain A residue  599 ARG
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  612 PHE
Chi-restraints excluded: chain A residue  615 MET
Chi-restraints excluded: chain A residue  723 VAL
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:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0370
   chunk 30 optimal weight:    8.9990
   chunk 72 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 24 optimal weight:   20.0000
   chunk 49 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9980
   chunk 88 optimal weight:   10.0000
   overall best weight:    0.9460

-------------------------------------------------------------------------------
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 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 712 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 = 0.4883 r_free = 0.4883 target = 0.199542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4756 r_free = 0.4756 target = 0.188735 restraints weight = 29953.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4785 r_free = 0.4785 target = 0.191021 restraints weight = 17450.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.4804 r_free = 0.4804 target = 0.192638 restraints weight = 11033.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.4794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4180
moved from start:          0.3955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8595  Z= 0.109
  Angle     :  0.599   9.442  11917  Z= 0.306
  Chirality :  0.038   0.220   1335
  Planarity :  0.005   0.053   1270
  Dihedral  : 18.634 115.158   1942
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 17.73 %
    Favored  : 79.84 %
  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: -1.47 (0.28), residues: 830
  helix:  0.12 (0.27), residues: 370
  sheet: -1.10 (0.60), residues: 72
  loop : -2.07 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 382 
 HIS   0.004   0.001   HIS A 216 
 PHE   0.013   0.001   PHE A 674 
 TYR   0.010   0.001   TYR A 607 
 ARG   0.005   0.000   ARG A 599 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04345 (  320)
  hydrogen bonds       : angle       4.86688 (  866)
  metal coordination   : bond        0.01604 (    7)
  metal coordination   : angle       3.66437 (    2)
  covalent geometry    : bond        0.00239 ( 8588)
  covalent geometry    : angle       0.59667 (11915)

*********************** 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: 18
    poor density    : 79
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.3836 (mmp) cc_final: 0.2958 (mtt)
REVERT: A  245 MET cc_start: 0.1021 (ptt) cc_final: 0.0788 (ptt)
REVERT: A  246 ARG cc_start: 0.4932 (mpt90) cc_final: 0.1608 (ptp90)
REVERT: A  327 LEU cc_start: 0.1770 (OUTLIER) cc_final: 0.1269 (pp)
REVERT: A  668 LYS cc_start: 0.6941 (tttm) cc_final: 0.6671 (tttm)
REVERT: A  689 LYS cc_start: 0.7054 (pptt) cc_final: 0.6616 (tptt)
REVERT: A  770 ARG cc_start: 0.3382 (mtt90) cc_final: 0.1974 (ptp-170)
REVERT: A  824 MET cc_start: 0.5172 (OUTLIER) cc_final: 0.4147 (mtp)
REVERT: A  882 TYR cc_start: 0.3783 (m-80) cc_final: 0.3418 (m-80)
  outliers start: 18
  outliers final: 11
  residues processed: 92
  average time/residue: 0.2351
  time to fit residues: 28.9587
Evaluate side-chains
  90 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
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  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  609 LEU
Chi-restraints excluded: chain A residue  612 PHE
Chi-restraints excluded: chain A residue  723 VAL
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 50 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 74 optimal weight:    9.9990
   chunk 38 optimal weight:    4.9990
   chunk 52 optimal weight:    9.9990
   chunk 72 optimal weight:    0.9990
   chunk 44 optimal weight:    8.9990
   chunk 2 optimal weight:    5.9990
   chunk 20 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    1.3990

-------------------------------------------------------------------------------
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 = 0.4873 r_free = 0.4873 target = 0.198803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4753 r_free = 0.4753 target = 0.188567 restraints weight = 29635.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4779 r_free = 0.4779 target = 0.190645 restraints weight = 17604.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.4796 r_free = 0.4796 target = 0.192055 restraints weight = 11292.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.4791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4195
moved from start:          0.4062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8595  Z= 0.117
  Angle     :  0.610   8.478  11917  Z= 0.314
  Chirality :  0.039   0.215   1335
  Planarity :  0.005   0.058   1270
  Dihedral  : 18.576 113.972   1942
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 14.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 18.00 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.28), residues: 830
  helix:  0.12 (0.27), residues: 370
  sheet: -1.09 (0.65), residues: 62
  loop : -2.08 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 382 
 HIS   0.004   0.001   HIS A 768 
 PHE   0.016   0.002   PHE A 708 
 TYR   0.011   0.001   TYR A 186 
 ARG   0.008   0.000   ARG A 739 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04431 (  320)
  hydrogen bonds       : angle       4.86478 (  866)
  metal coordination   : bond        0.01475 (    7)
  metal coordination   : angle       3.98393 (    2)
  covalent geometry    : bond        0.00259 ( 8588)
  covalent geometry    : angle       0.60786 (11915)

********************** 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
  96 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.3669 (mmp) cc_final: 0.2830 (mtt)
REVERT: A  245 MET cc_start: 0.1027 (ptt) cc_final: 0.0782 (ptt)
REVERT: A  246 ARG cc_start: 0.4900 (mpt90) cc_final: 0.1589 (ptp90)
REVERT: A  327 LEU cc_start: 0.1841 (OUTLIER) cc_final: 0.1210 (pp)
REVERT: A  623 MET cc_start: 0.2668 (ptp) cc_final: 0.2430 (ptm)
REVERT: A  668 LYS cc_start: 0.6912 (tttm) cc_final: 0.6559 (tttm)
REVERT: A  689 LYS cc_start: 0.7114 (pptt) cc_final: 0.6766 (tptt)
REVERT: A  770 ARG cc_start: 0.3249 (mtt90) cc_final: 0.1802 (ptp-170)
REVERT: A  824 MET cc_start: 0.5160 (OUTLIER) cc_final: 0.4089 (mtp)
REVERT: A  882 TYR cc_start: 0.3780 (m-80) cc_final: 0.3427 (m-80)
  outliers start: 17
  outliers final: 13
  residues processed: 92
  average time/residue: 0.2364
  time to fit residues: 29.5122
Evaluate side-chains
  92 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
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  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  483 PHE
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  612 PHE
Chi-restraints excluded: chain A residue  615 MET
Chi-restraints excluded: chain A residue  723 VAL
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:    1.9990
   chunk 25 optimal weight:    0.0010
   chunk 85 optimal weight:   10.0000
   chunk 72 optimal weight:    7.9990
   chunk 18 optimal weight:    0.1980
   chunk 62 optimal weight:    9.9990
   chunk 43 optimal weight:    0.0040
   chunk 9 optimal weight:    9.9990
   chunk 34 optimal weight:    1.9990
   chunk 69 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.6400

-------------------------------------------------------------------------------
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
** A 712 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 = 0.4893 r_free = 0.4893 target = 0.200724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4772 r_free = 0.4772 target = 0.190478 restraints weight = 29982.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4799 r_free = 0.4799 target = 0.192591 restraints weight = 17854.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.4816 r_free = 0.4816 target = 0.193986 restraints weight = 11390.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.4808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4103
moved from start:          0.4113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.086   8595  Z= 0.105
  Angle     :  0.595  10.139  11917  Z= 0.303
  Chirality :  0.037   0.213   1335
  Planarity :  0.005   0.052   1270
  Dihedral  : 18.420 112.625   1942
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 18.13 %
    Favored  : 79.57 %
  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: -1.32 (0.29), residues: 830
  helix:  0.27 (0.27), residues: 373
  sheet: -1.36 (0.56), residues: 82
  loop : -1.96 (0.30), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 382 
 HIS   0.005   0.001   HIS A 712 
 PHE   0.019   0.001   PHE A 708 
 TYR   0.008   0.001   TYR A 186 
 ARG   0.007   0.000   ARG A 739 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04119 (  320)
  hydrogen bonds       : angle       4.78035 (  866)
  metal coordination   : bond        0.03711 (    7)
  metal coordination   : angle       6.46733 (    2)
  covalent geometry    : bond        0.00226 ( 8588)
  covalent geometry    : angle       0.58916 (11915)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3311.84 seconds
wall clock time: 58 minutes 45.00 seconds (3525.00 seconds total)