Starting phenix.real_space_refine
on Fri Jun  6 04:47:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hhl_34803/06_2025/8hhl_34803.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hhl_34803/06_2025/8hhl_34803.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hhl_34803/06_2025/8hhl_34803.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hhl_34803/06_2025/8hhl_34803.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hhl_34803/06_2025/8hhl_34803.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hhl_34803/06_2025/8hhl_34803.cif"
  }
  resolution = 2.87
  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
-------------------------------------------------------------------------------
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=  -0.012 sd=   0.253
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: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     111      5.49       5
     Mg      3      5.21       5
     S      19      5.16       5
     C    3939      2.51       5
     N    1321      2.21       5
     O    1577      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6971
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1066
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 1066
          Classifications: {'RNA': 49}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 28, 'rna3p_pyr': 16}
          Link IDs: {'rna2p': 5, 'rna3p': 43}
    Chain: "C"
      Number of atoms: 624
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 624
          Classifications: {'DNA': 31}
          Link IDs: {'rna3p': 30}
    Chain: "D"
      Number of atoms: 647
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 647
          Classifications: {'DNA': 31}
          Link IDs: {'rna3p': 30}
    Chain: "A"
      Number of atoms: 4630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 592, 4630
          Classifications: {'peptide': 592}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 567}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 1, ' ZN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   6663  SG  CYS A 552      87.861  24.922  31.530  1.00120.60           S
  ATOM   6796  SG  CYS A 569      84.715  23.574  29.746  1.00120.99           S
  ATOM   6814  SG  CYS A 572      86.921  21.084  31.118  1.00121.86           S

  Time building chain proxies: 5.01, per 1000 atoms: 0.72
  Number of scatterers: 6971
  At special positions: 0
  Unit cell: (101.094, 89.474, 103.418, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      19     16.00
     P     111     15.00
     Mg      3     11.99
     O    1577      8.00
     N    1321      7.00
     C    3939      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: 2.26
  Conformation dependent library (CDL) restraints added in 608.0 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 602 "
        pdb="ZN    ZN A 602 " - pdb=" ND1 HIS A 549 "
        pdb="ZN    ZN A 602 " - pdb=" SG  CYS A 572 "
        pdb="ZN    ZN A 602 " - pdb=" SG  CYS A 552 "
        pdb="ZN    ZN A 602 " - pdb=" SG  CYS A 569 "
      Number of angles added : 3


  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1120

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 3 sheets defined
      58.1% alpha, 14.4% beta
      40 base pairs and 72 stacking pairs defined.
    Time for finding SS restraints: 3.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 52
    Processing helix  chain 'A' and resid 53 through 85
    Processing helix  chain 'A' and resid 90 through 118
      removed outlier: 3.558A  pdb=" N   THR A  94 " --> pdb=" O   SER A  90 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   VAL A 118 " --> pdb=" O   ALA A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 121
      No H-bonds generated for 'chain 'A' and resid 119 through 121'
    Processing helix  chain 'A' and resid 122 through 145
    Processing helix  chain 'A' and resid 151 through 176
    Processing helix  chain 'A' and resid 206 through 211
      removed outlier: 3.605A  pdb=" N   LEU A 210 " --> pdb=" O   THR A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 233
    Processing helix  chain 'A' and resid 236 through 244
    Processing helix  chain 'A' and resid 341 through 345
    Processing helix  chain 'A' and resid 362 through 397
      removed outlier: 4.195A  pdb=" N   GLU A 366 " --> pdb=" O   PRO A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 414
    Processing helix  chain 'A' and resid 417 through 428
      removed outlier: 4.230A  pdb=" N   PHE A 421 " --> pdb=" O   SER A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 431
      No H-bonds generated for 'chain 'A' and resid 429 through 431'
    Processing helix  chain 'A' and resid 434 through 479
      removed outlier: 3.520A  pdb=" N   TRP A 442 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   PHE A 443 " --> pdb=" O   LEU A 439 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU A 445 " --> pdb=" O   ALA A 441 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   ALA A 451 " --> pdb=" O   ARG A 447 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   ARG A 457 " --> pdb=" O   GLN A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 500
      removed outlier: 4.495A  pdb=" N   MET A 497 " --> pdb=" O   SER A 493 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   GLU A 498 " --> pdb=" O   ALA A 494 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ARG A 499 " --> pdb=" O   ARG A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 518
    Processing helix  chain 'A' and resid 518 through 534
    Processing helix  chain 'A' and resid 560 through 564
      removed outlier: 3.570A  pdb=" N   LEU A 563 " --> pdb=" O   ASP A 560 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   SER A 564 " --> pdb=" O   ARG A 561 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 560 through 564'
    Processing helix  chain 'A' and resid 579 through 591
    Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 195
      removed outlier: 6.076A  pdb=" N   ILE A 278 " --> pdb=" O   ARG A 301 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   ARG A 301 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLY A 280 " --> pdb=" O   THR A 299 " (cutoff:3.500A)
      removed outlier: 5.644A  pdb=" N   ALA A 294 " --> pdb=" O   VAL A  11 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLY A  10 " --> pdb=" O   GLN A 267 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   GLY A 253 " --> pdb=" O   GLN A 260 " (cutoff:3.500A)
      removed outlier: 5.892A  pdb=" N   ILE A 262 " --> pdb=" O   ARG A 251 " (cutoff:3.500A)
      removed outlier: 5.514A  pdb=" N   ARG A 251 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   LEU A 264 " --> pdb=" O   ARG A 249 " (cutoff:3.500A)
      removed outlier: 5.558A  pdb=" N   ARG A 249 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   VAL A 266 " --> pdb=" O   THR A 247 " (cutoff:3.500A)
      removed outlier: 5.267A  pdb=" N   THR A 247 " --> pdb=" O   VAL A 266 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 356 through 360
      removed outlier: 4.813A  pdb=" N   THR A 327 " --> pdb=" O   ARG A 321 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   ARG A 321 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   VAL A 329 " --> pdb=" O   GLY A 319 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ASP A 485 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
      removed outlier: 7.238A  pdb=" N   LEU A 318 " --> pdb=" O   ASP A 485 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 567 through 568

    300 hydrogen bonds defined for protein.
    879 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      105 hydrogen bonds
      206 hydrogen bond angles
      0 basepair planarities
      40 basepair parallelities
      72 stacking parallelities
  Total time for adding SS restraints: 2.97

  Time building geometry restraints manager: 2.61 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1580
        1.33 -     1.45: 2077
        1.45 -     1.57: 3432
        1.57 -     1.69: 219
        1.69 -     1.81: 31
  Bond restraints: 7339
  Sorted by residual:
  bond pdb=" C3'  DG D  -9 "
       pdb=" O3'  DG D  -9 "
    ideal  model  delta    sigma   weight residual
    1.422  1.484 -0.062 3.00e-02 1.11e+03 4.24e+00
  bond pdb=" C3'  DT D -10 "
       pdb=" O3'  DT D -10 "
    ideal  model  delta    sigma   weight residual
    1.422  1.460 -0.038 3.00e-02 1.11e+03 1.59e+00
  bond pdb=" C2'  DG D   0 "
       pdb=" C1'  DG D   0 "
    ideal  model  delta    sigma   weight residual
    1.525  1.504  0.021 2.00e-02 2.50e+03 1.07e+00
  bond pdb=" CA  ASP A 560 "
       pdb=" CB  ASP A 560 "
    ideal  model  delta    sigma   weight residual
    1.532  1.547 -0.015 1.51e-02 4.39e+03 9.66e-01
  bond pdb=" O4'  DG D   0 "
       pdb=" C1'  DG D   0 "
    ideal  model  delta    sigma   weight residual
    1.414  1.395  0.019 2.00e-02 2.50e+03 9.01e-01
  ... (remaining 7334 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.18: 10112
        1.18 -     2.36: 291
        2.36 -     3.55: 57
        3.55 -     4.73: 8
        4.73 -     5.91: 2
  Bond angle restraints: 10470
  Sorted by residual:
  angle pdb=" C2'  DG D   0 "
        pdb=" C1'  DG D   0 "
        pdb=" N9   DG D   0 "
      ideal   model   delta    sigma   weight residual
     113.50  117.07   -3.57 1.50e+00 4.44e-01 5.66e+00
  angle pdb=" C   ASP A 559 "
        pdb=" N   ASP A 560 "
        pdb=" CA  ASP A 560 "
      ideal   model   delta    sigma   weight residual
     122.61  126.22   -3.61 1.56e+00 4.11e-01 5.36e+00
  angle pdb=" C4'  DG D   0 "
        pdb=" O4'  DG D   0 "
        pdb=" C1'  DG D   0 "
      ideal   model   delta    sigma   weight residual
     109.70  106.45    3.25 1.50e+00 4.44e-01 4.70e+00
  angle pdb=" CA  ASP A 560 "
        pdb=" CB  ASP A 560 "
        pdb=" CG  ASP A 560 "
      ideal   model   delta    sigma   weight residual
     112.60  114.65   -2.05 1.00e+00 1.00e+00 4.21e+00
  angle pdb=" OP2  DT D  -8 "
        pdb=" P    DT D  -8 "
        pdb=" O5'  DT D  -8 "
      ideal   model   delta    sigma   weight residual
     108.00  102.09    5.91 3.00e+00 1.11e-01 3.88e+00
  ... (remaining 10465 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.75: 3630
       23.75 -    47.50: 449
       47.50 -    71.25: 226
       71.25 -    95.00: 19
       95.00 -   118.75: 1
  Dihedral angle restraints: 4325
    sinusoidal: 2602
      harmonic: 1723
  Sorted by residual:
  dihedral pdb=" O4'   G B -11 "
           pdb=" C1'   G B -11 "
           pdb=" N9    G B -11 "
           pdb=" C4    G B -11 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -172.34   66.34     1      1.70e+01 3.46e-03 1.99e+01
  dihedral pdb=" C4'  DG D  -9 "
           pdb=" C3'  DG D  -9 "
           pdb=" O3'  DG D  -9 "
           pdb=" P    DT D  -8 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00  101.25  118.75     1      3.50e+01 8.16e-04 1.16e+01
  dihedral pdb=" CA  ASP A 477 "
           pdb=" CB  ASP A 477 "
           pdb=" CG  ASP A 477 "
           pdb=" OD1 ASP A 477 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.97   56.97     1      2.00e+01 2.50e-03 1.09e+01
  ... (remaining 4322 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 889
       0.033 -    0.066: 241
       0.066 -    0.099: 58
       0.099 -    0.133: 17
       0.133 -    0.166: 5
  Chirality restraints: 1210
  Sorted by residual:
  chirality pdb=" C1'  DG D   0 "
            pdb=" O4'  DG D   0 "
            pdb=" C2'  DG D   0 "
            pdb=" N9   DG D   0 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.25    0.17 2.00e-01 2.50e+01 6.87e-01
  chirality pdb=" CA  ASP A 560 "
            pdb=" N   ASP A 560 "
            pdb=" C   ASP A 560 "
            pdb=" CB  ASP A 560 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.69e-01
  chirality pdb=" CA  ILE A 358 "
            pdb=" N   ILE A 358 "
            pdb=" C   ILE A 358 "
            pdb=" CB  ILE A 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.67e-01
  ... (remaining 1207 not shown)

  Planarity restraints: 951
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG D   0 "    0.027 2.00e-02 2.50e+03   1.15e-02 3.97e+00
        pdb=" N9   DG D   0 "   -0.028 2.00e-02 2.50e+03
        pdb=" C8   DG D   0 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7   DG D   0 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5   DG D   0 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG D   0 "    0.004 2.00e-02 2.50e+03
        pdb=" O6   DG D   0 "    0.007 2.00e-02 2.50e+03
        pdb=" N1   DG D   0 "    0.002 2.00e-02 2.50e+03
        pdb=" C2   DG D   0 "   -0.002 2.00e-02 2.50e+03
        pdb=" N2   DG D   0 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3   DG D   0 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DG D   0 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B   2 "    0.025 2.00e-02 2.50e+03   1.06e-02 3.34e+00
        pdb=" N9    G B   2 "   -0.024 2.00e-02 2.50e+03
        pdb=" C8    G B   2 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7    G B   2 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G B   2 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    G B   2 "    0.004 2.00e-02 2.50e+03
        pdb=" O6    G B   2 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    G B   2 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    G B   2 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G B   2 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    G B   2 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4    G B   2 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 452 "    0.009 2.00e-02 2.50e+03   1.78e-02 3.18e+00
        pdb=" C   GLN A 452 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   GLN A 452 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLN A 453 "    0.010 2.00e-02 2.50e+03
  ... (remaining 948 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 215
        2.68 -     3.24: 6117
        3.24 -     3.79: 12497
        3.79 -     4.35: 16282
        4.35 -     4.90: 24625
  Nonbonded interactions: 59736
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 579 "
            pdb="MG    MG A 601 "
     model   vdw
     2.126 2.170
  nonbonded pdb=" OP1   G B -22 "
            pdb="MG    MG B 101 "
     model   vdw
     2.134 2.170
  nonbonded pdb=" OP1  DG D  15 "
            pdb="MG    MG A 601 "
     model   vdw
     2.143 2.170
  nonbonded pdb=" OG  SER A 334 "
            pdb=" O   ALA A 336 "
     model   vdw
     2.154 3.040
  nonbonded pdb=" NE2 HIS A 317 "
            pdb="MG    MG A 601 "
     model   vdw
     2.198 2.250
  ... (remaining 59731 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 individual isotropic
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:             0.080
  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:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     25.540
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
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      :  0.004   0.062   7343  Z= 0.172
  Angle     :  0.513   9.011  10473  Z= 0.285
  Chirality :  0.035   0.166   1210
  Planarity :  0.004   0.042    951
  Dihedral  : 22.356 118.750   3205
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 12.29 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.35), residues: 590
  helix:  2.63 (0.29), residues: 323
  sheet:  1.62 (0.63), residues: 60
  loop : -0.37 (0.41), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 232 
 HIS   0.002   0.000   HIS A  12 
 PHE   0.006   0.001   PHE A 443 
 TYR   0.010   0.001   TYR A  42 
 ARG   0.002   0.000   ARG A 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12160 (  405)
  hydrogen bonds       : angle       5.09844 ( 1085)
  metal coordination   : bond        0.03038 (    4)
  metal coordination   : angle       7.17526 (    3)
  covalent geometry    : bond        0.00366 ( 7339)
  covalent geometry    : angle       0.49870 (10470)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.654 
Fit side-chains
REVERT: A   63 MET cc_start: 0.8112 (ttt) cc_final: 0.7844 (ttp)
REVERT: A  160 ASP cc_start: 0.7952 (m-30) cc_final: 0.7678 (m-30)
REVERT: A  172 GLN cc_start: 0.7385 (mm-40) cc_final: 0.7002 (mm-40)
REVERT: A  199 GLN cc_start: 0.7801 (mm-40) cc_final: 0.7586 (tt0)
REVERT: A  264 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8790 (mt)
REVERT: A  404 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7712 (p0)
REVERT: A  416 LYS cc_start: 0.6723 (mttt) cc_final: 0.5308 (tttm)
REVERT: A  458 ARG cc_start: 0.8083 (mmm160) cc_final: 0.7644 (mmm-85)
REVERT: A  575 MET cc_start: 0.8659 (mtp) cc_final: 0.8283 (mtt)
  outliers start: 11
  outliers final: 2
  residues processed: 82
  average time/residue: 1.6501
  time to fit residues: 140.7976
Evaluate side-chains
  51 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  404 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 58 optimal weight:    9.9990
   chunk 52 optimal weight:    3.9990
   chunk 29 optimal weight:   10.0000
   chunk 17 optimal weight:   20.0000
   chunk 35 optimal weight:   10.0000
   chunk 27 optimal weight:    8.9990
   chunk 54 optimal weight:    4.9990
   chunk 20 optimal weight:    6.9990
   chunk 32 optimal weight:    0.0670
   chunk 40 optimal weight:   10.0000
   chunk 62 optimal weight:    4.9990
   overall best weight:    4.2126

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN
A 242 GLN
A 478 GLN
A 556 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.136441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.104158 restraints weight = 9684.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 1.50
r_work: 0.3198 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.1171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   7343  Z= 0.215
  Angle     :  0.569   8.867  10473  Z= 0.314
  Chirality :  0.038   0.166   1210
  Planarity :  0.006   0.110    951
  Dihedral  : 23.885 118.270   2123
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 16.88 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.74 (0.34), residues: 590
  helix:  3.07 (0.28), residues: 323
  sheet:  1.81 (0.62), residues: 60
  loop : -0.30 (0.41), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 232 
 HIS   0.002   0.001   HIS A 183 
 PHE   0.005   0.001   PHE A 421 
 TYR   0.009   0.001   TYR A  42 
 ARG   0.010   0.001   ARG A  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05033 (  405)
  hydrogen bonds       : angle       3.65714 ( 1085)
  metal coordination   : bond        0.00356 (    4)
  metal coordination   : angle       1.00980 (    3)
  covalent geometry    : bond        0.00475 ( 7339)
  covalent geometry    : angle       0.56879 (10470)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 49
  time to evaluate  : 0.539 
Fit side-chains
REVERT: A   63 MET cc_start: 0.8333 (ttt) cc_final: 0.8067 (ttp)
REVERT: A   89 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8246 (pp)
REVERT: A  103 ARG cc_start: 0.8330 (mtp180) cc_final: 0.8048 (mtm180)
REVERT: A  160 ASP cc_start: 0.7986 (m-30) cc_final: 0.7704 (m-30)
REVERT: A  172 GLN cc_start: 0.7644 (mm-40) cc_final: 0.7415 (mm-40)
REVERT: A  199 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7828 (tt0)
REVERT: A  416 LYS cc_start: 0.6805 (mttt) cc_final: 0.5463 (tttm)
REVERT: A  458 ARG cc_start: 0.8756 (mmm160) cc_final: 0.8348 (mmm-85)
REVERT: A  459 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8081 (mttp)
REVERT: A  498 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6651 (pm20)
REVERT: A  575 MET cc_start: 0.8607 (mtp) cc_final: 0.8222 (mtt)
  outliers start: 17
  outliers final: 8
  residues processed: 62
  average time/residue: 1.8564
  time to fit residues: 119.4089
Evaluate side-chains
  54 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 THR
Chi-restraints excluded: chain A residue   69 ASP
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  459 LYS
Chi-restraints excluded: chain A residue  498 GLU
Chi-restraints excluded: chain A residue  560 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 43 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   chunk 44 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   chunk 48 optimal weight:    2.9990
   chunk 9 optimal weight:   10.0000
   chunk 29 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9990
   chunk 14 optimal weight:    9.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN
A 478 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.137006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.104698 restraints weight = 9812.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 1.50
r_work: 0.3215 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3090 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.1466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   7343  Z= 0.175
  Angle     :  0.527   8.351  10473  Z= 0.293
  Chirality :  0.036   0.154   1210
  Planarity :  0.004   0.063    951
  Dihedral  : 23.806 116.037   2119
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 18.54 %
    Favored  : 77.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.92 (0.34), residues: 590
  helix:  3.22 (0.27), residues: 324
  sheet:  1.62 (0.60), residues: 62
  loop : -0.15 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 232 
 HIS   0.002   0.000   HIS A 269 
 PHE   0.005   0.001   PHE A 443 
 TYR   0.008   0.001   TYR A  42 
 ARG   0.008   0.000   ARG A 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04557 (  405)
  hydrogen bonds       : angle       3.47153 ( 1085)
  metal coordination   : bond        0.00211 (    4)
  metal coordination   : angle       0.70440 (    3)
  covalent geometry    : bond        0.00385 ( 7339)
  covalent geometry    : angle       0.52709 (10470)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 48
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 MET cc_start: 0.8331 (ttt) cc_final: 0.8061 (ttp)
REVERT: A  146 ARG cc_start: 0.8626 (mtp85) cc_final: 0.8101 (mtm-85)
REVERT: A  172 GLN cc_start: 0.7663 (mm-40) cc_final: 0.7423 (mm-40)
REVERT: A  199 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7853 (tp40)
REVERT: A  416 LYS cc_start: 0.6633 (mttt) cc_final: 0.5325 (tttm)
REVERT: A  458 ARG cc_start: 0.8719 (mmm160) cc_final: 0.8364 (mmm-85)
REVERT: A  459 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8055 (mttp)
REVERT: A  498 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6552 (pm20)
REVERT: A  575 MET cc_start: 0.8586 (mtp) cc_final: 0.8218 (mtt)
  outliers start: 18
  outliers final: 6
  residues processed: 61
  average time/residue: 1.8627
  time to fit residues: 118.1135
Evaluate side-chains
  50 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 THR
Chi-restraints excluded: chain A residue   69 ASP
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  459 LYS
Chi-restraints excluded: chain A residue  498 GLU
Chi-restraints excluded: chain A residue  560 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 55 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9990
   chunk 57 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   chunk 38 optimal weight:    8.9990
   chunk 1 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.136965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.104565 restraints weight = 9929.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 1.51
r_work: 0.3206 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   7343  Z= 0.181
  Angle     :  0.528   7.584  10473  Z= 0.294
  Chirality :  0.036   0.153   1210
  Planarity :  0.004   0.033    951
  Dihedral  : 23.792 114.406   2118
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 18.12 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.94 (0.34), residues: 590
  helix:  3.25 (0.27), residues: 324
  sheet:  1.54 (0.60), residues: 62
  loop : -0.15 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 232 
 HIS   0.002   0.000   HIS A  12 
 PHE   0.006   0.001   PHE A 155 
 TYR   0.008   0.001   TYR A  42 
 ARG   0.003   0.000   ARG A 205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04530 (  405)
  hydrogen bonds       : angle       3.42022 ( 1085)
  metal coordination   : bond        0.00235 (    4)
  metal coordination   : angle       0.69194 (    3)
  covalent geometry    : bond        0.00400 ( 7339)
  covalent geometry    : angle       0.52754 (10470)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 46
  time to evaluate  : 0.636 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 MET cc_start: 0.8321 (ttt) cc_final: 0.8016 (ttp)
REVERT: A  172 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7430 (mm-40)
REVERT: A  199 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7841 (tp40)
REVERT: A  335 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8827 (t0)
REVERT: A  367 ARG cc_start: 0.8077 (mtp85) cc_final: 0.7807 (ttp-110)
REVERT: A  413 LYS cc_start: 0.8098 (tttt) cc_final: 0.7085 (tptp)
REVERT: A  416 LYS cc_start: 0.6707 (mttt) cc_final: 0.5309 (tttm)
REVERT: A  458 ARG cc_start: 0.8755 (mmm160) cc_final: 0.8314 (mmm-85)
REVERT: A  459 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8062 (mttp)
REVERT: A  575 MET cc_start: 0.8583 (mtp) cc_final: 0.8230 (mtt)
  outliers start: 21
  outliers final: 11
  residues processed: 62
  average time/residue: 1.7764
  time to fit residues: 114.4787
Evaluate side-chains
  59 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 THR
Chi-restraints excluded: chain A residue   69 ASP
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  335 ASP
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  459 LYS
Chi-restraints excluded: chain A residue  530 MET
Chi-restraints excluded: chain A residue  560 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 16 optimal weight:   20.0000
   chunk 40 optimal weight:   10.0000
   chunk 57 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 41 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 42 optimal weight:   10.0000
   chunk 46 optimal weight:    6.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.136187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.103857 restraints weight = 9801.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 1.49
r_work: 0.3196 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   7343  Z= 0.200
  Angle     :  0.540   7.655  10473  Z= 0.299
  Chirality :  0.037   0.156   1210
  Planarity :  0.004   0.045    951
  Dihedral  : 23.820 114.330   2118
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 17.50 %
    Favored  : 78.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.89 (0.34), residues: 590
  helix:  3.21 (0.27), residues: 324
  sheet:  1.50 (0.60), residues: 62
  loop : -0.15 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 232 
 HIS   0.002   0.001   HIS A  12 
 PHE   0.006   0.001   PHE A 443 
 TYR   0.009   0.001   TYR A  42 
 ARG   0.004   0.000   ARG A  85 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04682 (  405)
  hydrogen bonds       : angle       3.44042 ( 1085)
  metal coordination   : bond        0.00260 (    4)
  metal coordination   : angle       0.77986 (    3)
  covalent geometry    : bond        0.00442 ( 7339)
  covalent geometry    : angle       0.53996 (10470)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 47
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 MET cc_start: 0.8323 (ttt) cc_final: 0.8066 (ttp)
REVERT: A  172 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7468 (mm-40)
REVERT: A  335 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8827 (t0)
REVERT: A  367 ARG cc_start: 0.8116 (mtp85) cc_final: 0.7830 (ttp-110)
REVERT: A  413 LYS cc_start: 0.8125 (tttt) cc_final: 0.7142 (tptp)
REVERT: A  416 LYS cc_start: 0.6702 (mttt) cc_final: 0.5307 (tttm)
REVERT: A  458 ARG cc_start: 0.8754 (mmm160) cc_final: 0.8322 (mmm-85)
REVERT: A  459 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.8052 (mttp)
REVERT: A  575 MET cc_start: 0.8591 (mtp) cc_final: 0.8238 (mtt)
  outliers start: 18
  outliers final: 10
  residues processed: 60
  average time/residue: 1.8004
  time to fit residues: 112.2423
Evaluate side-chains
  58 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 THR
Chi-restraints excluded: chain A residue   69 ASP
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  335 ASP
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  459 LYS
Chi-restraints excluded: chain A residue  530 MET
Chi-restraints excluded: chain A residue  560 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 59 optimal weight:    0.7980
   chunk 19 optimal weight:    8.9990
   chunk 50 optimal weight:    0.5980
   chunk 29 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 65 optimal weight:   20.0000
   chunk 28 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 9 optimal weight:   10.0000
   overall best weight:    2.4786

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.137386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.104854 restraints weight = 9810.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 1.50
r_work: 0.3223 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3097 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   7343  Z= 0.156
  Angle     :  0.519   8.913  10473  Z= 0.288
  Chirality :  0.035   0.144   1210
  Planarity :  0.004   0.039    951
  Dihedral  : 23.765 112.510   2118
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 18.96 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  3.07 (0.34), residues: 590
  helix:  3.37 (0.27), residues: 324
  sheet:  1.49 (0.60), residues: 62
  loop : -0.09 (0.44), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 232 
 HIS   0.001   0.000   HIS A 269 
 PHE   0.006   0.001   PHE A 155 
 TYR   0.007   0.001   TYR A  42 
 ARG   0.004   0.000   ARG A 499 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04217 (  405)
  hydrogen bonds       : angle       3.29089 ( 1085)
  metal coordination   : bond        0.00156 (    4)
  metal coordination   : angle       0.60355 (    3)
  covalent geometry    : bond        0.00342 ( 7339)
  covalent geometry    : angle       0.51875 (10470)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 49
  time to evaluate  : 0.619 
Fit side-chains
REVERT: A   63 MET cc_start: 0.8290 (ttt) cc_final: 0.7984 (ttp)
REVERT: A  172 GLN cc_start: 0.7640 (mm-40) cc_final: 0.7401 (mm-40)
REVERT: A  367 ARG cc_start: 0.8099 (mtp85) cc_final: 0.7816 (ttp-110)
REVERT: A  413 LYS cc_start: 0.8077 (tttt) cc_final: 0.7097 (tptp)
REVERT: A  416 LYS cc_start: 0.6619 (mttt) cc_final: 0.5284 (tttm)
REVERT: A  458 ARG cc_start: 0.8762 (mmm160) cc_final: 0.8315 (mmm-85)
REVERT: A  459 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.8033 (mttp)
REVERT: A  575 MET cc_start: 0.8579 (mtp) cc_final: 0.8218 (mtt)
  outliers start: 17
  outliers final: 10
  residues processed: 61
  average time/residue: 1.7782
  time to fit residues: 112.6659
Evaluate side-chains
  56 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LYS
Chi-restraints excluded: chain A residue   69 ASP
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  459 LYS
Chi-restraints excluded: chain A residue  530 MET
Chi-restraints excluded: chain A residue  560 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:    8.9990
   chunk 47 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 64 optimal weight:    8.9990
   chunk 17 optimal weight:   20.0000
   chunk 15 optimal weight:    8.9990
   chunk 31 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 7 optimal weight:    6.9990
   chunk 29 optimal weight:    6.9990
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.133302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.100979 restraints weight = 9869.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 1.56
r_work: 0.3151 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059   7343  Z= 0.316
  Angle     :  0.624   6.296  10473  Z= 0.341
  Chirality :  0.042   0.175   1210
  Planarity :  0.005   0.042    951
  Dihedral  : 23.986 116.033   2118
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 19.58 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.34), residues: 590
  helix:  2.85 (0.27), residues: 324
  sheet:  1.42 (0.61), residues: 62
  loop : -0.32 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 232 
 HIS   0.003   0.001   HIS A 183 
 PHE   0.008   0.002   PHE A 443 
 TYR   0.012   0.002   TYR A  42 
 ARG   0.003   0.001   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05551 (  405)
  hydrogen bonds       : angle       3.68671 ( 1085)
  metal coordination   : bond        0.00398 (    4)
  metal coordination   : angle       1.04933 (    3)
  covalent geometry    : bond        0.00707 ( 7339)
  covalent geometry    : angle       0.62349 (10470)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 46
  time to evaluate  : 1.551 
Fit side-chains
REVERT: A   63 MET cc_start: 0.8339 (ttt) cc_final: 0.8081 (ttp)
REVERT: A  172 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7603 (mm110)
REVERT: A  335 ASP cc_start: 0.9064 (OUTLIER) cc_final: 0.8838 (t0)
REVERT: A  367 ARG cc_start: 0.8119 (mtp85) cc_final: 0.7904 (ttp-110)
REVERT: A  413 LYS cc_start: 0.8156 (tttt) cc_final: 0.7140 (tptp)
REVERT: A  416 LYS cc_start: 0.6751 (mttt) cc_final: 0.5340 (tttm)
REVERT: A  458 ARG cc_start: 0.8797 (mmm160) cc_final: 0.8359 (mmm-85)
REVERT: A  459 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8098 (mttp)
REVERT: A  575 MET cc_start: 0.8598 (mtp) cc_final: 0.8279 (mtt)
  outliers start: 18
  outliers final: 12
  residues processed: 60
  average time/residue: 2.1043
  time to fit residues: 132.1340
Evaluate side-chains
  59 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 THR
Chi-restraints excluded: chain A residue   69 ASP
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  304 ASP
Chi-restraints excluded: chain A residue  335 ASP
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  459 LYS
Chi-restraints excluded: chain A residue  530 MET
Chi-restraints excluded: chain A residue  560 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 2 optimal weight:   10.0000
   chunk 15 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 38 optimal weight:    9.9990
   chunk 17 optimal weight:    8.9990
   chunk 8 optimal weight:   10.0000
   chunk 61 optimal weight:    2.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.137744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.105773 restraints weight = 9444.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 1.37
r_work: 0.3301 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3177 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   7343  Z= 0.168
  Angle     :  0.544   9.712  10473  Z= 0.299
  Chirality :  0.036   0.145   1210
  Planarity :  0.004   0.038    951
  Dihedral  : 23.873 113.536   2118
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 21.04 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.80 (0.34), residues: 590
  helix:  3.20 (0.27), residues: 324
  sheet:  1.38 (0.61), residues: 62
  loop : -0.27 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 232 
 HIS   0.002   0.000   HIS A 269 
 PHE   0.006   0.001   PHE A 155 
 TYR   0.008   0.001   TYR A  42 
 ARG   0.004   0.000   ARG A 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04413 (  405)
  hydrogen bonds       : angle       3.37284 ( 1085)
  metal coordination   : bond        0.00163 (    4)
  metal coordination   : angle       0.61805 (    3)
  covalent geometry    : bond        0.00370 ( 7339)
  covalent geometry    : angle       0.54386 (10470)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 47
  time to evaluate  : 0.617 
Fit side-chains
REVERT: A   63 MET cc_start: 0.8335 (ttt) cc_final: 0.8095 (ttp)
REVERT: A   98 ARG cc_start: 0.8167 (mtp-110) cc_final: 0.7661 (mtm110)
REVERT: A  172 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7488 (mm-40)
REVERT: A  335 ASP cc_start: 0.8998 (OUTLIER) cc_final: 0.8769 (t0)
REVERT: A  367 ARG cc_start: 0.8135 (mtp85) cc_final: 0.7887 (ttp-110)
REVERT: A  413 LYS cc_start: 0.8169 (tttt) cc_final: 0.7217 (tptp)
REVERT: A  416 LYS cc_start: 0.6603 (mttt) cc_final: 0.5359 (tttm)
REVERT: A  458 ARG cc_start: 0.8729 (mmm160) cc_final: 0.8366 (mmm-85)
REVERT: A  459 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8086 (mttp)
REVERT: A  575 MET cc_start: 0.8491 (mtp) cc_final: 0.8170 (mtt)
  outliers start: 12
  outliers final: 8
  residues processed: 56
  average time/residue: 2.1591
  time to fit residues: 125.5073
Evaluate side-chains
  56 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 ASP
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  335 ASP
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  459 LYS
Chi-restraints excluded: chain A residue  530 MET
Chi-restraints excluded: chain A residue  560 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 61 optimal weight:    6.9990
   chunk 20 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 66 optimal weight:    5.9990
   chunk 37 optimal weight:    9.9990
   chunk 32 optimal weight:    6.9990
   chunk 21 optimal weight:    7.9990
   chunk 42 optimal weight:    0.0670
   chunk 43 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 40 optimal weight:    6.9990
   overall best weight:    3.4124

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.137028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.104754 restraints weight = 9444.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 1.36
r_work: 0.3285 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   7343  Z= 0.183
  Angle     :  0.555  11.296  10473  Z= 0.304
  Chirality :  0.036   0.146   1210
  Planarity :  0.004   0.039    951
  Dihedral  : 23.890 112.196   2118
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 21.46 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.80 (0.34), residues: 590
  helix:  3.20 (0.27), residues: 324
  sheet:  1.35 (0.60), residues: 62
  loop : -0.29 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 232 
 HIS   0.002   0.000   HIS A 183 
 PHE   0.007   0.001   PHE A 443 
 TYR   0.009   0.001   TYR A  42 
 ARG   0.002   0.000   ARG A 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04498 (  405)
  hydrogen bonds       : angle       3.37192 ( 1085)
  metal coordination   : bond        0.00164 (    4)
  metal coordination   : angle       0.67526 (    3)
  covalent geometry    : bond        0.00408 ( 7339)
  covalent geometry    : angle       0.55476 (10470)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 47
  time to evaluate  : 0.753 
Fit side-chains
REVERT: A   63 MET cc_start: 0.8331 (ttt) cc_final: 0.8100 (ttp)
REVERT: A  172 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7509 (mm-40)
REVERT: A  335 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8741 (t0)
REVERT: A  367 ARG cc_start: 0.8137 (mtp85) cc_final: 0.7894 (ttp-110)
REVERT: A  413 LYS cc_start: 0.8170 (tttt) cc_final: 0.7237 (tptp)
REVERT: A  416 LYS cc_start: 0.6631 (mttt) cc_final: 0.5346 (tttm)
REVERT: A  458 ARG cc_start: 0.8613 (mmm160) cc_final: 0.8363 (mmm-85)
REVERT: A  459 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8117 (mttp)
REVERT: A  575 MET cc_start: 0.8519 (mtp) cc_final: 0.8175 (mtt)
  outliers start: 13
  outliers final: 10
  residues processed: 57
  average time/residue: 3.0719
  time to fit residues: 180.7477
Evaluate side-chains
  57 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 45
  time to evaluate  : 1.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 ASP
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  335 ASP
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  459 LYS
Chi-restraints excluded: chain A residue  530 MET
Chi-restraints excluded: chain A residue  560 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 18 optimal weight:    7.9990
   chunk 44 optimal weight:    8.9990
   chunk 67 optimal weight:    0.9980
   chunk 8 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 42 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 43 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    3.7988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.137955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.105344 restraints weight = 9514.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 1.42
r_work: 0.3278 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   7343  Z= 0.196
  Angle     :  0.561   9.875  10473  Z= 0.308
  Chirality :  0.037   0.193   1210
  Planarity :  0.004   0.039    951
  Dihedral  : 23.840 112.385   2118
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 21.25 %
    Favored  : 75.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.74 (0.34), residues: 590
  helix:  3.14 (0.27), residues: 324
  sheet:  1.37 (0.60), residues: 62
  loop : -0.29 (0.42), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 232 
 HIS   0.002   0.001   HIS A 426 
 PHE   0.006   0.001   PHE A 443 
 TYR   0.009   0.001   TYR A  42 
 ARG   0.002   0.000   ARG A 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04600 (  405)
  hydrogen bonds       : angle       3.41194 ( 1085)
  metal coordination   : bond        0.00188 (    4)
  metal coordination   : angle       0.72263 (    3)
  covalent geometry    : bond        0.00437 ( 7339)
  covalent geometry    : angle       0.56081 (10470)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 0.893 
Fit side-chains
REVERT: A   63 MET cc_start: 0.8306 (ttt) cc_final: 0.8064 (ttp)
REVERT: A  172 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7485 (mm-40)
REVERT: A  335 ASP cc_start: 0.9010 (OUTLIER) cc_final: 0.8781 (t0)
REVERT: A  367 ARG cc_start: 0.8124 (mtp85) cc_final: 0.7859 (ttp-110)
REVERT: A  413 LYS cc_start: 0.7981 (tttt) cc_final: 0.6995 (tptp)
REVERT: A  416 LYS cc_start: 0.6639 (mttt) cc_final: 0.5325 (tttm)
REVERT: A  458 ARG cc_start: 0.8599 (mmm160) cc_final: 0.8343 (mmm-85)
REVERT: A  459 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8098 (mttp)
REVERT: A  575 MET cc_start: 0.8572 (mtp) cc_final: 0.8222 (mtt)
  outliers start: 15
  outliers final: 10
  residues processed: 59
  average time/residue: 3.9623
  time to fit residues: 245.2783
Evaluate side-chains
  59 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 47
  time to evaluate  : 1.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 ASP
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  335 ASP
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  459 LYS
Chi-restraints excluded: chain A residue  530 MET
Chi-restraints excluded: chain A residue  560 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 5 optimal weight:    8.9990
   chunk 44 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 18 optimal weight:    9.9990
   chunk 25 optimal weight:    5.9990
   chunk 28 optimal weight:    8.9990
   chunk 31 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 51 optimal weight:    7.9990
   chunk 32 optimal weight:    0.5980
   overall best weight:    3.1188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.139538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.107672 restraints weight = 9438.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.38
r_work: 0.3298 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   7343  Z= 0.175
  Angle     :  0.565  11.301  10473  Z= 0.306
  Chirality :  0.036   0.170   1210
  Planarity :  0.004   0.038    951
  Dihedral  : 23.781 111.885   2118
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 21.88 %
    Favored  : 75.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.82 (0.34), residues: 590
  helix:  3.20 (0.27), residues: 324
  sheet:  1.36 (0.60), residues: 62
  loop : -0.25 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 232 
 HIS   0.002   0.001   HIS A  12 
 PHE   0.006   0.001   PHE A 443 
 TYR   0.008   0.001   TYR A  42 
 ARG   0.006   0.000   ARG A 580 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04409 (  405)
  hydrogen bonds       : angle       3.35259 ( 1085)
  metal coordination   : bond        0.00156 (    4)
  metal coordination   : angle       0.65836 (    3)
  covalent geometry    : bond        0.00390 ( 7339)
  covalent geometry    : angle       0.56463 (10470)

===============================================================================
Job complete
usr+sys time: 5954.14 seconds
wall clock time: 106 minutes 55.86 seconds (6415.86 seconds total)