Starting phenix.real_space_refine
on Tue Mar 11 15:52:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cal_45395/03_2025/9cal_45395_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cal_45395/03_2025/9cal_45395.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cal_45395/03_2025/9cal_45395.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cal_45395/03_2025/9cal_45395.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cal_45395/03_2025/9cal_45395_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cal_45395/03_2025/9cal_45395_neut.cif"
  }
  resolution = 3.15
  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=   0.020
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
     Mn      1      7.51       5
     P      10      5.49       5
     S      39      5.16       5
     C    3928      2.51       5
     N    1084      2.21       5
     O    1206      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6268
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 612, 4845
          Classifications: {'peptide': 612}
          Link IDs: {'PTRANS': 30, 'TRANS': 581}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'PTR:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 1219
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1219
          Classifications: {'peptide': 161}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 153}
    Chain: "D"
      Number of atoms: 146
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 146
          Classifications: {'DNA': 7}
          Link IDs: {'rna3p': 6}
    Chain: "E"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 57
          Classifications: {'DNA': 3}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.14, per 1000 atoms: 0.82
  Number of scatterers: 6268
  At special positions: 0
  Unit cell: (72.16, 86.1, 137.76, 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)
     Mn      1     24.99
     S      39     16.00
     P      10     15.00
     O    1206      8.00
     N    1084      7.00
     C    3928      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.64
  Conformation dependent library (CDL) restraints added in 890.0 milliseconds
  

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1442

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 6 sheets defined
      42.8% alpha, 14.7% beta
      0 base pairs and 5 stacking pairs defined.
    Time for finding SS restraints: 1.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 22
    Processing helix  chain 'A' and resid 68 through 72
    Processing helix  chain 'A' and resid 77 through 82
      removed outlier: 3.997A  pdb=" N   PHE A  82 " --> pdb=" O   ALA A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 106
    Processing helix  chain 'A' and resid 119 through 134
    Processing helix  chain 'A' and resid 135 through 137
      No H-bonds generated for 'chain 'A' and resid 135 through 137'
    Processing helix  chain 'A' and resid 156 through 166
    Processing helix  chain 'A' and resid 171 through 201
      removed outlier: 3.743A  pdb=" N   ALA A 191 " --> pdb=" O   ARG A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 234
      removed outlier: 3.725A  pdb=" N   CYS A 225 " --> pdb=" O   THR A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 277
      removed outlier: 3.523A  pdb=" N   THR A 277 " --> pdb=" O   PHE A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 313
    Processing helix  chain 'A' and resid 317 through 332
    Processing helix  chain 'A' and resid 349 through 357
      removed outlier: 4.146A  pdb=" N   GLN A 357 " --> pdb=" O   SER A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 373
    Processing helix  chain 'A' and resid 404 through 421
      removed outlier: 3.730A  pdb=" N   LEU A 408 " --> pdb=" O   ASP A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 455
    Processing helix  chain 'A' and resid 495 through 507
    Processing helix  chain 'A' and resid 513 through 524
    Processing helix  chain 'A' and resid 538 through 552
    Processing helix  chain 'A' and resid 553 through 556
    Processing helix  chain 'A' and resid 559 through 573
      removed outlier: 3.923A  pdb=" N   LEU A 570 " --> pdb=" O   LYS A 566 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   ILE A 571 " --> pdb=" O   GLN A 567 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ALA A 572 " --> pdb=" O   LEU A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 599
    Processing helix  chain 'A' and resid 600 through 611
      removed outlier: 3.742A  pdb=" N   LEU A 606 " --> pdb=" O   GLY A 602 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   VAL A 609 " --> pdb=" O   GLU A 605 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   SER A 610 " --> pdb=" O   LEU A 606 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 13
    Processing helix  chain 'B' and resid 17 through 25
      removed outlier: 3.505A  pdb=" N   THR B  25 " --> pdb=" O   ILE B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 41
    Processing helix  chain 'B' and resid 44 through 48
    Processing helix  chain 'B' and resid 56 through 60
      removed outlier: 4.256A  pdb=" N   GLY B  60 " --> pdb=" O   ILE B  57 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30
      removed outlier: 6.557A  pdb=" N   LYS A   2 " --> pdb=" O   ARG A  51 " (cutoff:3.500A)
      removed outlier: 7.686A  pdb=" N   LYS A  53 " --> pdb=" O   LYS A   2 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   VAL A   4 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   THR A   3 " --> pdb=" O   TYR A 111 " (cutoff:3.500A)
      removed outlier: 8.208A  pdb=" N   VAL A 113 " --> pdb=" O   THR A   3 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   LEU A   5 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ILE A 112 " --> pdb=" O   PHE A 148 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 66
    Processing sheet with id=AA3, first strand: chain 'A' and resid 254 through 256
      removed outlier: 6.569A  pdb=" N   VAL A 242 " --> pdb=" O   MET A 483 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   MET A 483 " --> pdb=" O   VAL A 242 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   GLN A 244 " --> pdb=" O   VAL A 481 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   VAL A 481 " --> pdb=" O   GLN A 244 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   LYS A 246 " --> pdb=" O   GLY A 479 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 259
      removed outlier: 7.258A  pdb=" N   LYS A 425 " --> pdb=" O   LEU A 448 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   TYR A 426 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR A 430 " --> pdb=" O   SER A 289 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ALA A 287 " --> pdb=" O   SER A 432 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   ARG A 434 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 5.766A  pdb=" N   VAL A 285 " --> pdb=" O   ARG A 434 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 527 through 529
    Processing sheet with id=AA6, first strand: chain 'B' and resid 135 through 136
      removed outlier: 9.347A  pdb=" N   LEU B 140 " --> pdb=" O   SER B 105 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   THR B 107 " --> pdb=" O   LEU B 140 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   LEU B 142 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   VAL B 109 " --> pdb=" O   LEU B 142 " (cutoff:3.500A)
      removed outlier: 4.951A  pdb=" N   LEU B  95 " --> pdb=" O   GLU B 110 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ARG B  96 " --> pdb=" O   ILE B  76 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   ILE B  76 " --> pdb=" O   ARG B  96 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   GLN B  98 " --> pdb=" O   GLN B  74 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   CYS B  69 " --> pdb=" O   LEU B 129 " (cutoff:3.500A)
      removed outlier: 5.802A  pdb=" N   LYS B 126 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)

    267 hydrogen bonds defined for protein.
    756 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      5 stacking parallelities
  Total time for adding SS restraints: 1.83

  Time building geometry restraints manager: 1.93 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: 1966
        1.34 -     1.45: 875
        1.45 -     1.57: 3495
        1.57 -     1.69: 18
        1.69 -     1.81: 61
  Bond restraints: 6415
  Sorted by residual:
  bond pdb=" OH  PTR A 336 "
       pdb=" P   PTR A 336 "
    ideal  model  delta    sigma   weight residual
    1.769  1.608  0.161 2.00e-02 2.50e+03 6.49e+01
  bond pdb=" C   SER A 335 "
       pdb=" N   PTR A 336 "
    ideal  model  delta    sigma   weight residual
    1.329  1.430 -0.101 1.40e-02 5.10e+03 5.18e+01
  bond pdb=" O1P PTR A 336 "
       pdb=" P   PTR A 336 "
    ideal  model  delta    sigma   weight residual
    1.522  1.477  0.045 2.00e-02 2.50e+03 5.03e+00
  bond pdb=" CZ  PTR A 336 "
       pdb=" OH  PTR A 336 "
    ideal  model  delta    sigma   weight residual
    1.339  1.300  0.039 2.00e-02 2.50e+03 3.84e+00
  bond pdb=" O3'  DA D   3 "
       pdb=" P    DT D   4 "
    ideal  model  delta    sigma   weight residual
    1.607  1.583  0.024 1.50e-02 4.44e+03 2.58e+00
  ... (remaining 6410 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.17: 8716
        6.17 -    12.34: 4
       12.34 -    18.51: 1
       18.51 -    24.68: 0
       24.68 -    30.85: 1
  Bond angle restraints: 8722
  Sorted by residual:
  angle pdb=" O   SER A 335 "
        pdb=" C   SER A 335 "
        pdb=" N   PTR A 336 "
      ideal   model   delta    sigma   weight residual
     123.00   92.15   30.85 1.60e+00 3.91e-01 3.72e+02
  angle pdb=" CA  SER A 335 "
        pdb=" C   SER A 335 "
        pdb=" N   PTR A 336 "
      ideal   model   delta    sigma   weight residual
     116.20  132.42  -16.22 2.00e+00 2.50e-01 6.58e+01
  angle pdb=" N   ASN A  33 "
        pdb=" CA  ASN A  33 "
        pdb=" C   ASN A  33 "
      ideal   model   delta    sigma   weight residual
     114.62  109.58    5.04 1.14e+00 7.69e-01 1.95e+01
  angle pdb=" C   SER A 335 "
        pdb=" N   PTR A 336 "
        pdb=" CA  PTR A 336 "
      ideal   model   delta    sigma   weight residual
     121.70  129.53   -7.83 1.80e+00 3.09e-01 1.89e+01
  angle pdb=" OH  PTR A 336 "
        pdb=" P   PTR A 336 "
        pdb=" O2P PTR A 336 "
      ideal   model   delta    sigma   weight residual
      99.92  109.91   -9.99 3.00e+00 1.11e-01 1.11e+01
  ... (remaining 8717 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 3434
       17.94 -    35.88: 344
       35.88 -    53.81: 78
       53.81 -    71.75: 9
       71.75 -    89.69: 9
  Dihedral angle restraints: 3874
    sinusoidal: 1640
      harmonic: 2234
  Sorted by residual:
  dihedral pdb=" CA  LEU A  67 "
           pdb=" C   LEU A  67 "
           pdb=" N   GLY A  68 "
           pdb=" CA  GLY A  68 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.78   17.22     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CG  ARG A 407 "
           pdb=" CD  ARG A 407 "
           pdb=" NE  ARG A 407 "
           pdb=" CZ  ARG A 407 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -135.06  -44.94     2      1.50e+01 4.44e-03 1.06e+01
  dihedral pdb=" CB  GLU A 238 "
           pdb=" CG  GLU A 238 "
           pdb=" CD  GLU A 238 "
           pdb=" OE1 GLU A 238 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.69  -89.69     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 3871 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 630
       0.032 -    0.064: 248
       0.064 -    0.096: 61
       0.096 -    0.128: 33
       0.128 -    0.160: 5
  Chirality restraints: 977
  Sorted by residual:
  chirality pdb=" CA  PTR A 336 "
            pdb=" N   PTR A 336 "
            pdb=" C   PTR A 336 "
            pdb=" CB  PTR A 336 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.51   -0.16 2.00e-01 2.50e+01 6.44e-01
  chirality pdb=" CA  VAL B  31 "
            pdb=" N   VAL B  31 "
            pdb=" C   VAL B  31 "
            pdb=" CB  VAL B  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.28e-01
  chirality pdb=" CB  VAL A 136 "
            pdb=" CA  VAL A 136 "
            pdb=" CG1 VAL A 136 "
            pdb=" CG2 VAL A 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.13 2.00e-01 2.50e+01 4.53e-01
  ... (remaining 974 not shown)

  Planarity restraints: 1092
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 335 "    0.084 2.00e-02 2.50e+03   1.31e-01 1.73e+02
        pdb=" C   SER A 335 "   -0.227 2.00e-02 2.50e+03
        pdb=" O   SER A 335 "    0.070 2.00e-02 2.50e+03
        pdb=" N   PTR A 336 "    0.073 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 476 "   -0.067 5.00e-02 4.00e+02   1.01e-01 1.64e+01
        pdb=" N   PRO A 477 "    0.175 5.00e-02 4.00e+02
        pdb=" CA  PRO A 477 "   -0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO A 477 "   -0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 436 "   -0.028 5.00e-02 4.00e+02   4.38e-02 3.06e+00
        pdb=" N   PRO A 437 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 437 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 437 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1089 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 118
        2.69 -     3.24: 5871
        3.24 -     3.79: 9334
        3.79 -     4.35: 12400
        4.35 -     4.90: 20681
  Nonbonded interactions: 48404
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 117 "
            pdb="MN    MN A 701 "
     model   vdw
     2.136 2.320
  nonbonded pdb=" OD2 ASP A 119 "
            pdb="MN    MN A 701 "
     model   vdw
     2.173 2.320
  nonbonded pdb=" OE1 GLN A 196 "
            pdb=" OH  TYR A 548 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OH  TYR A 199 "
            pdb=" OD2 ASP A 604 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OD1 ASP A 208 "
            pdb=" N   SER A 209 "
     model   vdw
     2.291 3.120
  ... (remaining 48399 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:             1.870
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.810
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
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   0.161   6415  Z= 0.266
  Angle     :  0.680  30.854   8722  Z= 0.369
  Chirality :  0.040   0.160    977
  Planarity :  0.006   0.131   1092
  Dihedral  : 15.357  89.687   2432
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  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: -0.07 (0.31), residues: 766
  helix:  0.71 (0.30), residues: 309
  sheet: -0.49 (0.49), residues: 127
  loop : -0.46 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 115 
 HIS   0.003   0.001   HIS A  29 
 PHE   0.009   0.001   PHE A 101 
 TYR   0.010   0.001   TYR A 240 
 ARG   0.006   0.000   ARG A 107 

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
REVERT: A   48 GLN cc_start: 0.8056 (mm110) cc_final: 0.7737 (tp40)
REVERT: A  246 LYS cc_start: 0.8427 (mttm) cc_final: 0.8206 (mttp)
REVERT: A  284 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7280 (mm-40)
REVERT: A  425 LYS cc_start: 0.8154 (mttm) cc_final: 0.7927 (mttm)
REVERT: A  434 ARG cc_start: 0.7894 (ttm170) cc_final: 0.7691 (ttm-80)
REVERT: A  599 SER cc_start: 0.7741 (t) cc_final: 0.7518 (t)
REVERT: B  132 ILE cc_start: 0.8605 (mm) cc_final: 0.8375 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.2305
  time to fit residues: 49.3064
Evaluate side-chains
  161 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 39 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0670
   chunk 44 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.5720

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

Flipped N/Q/H residues before XYZ refinement:
A 196 GLN
A 218 GLN
B  11 GLN
B 156 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.109151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.098067 restraints weight = 9697.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.04
r_work: 0.3129 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.0885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6415  Z= 0.268
  Angle     :  0.541   6.562   8722  Z= 0.287
  Chirality :  0.042   0.200    977
  Planarity :  0.004   0.071   1092
  Dihedral  : 11.256  88.966    946
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  7.95 %
    Favored  : 90.70 %
  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:  0.37 (0.31), residues: 766
  helix:  1.36 (0.30), residues: 306
  sheet: -0.45 (0.49), residues: 125
  loop : -0.44 (0.34), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 458 
 HIS   0.004   0.001   HIS A 172 
 PHE   0.011   0.001   PHE A 433 
 TYR   0.013   0.002   TYR A 578 
 ARG   0.004   0.000   ARG A 107 

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 163
  time to evaluate  : 0.691 
Fit side-chains
REVERT: A  423 ASP cc_start: 0.8259 (m-30) cc_final: 0.7954 (m-30)
REVERT: A  587 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7863 (m-30)
REVERT: A  599 SER cc_start: 0.8321 (t) cc_final: 0.8047 (t)
REVERT: B  132 ILE cc_start: 0.8676 (mm) cc_final: 0.8430 (mm)
  outliers start: 9
  outliers final: 3
  residues processed: 163
  average time/residue: 0.2216
  time to fit residues: 45.6608
Evaluate side-chains
  162 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 158
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 CYS
Chi-restraints excluded: chain A residue  587 ASP
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   21 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 58 optimal weight:    0.9990
   chunk 63 optimal weight:    0.4980
   chunk 37 optimal weight:    0.3980
   chunk 47 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0570
   chunk 30 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
A 573 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.109498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.098448 restraints weight = 9744.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.03
r_work: 0.3133 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.1148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6415  Z= 0.245
  Angle     :  0.520   5.823   8722  Z= 0.276
  Chirality :  0.041   0.184    977
  Planarity :  0.004   0.060   1092
  Dihedral  : 11.174  88.656    946
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 11.39 %
    Favored  : 86.81 %
  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:  0.50 (0.31), residues: 766
  helix:  1.55 (0.30), residues: 304
  sheet: -0.34 (0.46), residues: 142
  loop : -0.46 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 115 
 HIS   0.004   0.001   HIS A 172 
 PHE   0.010   0.001   PHE A 101 
 TYR   0.015   0.001   TYR A 578 
 ARG   0.003   0.000   ARG A 107 

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 163
  time to evaluate  : 0.840 
Fit side-chains
REVERT: A   48 GLN cc_start: 0.8235 (mm110) cc_final: 0.8008 (tp40)
REVERT: A  423 ASP cc_start: 0.8297 (m-30) cc_final: 0.7911 (m-30)
REVERT: A  504 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7130 (tm-30)
REVERT: A  587 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7814 (m-30)
REVERT: A  598 ASP cc_start: 0.8313 (m-30) cc_final: 0.7196 (t0)
REVERT: A  599 SER cc_start: 0.8279 (t) cc_final: 0.8008 (t)
REVERT: B  132 ILE cc_start: 0.8674 (mm) cc_final: 0.8438 (mm)
  outliers start: 12
  outliers final: 8
  residues processed: 165
  average time/residue: 0.2230
  time to fit residues: 46.3144
Evaluate side-chains
  169 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 160
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   65 ASP
Chi-restraints excluded: chain A residue  161 CYS
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  425 LYS
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  587 ASP
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   51 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0970
   chunk 34 optimal weight:    0.9980
   chunk 54 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A 201 GLN
A 573 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.109321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.098228 restraints weight = 9781.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 2.04
r_work: 0.3130 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.1294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6415  Z= 0.247
  Angle     :  0.516   5.790   8722  Z= 0.273
  Chirality :  0.041   0.171    977
  Planarity :  0.004   0.055   1092
  Dihedral  : 11.069  84.161    946
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 13.64 %
    Favored  : 84.11 %
  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:  0.54 (0.31), residues: 766
  helix:  1.59 (0.30), residues: 305
  sheet: -0.34 (0.47), residues: 140
  loop : -0.44 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 115 
 HIS   0.004   0.001   HIS A 172 
 PHE   0.009   0.001   PHE A 101 
 TYR   0.016   0.001   TYR A 578 
 ARG   0.004   0.000   ARG A 107 

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 163
  time to evaluate  : 0.767 
Fit side-chains
REVERT: A   48 GLN cc_start: 0.8238 (mm110) cc_final: 0.8012 (tp40)
REVERT: A  423 ASP cc_start: 0.8295 (m-30) cc_final: 0.7925 (m-30)
REVERT: A  504 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7155 (tm-30)
REVERT: A  587 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7798 (m-30)
REVERT: A  598 ASP cc_start: 0.8281 (m-30) cc_final: 0.7223 (t0)
REVERT: A  599 SER cc_start: 0.8292 (t) cc_final: 0.7996 (t)
REVERT: B  132 ILE cc_start: 0.8688 (mm) cc_final: 0.8448 (mm)
  outliers start: 15
  outliers final: 10
  residues processed: 163
  average time/residue: 0.2300
  time to fit residues: 47.8422
Evaluate side-chains
  171 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 160
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   65 ASP
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  161 CYS
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  327 ARG
Chi-restraints excluded: chain A residue  373 GLU
Chi-restraints excluded: chain A residue  425 LYS
Chi-restraints excluded: chain A residue  587 ASP
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   51 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0000
   chunk 62 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0980
   chunk 39 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.4584

-------------------------------------------------------------------------------
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 = 0.3418 r_free = 0.3418 target = 0.109697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.098553 restraints weight = 9704.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 2.04
r_work: 0.3139 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.1386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6415  Z= 0.220
  Angle     :  0.506   5.731   8722  Z= 0.268
  Chirality :  0.041   0.168    977
  Planarity :  0.004   0.051   1092
  Dihedral  : 10.996  80.102    946
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.84 %
    Favored  : 83.21 %
  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:  0.61 (0.31), residues: 766
  helix:  1.66 (0.31), residues: 304
  sheet: -0.25 (0.48), residues: 140
  loop : -0.43 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 458 
 HIS   0.004   0.001   HIS A 172 
 PHE   0.008   0.001   PHE A 127 
 TYR   0.015   0.001   TYR A 578 
 ARG   0.004   0.000   ARG A 107 

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 165
  time to evaluate  : 0.808 
Fit side-chains
REVERT: A   48 GLN cc_start: 0.8228 (mm110) cc_final: 0.8011 (tp40)
REVERT: A  423 ASP cc_start: 0.8300 (m-30) cc_final: 0.8077 (m-30)
REVERT: A  504 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7159 (tm-30)
REVERT: A  587 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7802 (m-30)
REVERT: A  598 ASP cc_start: 0.8268 (m-30) cc_final: 0.7587 (m-30)
REVERT: A  599 SER cc_start: 0.8278 (t) cc_final: 0.7974 (t)
REVERT: B  132 ILE cc_start: 0.8700 (mm) cc_final: 0.8458 (mm)
  outliers start: 13
  outliers final: 10
  residues processed: 165
  average time/residue: 0.2352
  time to fit residues: 49.2191
Evaluate side-chains
  169 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 158
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   65 ASP
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  161 CYS
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  276 MET
Chi-restraints excluded: chain A residue  327 ARG
Chi-restraints excluded: chain A residue  425 LYS
Chi-restraints excluded: chain A residue  587 ASP
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   51 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0970
   chunk 43 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.6978

-------------------------------------------------------------------------------
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 = 0.3400 r_free = 0.3400 target = 0.108546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.097498 restraints weight = 9666.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 2.02
r_work: 0.3124 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.1475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6415  Z= 0.307
  Angle     :  0.533   5.773   8722  Z= 0.282
  Chirality :  0.042   0.171    977
  Planarity :  0.004   0.056   1092
  Dihedral  : 10.975  76.251    946
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 15.74 %
    Favored  : 81.86 %
  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:  0.60 (0.31), residues: 766
  helix:  1.63 (0.31), residues: 301
  sheet: -0.16 (0.48), residues: 140
  loop : -0.44 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 115 
 HIS   0.005   0.001   HIS A 172 
 PHE   0.011   0.001   PHE A 127 
 TYR   0.017   0.002   TYR A 578 
 ARG   0.004   0.000   ARG A 107 

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 166
  time to evaluate  : 0.738 
Fit side-chains
REVERT: A   33 ASN cc_start: 0.8037 (m-40) cc_final: 0.7823 (t0)
REVERT: A   48 GLN cc_start: 0.8254 (mm110) cc_final: 0.8029 (tp40)
REVERT: A  145 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8535 (mtpp)
REVERT: A  423 ASP cc_start: 0.8319 (m-30) cc_final: 0.7899 (m-30)
REVERT: A  504 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7183 (tm-30)
REVERT: A  587 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7812 (m-30)
REVERT: A  598 ASP cc_start: 0.8284 (m-30) cc_final: 0.7646 (m-30)
REVERT: A  599 SER cc_start: 0.8335 (t) cc_final: 0.8018 (t)
REVERT: B  132 ILE cc_start: 0.8715 (mm) cc_final: 0.8488 (mm)
  outliers start: 16
  outliers final: 12
  residues processed: 169
  average time/residue: 0.2276
  time to fit residues: 48.5023
Evaluate side-chains
  174 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 161
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  161 CYS
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  327 ARG
Chi-restraints excluded: chain A residue  425 LYS
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  587 ASP
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   26 SER
Chi-restraints excluded: chain B residue   51 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 66 optimal weight:    0.2980
   chunk 45 optimal weight:    0.0980
   chunk 44 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 65 optimal weight:    0.4980
   chunk 75 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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 = 0.3412 r_free = 0.3412 target = 0.109338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.098290 restraints weight = 9698.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 2.01
r_work: 0.3140 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6415  Z= 0.215
  Angle     :  0.515   5.860   8722  Z= 0.273
  Chirality :  0.041   0.167    977
  Planarity :  0.004   0.051   1092
  Dihedral  : 10.996  73.776    946
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 16.19 %
    Favored  : 81.86 %
  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:  0.61 (0.31), residues: 766
  helix:  1.61 (0.31), residues: 303
  sheet: -0.20 (0.47), residues: 140
  loop : -0.41 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 241 
 HIS   0.003   0.001   HIS A 172 
 PHE   0.008   0.001   PHE A 127 
 TYR   0.015   0.001   TYR A 578 
 ARG   0.005   0.000   ARG A 107 

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 159
  time to evaluate  : 0.703 
Fit side-chains
REVERT: A   32 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8637 (pp)
REVERT: A   33 ASN cc_start: 0.7977 (m-40) cc_final: 0.7697 (t0)
REVERT: A   48 GLN cc_start: 0.8231 (mm110) cc_final: 0.8018 (tp40)
REVERT: A  145 LYS cc_start: 0.8761 (mtpt) cc_final: 0.8520 (mtpp)
REVERT: A  423 ASP cc_start: 0.8303 (m-30) cc_final: 0.7894 (m-30)
REVERT: A  504 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7151 (tm-30)
REVERT: A  587 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7804 (m-30)
REVERT: A  598 ASP cc_start: 0.8263 (m-30) cc_final: 0.7576 (m-30)
REVERT: A  599 SER cc_start: 0.8324 (t) cc_final: 0.7993 (t)
  outliers start: 13
  outliers final: 9
  residues processed: 163
  average time/residue: 0.2186
  time to fit residues: 45.1162
Evaluate side-chains
  169 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 158
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   65 ASP
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  327 ARG
Chi-restraints excluded: chain A residue  425 LYS
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  587 ASP
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   26 SER
Chi-restraints excluded: chain B residue   51 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 19 optimal weight:    0.2980
   chunk 12 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0980
   chunk 13 optimal weight:    0.0270
   overall best weight:    0.3238

-------------------------------------------------------------------------------
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 = 0.3425 r_free = 0.3425 target = 0.110228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.099100 restraints weight = 9630.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.02
r_work: 0.3153 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6415  Z= 0.180
  Angle     :  0.506   7.507   8722  Z= 0.265
  Chirality :  0.040   0.161    977
  Planarity :  0.004   0.049   1092
  Dihedral  : 11.136  71.668    946
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 16.79 %
    Favored  : 81.11 %
  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:  0.74 (0.31), residues: 766
  helix:  1.72 (0.31), residues: 302
  sheet: -0.15 (0.47), residues: 140
  loop : -0.31 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 241 
 HIS   0.003   0.001   HIS A 229 
 PHE   0.009   0.001   PHE A 433 
 TYR   0.014   0.001   TYR A 578 
 ARG   0.006   0.000   ARG A 107 

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 160
  time to evaluate  : 0.690 
Fit side-chains
REVERT: A   32 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8622 (pp)
REVERT: A   33 ASN cc_start: 0.7984 (m-40) cc_final: 0.7720 (t0)
REVERT: A   48 GLN cc_start: 0.8197 (mm110) cc_final: 0.7977 (tp40)
REVERT: A  145 LYS cc_start: 0.8760 (mtpt) cc_final: 0.8521 (mtpp)
REVERT: A  423 ASP cc_start: 0.8298 (m-30) cc_final: 0.7874 (m-30)
REVERT: A  504 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7106 (tm-30)
REVERT: A  598 ASP cc_start: 0.8242 (m-30) cc_final: 0.7473 (m-30)
REVERT: A  599 SER cc_start: 0.8297 (t) cc_final: 0.7958 (t)
  outliers start: 14
  outliers final: 9
  residues processed: 166
  average time/residue: 0.2245
  time to fit residues: 47.2621
Evaluate side-chains
  165 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 155
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   65 ASP
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  327 ARG
Chi-restraints excluded: chain A residue  425 LYS
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   51 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0470
   chunk 32 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 14 optimal weight:    0.2980
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.4478

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

Flipped N/Q/H residues before XYZ refinement:
A 201 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.109766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.098577 restraints weight = 9637.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 2.02
r_work: 0.3145 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
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      :  0.003   0.038   6415  Z= 0.220
  Angle     :  0.526   8.109   8722  Z= 0.272
  Chirality :  0.040   0.158    977
  Planarity :  0.004   0.048   1092
  Dihedral  : 11.281  70.340    946
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 17.54 %
    Favored  : 80.66 %
  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:  0.79 (0.31), residues: 766
  helix:  1.77 (0.31), residues: 299
  sheet: -0.07 (0.48), residues: 140
  loop : -0.31 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 458 
 HIS   0.003   0.001   HIS A 172 
 PHE   0.009   0.001   PHE A 127 
 TYR   0.015   0.001   TYR A 578 
 ARG   0.005   0.000   ARG A 107 

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 157
  time to evaluate  : 0.768 
Fit side-chains
REVERT: A   32 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8638 (pp)
REVERT: A   33 ASN cc_start: 0.7941 (m-40) cc_final: 0.7641 (t0)
REVERT: A   48 GLN cc_start: 0.8231 (mm110) cc_final: 0.8011 (tp40)
REVERT: A  145 LYS cc_start: 0.8760 (mtpt) cc_final: 0.8521 (mtpp)
REVERT: A  423 ASP cc_start: 0.8308 (m-30) cc_final: 0.7867 (m-30)
REVERT: A  427 LEU cc_start: 0.8616 (tt) cc_final: 0.8376 (tp)
REVERT: A  504 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7107 (tm-30)
REVERT: A  598 ASP cc_start: 0.8269 (m-30) cc_final: 0.7520 (m-30)
REVERT: A  599 SER cc_start: 0.8354 (t) cc_final: 0.8004 (t)
  outliers start: 12
  outliers final: 11
  residues processed: 159
  average time/residue: 0.2284
  time to fit residues: 46.2402
Evaluate side-chains
  167 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 155
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   65 ASP
Chi-restraints excluded: chain A residue   88 GLU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  327 ARG
Chi-restraints excluded: chain A residue  425 LYS
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   26 SER
Chi-restraints excluded: chain B residue   51 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3393 r_free = 0.3393 target = 0.107994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.096962 restraints weight = 9832.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 2.03
r_work: 0.3119 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   6415  Z= 0.358
  Angle     :  0.575   8.575   8722  Z= 0.298
  Chirality :  0.043   0.185    977
  Planarity :  0.004   0.050   1092
  Dihedral  : 11.368  71.227    946
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.09 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.31), residues: 766
  helix:  1.56 (0.31), residues: 302
  sheet: -0.18 (0.47), residues: 135
  loop : -0.43 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 115 
 HIS   0.006   0.001   HIS A  29 
 PHE   0.013   0.002   PHE A 127 
 TYR   0.019   0.002   TYR A 578 
 ARG   0.005   0.000   ARG A 107 

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 163
  time to evaluate  : 0.775 
Fit side-chains
REVERT: A   15 GLN cc_start: 0.8063 (tm-30) cc_final: 0.7611 (tt0)
REVERT: A   32 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8652 (pp)
REVERT: A   33 ASN cc_start: 0.7920 (m-40) cc_final: 0.7692 (t0)
REVERT: A   48 GLN cc_start: 0.8278 (mm110) cc_final: 0.8054 (tp40)
REVERT: A  145 LYS cc_start: 0.8774 (mtpt) cc_final: 0.8566 (mtpp)
REVERT: A  162 ASN cc_start: 0.7836 (m-40) cc_final: 0.7428 (m-40)
REVERT: A  423 ASP cc_start: 0.8352 (m-30) cc_final: 0.7882 (m-30)
REVERT: A  427 LEU cc_start: 0.8622 (tt) cc_final: 0.8407 (tp)
REVERT: A  504 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7144 (tm-30)
REVERT: A  598 ASP cc_start: 0.8300 (m-30) cc_final: 0.7633 (m-30)
REVERT: A  599 SER cc_start: 0.8251 (t) cc_final: 0.7918 (t)
  outliers start: 13
  outliers final: 12
  residues processed: 165
  average time/residue: 0.2333
  time to fit residues: 49.0871
Evaluate side-chains
  176 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 163
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   65 ASP
Chi-restraints excluded: chain A residue   88 GLU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  327 ARG
Chi-restraints excluded: chain A residue  425 LYS
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain B residue    9 LEU
Chi-restraints excluded: chain B residue   26 SER
Chi-restraints excluded: chain B residue   51 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 74 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 55 optimal weight:    0.4980
   chunk 41 optimal weight:    0.2980
   chunk 3 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0980
   chunk 61 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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 = 0.3413 r_free = 0.3413 target = 0.109462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.098206 restraints weight = 9784.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 2.04
r_work: 0.3138 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6415  Z= 0.218
  Angle     :  0.530   8.216   8722  Z= 0.276
  Chirality :  0.040   0.159    977
  Planarity :  0.004   0.048   1092
  Dihedral  : 11.323  70.421    946
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 17.39 %
    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:  0.64 (0.31), residues: 766
  helix:  1.60 (0.31), residues: 304
  sheet: -0.21 (0.47), residues: 135
  loop : -0.35 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 241 
 HIS   0.003   0.001   HIS A 172 
 PHE   0.009   0.001   PHE A 127 
 TYR   0.015   0.001   TYR A 578 
 ARG   0.005   0.000   ARG A 107 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3897.79 seconds
wall clock time: 67 minutes 34.44 seconds (4054.44 seconds total)