Starting phenix.real_space_refine
on Tue Mar  3 22:56:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8csz_26976/03_2026/8csz_26976.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8csz_26976/03_2026/8csz_26976.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8csz_26976/03_2026/8csz_26976.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8csz_26976/03_2026/8csz_26976.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8csz_26976/03_2026/8csz_26976.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8csz_26976/03_2026/8csz_26976.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.028
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     236      5.49       5
     Mg      2      5.21       5
     S      27      5.16       5
     C    4741      2.51       5
     N    1654      2.21       5
     O    2287      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8948
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "D"
      Number of atoms: 3950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 494, 3950
          Classifications: {'peptide': 494}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 472}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "C"
      Number of atoms: 3937
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 3937
          Classifications: {'RNA': 184}
          Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 13, 'rna3p_pur': 91, 'rna3p_pyr': 67}
          Link IDs: {'rna2p': 25, 'rna3p': 158}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 661
          Classifications: {'DNA': 33}
          Link IDs: {'rna3p': 32}
    Chain: "E"
      Number of atoms: 397
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 397
          Classifications: {'DNA': 19}
          Link IDs: {'rna3p': 18}
    Chain: "D"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MG': 2, ' ZN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2125  SG  CYS D 265      82.445  57.202  49.318  1.00 89.87           S

  Time building chain proxies: 2.44, per 1000 atoms: 0.27
  Number of scatterers: 8948
  At special positions: 0
  Unit cell: (99.51, 111.28, 131.61, 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      27     16.00
     P     236     15.00
     Mg      2     11.99
     O    2287      8.00
     N    1654      7.00
     C    4741      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: 0.80
  Conformation dependent library (CDL) restraints added in 166.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN D 503 "
        pdb="ZN    ZN D 503 " - pdb=" SG  CYS D 265 "
        pdb="ZN    ZN D 503 " - pdb=" NE2 HIS D 268 "


  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  922

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 7 sheets defined
      34.8% alpha, 17.8% beta
      82 base pairs and 139 stacking pairs defined.
    Time for finding SS restraints: 1.40
  Creating SS restraints...
    Processing helix  chain 'D' and resid 21 through 29
    Processing helix  chain 'D' and resid 85 through 87
      No H-bonds generated for 'chain 'D' and resid 85 through 87'
    Processing helix  chain 'D' and resid 88 through 109
      removed outlier: 4.413A  pdb=" N   LYS D  92 " --> pdb=" O   LYS D  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 109 through 121
    Processing helix  chain 'D' and resid 163 through 184
      removed outlier: 3.723A  pdb=" N   ILE D 183 " --> pdb=" O   LYS D 179 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 207 through 212
    Processing helix  chain 'D' and resid 221 through 230
    Processing helix  chain 'D' and resid 265 through 275
    Processing helix  chain 'D' and resid 275 through 286
      removed outlier: 3.715A  pdb=" N   GLU D 279 " --> pdb=" O   ASP D 275 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 294 through 314
      removed outlier: 3.870A  pdb=" N   VAL D 298 " --> pdb=" O   HIS D 294 " (cutoff:3.500A)
      Proline residue:  D 304  - end of helix
    Processing helix  chain 'D' and resid 323 through 334
    Processing helix  chain 'D' and resid 340 through 351
      removed outlier: 3.692A  pdb=" N   TYR D 344 " --> pdb=" O   TYR D 340 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ALA D 350 " --> pdb=" O   ILE D 346 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   LEU D 351 " --> pdb=" O   ALA D 347 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 408 through 416
    Processing helix  chain 'D' and resid 417 through 423
    Processing helix  chain 'D' and resid 480 through 482
      No H-bonds generated for 'chain 'D' and resid 480 through 482'
    Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 17
      removed outlier: 5.180A  pdb=" N   MET D  15 " --> pdb=" O   VAL D   6 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   VAL D   6 " --> pdb=" O   MET D  15 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   TYR D   5 " --> pdb=" O   ILE D  42 " (cutoff:3.500A)
      removed outlier: 7.387A  pdb=" N   LEU D  44 " --> pdb=" O   TYR D   5 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   ILE D   7 " --> pdb=" O   LEU D  44 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   THR D  41 " --> pdb=" O   VAL D  35 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 318 through 322
      removed outlier: 3.988A  pdb=" N   MET D  68 " --> pdb=" O   ALA D  81 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   PHE D  79 " --> pdb=" O   VAL D  70 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 129 through 131
    Processing sheet with id=AA4, first strand: chain 'D' and resid 243 through 246
    Processing sheet with id=AA5, first strand: chain 'D' and resid 378 through 380
      removed outlier: 6.593A  pdb=" N   GLN D 432 " --> pdb=" O   HIS D 379 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 392 through 395
      removed outlier: 5.883A  pdb=" N   LEU D 393 " --> pdb=" O   MET D 389 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   MET D 389 " --> pdb=" O   LEU D 393 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ALA D 395 " --> pdb=" O   TYR D 387 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   SER D 386 " --> pdb=" O   LYS D 427 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 476 through 478
      removed outlier: 6.997A  pdb=" N   GLY D 460 " --> pdb=" O   ASN D 467 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   PHE D 469 " --> pdb=" O   SER D 458 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   SER D 458 " --> pdb=" O   PHE D 469 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   SER D 471 " --> pdb=" O   SER D 456 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   SER D 456 " --> pdb=" O   SER D 471 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   ILE D 444 " --> pdb=" O   LEU D 485 " (cutoff:3.500A)

    156 hydrogen bonds defined for protein.
    429 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      208 hydrogen bonds
      388 hydrogen bond angles
      0 basepair planarities
      82 basepair parallelities
      139 stacking parallelities
  Total time for adding SS restraints: 2.04

  Time building geometry restraints manager: 1.09 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: 1542
        1.33 -     1.45: 3518
        1.45 -     1.57: 4051
        1.57 -     1.69: 467
        1.69 -     1.80: 42
  Bond restraints: 9620
  Sorted by residual:
  bond pdb=" O5'   G C 172 "
       pdb=" C5'   G C 172 "
    ideal  model  delta    sigma   weight residual
    1.420  1.443 -0.023 1.50e-02 4.44e+03 2.29e+00
  bond pdb=" O5'   A C  78 "
       pdb=" C5'   A C  78 "
    ideal  model  delta    sigma   weight residual
    1.420  1.440 -0.020 1.50e-02 4.44e+03 1.73e+00
  bond pdb=" CB  ARG D 101 "
       pdb=" CG  ARG D 101 "
    ideal  model  delta    sigma   weight residual
    1.520  1.484  0.036 3.00e-02 1.11e+03 1.47e+00
  bond pdb=" N   ASN D 203 "
       pdb=" CA  ASN D 203 "
    ideal  model  delta    sigma   weight residual
    1.463  1.451  0.011 9.30e-03 1.16e+04 1.47e+00
  bond pdb=" O5'   U C 205 "
       pdb=" C5'   U C 205 "
    ideal  model  delta    sigma   weight residual
    1.420  1.438 -0.018 1.50e-02 4.44e+03 1.47e+00
  ... (remaining 9615 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 13569
        1.54 -     3.08: 460
        3.08 -     4.62: 57
        4.62 -     6.16: 11
        6.16 -     7.70: 5
  Bond angle restraints: 14102
  Sorted by residual:
  angle pdb=" O3'  DG E 127 "
        pdb=" C3'  DG E 127 "
        pdb=" C2'  DG E 127 "
      ideal   model   delta    sigma   weight residual
     111.50  104.54    6.96 1.50e+00 4.44e-01 2.15e+01
  angle pdb=" C4'   U C 206 "
        pdb=" C3'   U C 206 "
        pdb=" O3'   U C 206 "
      ideal   model   delta    sigma   weight residual
     109.40  114.83   -5.43 1.50e+00 4.44e-01 1.31e+01
  angle pdb=" O3'  DA B  10 "
        pdb=" C3'  DA B  10 "
        pdb=" C2'  DA B  10 "
      ideal   model   delta    sigma   weight residual
     111.50  106.22    5.28 1.50e+00 4.44e-01 1.24e+01
  angle pdb=" C3'   A C 128 "
        pdb=" O3'   A C 128 "
        pdb=" P     U C 129 "
      ideal   model   delta    sigma   weight residual
     120.20  124.99   -4.79 1.50e+00 4.44e-01 1.02e+01
  angle pdb=" C4'   A C 128 "
        pdb=" C3'   A C 128 "
        pdb=" O3'   A C 128 "
      ideal   model   delta    sigma   weight residual
     109.40  114.19   -4.79 1.50e+00 4.44e-01 1.02e+01
  ... (remaining 14097 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.92: 5157
       34.92 -    69.84: 614
       69.84 -   104.77: 59
      104.77 -   139.69: 6
      139.69 -   174.61: 8
  Dihedral angle restraints: 5844
    sinusoidal: 4409
      harmonic: 1435
  Sorted by residual:
  dihedral pdb=" O4'   C C  60 "
           pdb=" C1'   C C  60 "
           pdb=" N1    C C  60 "
           pdb=" C2    C C  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   40.92  159.08     1      1.50e+01 4.44e-03 8.25e+01
  dihedral pdb=" O4'   C C  94 "
           pdb=" C1'   C C  94 "
           pdb=" N1    C C  94 "
           pdb=" C2    C C  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   57.39  174.61     1      1.70e+01 3.46e-03 6.63e+01
  dihedral pdb=" O4'   U C 107 "
           pdb=" C1'   U C 107 "
           pdb=" N1    U C 107 "
           pdb=" C2    U C 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   39.42 -167.42     1      1.70e+01 3.46e-03 6.56e+01
  ... (remaining 5841 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1544
       0.062 -    0.124: 138
       0.124 -    0.185: 15
       0.185 -    0.247: 7
       0.247 -    0.309: 1
  Chirality restraints: 1705
  Sorted by residual:
  chirality pdb=" C3'   U C 206 "
            pdb=" C4'   U C 206 "
            pdb=" O3'   U C 206 "
            pdb=" C2'   U C 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.44   -0.31 2.00e-01 2.50e+01 2.39e+00
  chirality pdb=" C3'   A C  78 "
            pdb=" C4'   A C  78 "
            pdb=" O3'   A C  78 "
            pdb=" C2'   A C  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.72    0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" C3'   A C 128 "
            pdb=" C4'   A C 128 "
            pdb=" O3'   A C 128 "
            pdb=" C2'   A C 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.52   -0.22 2.00e-01 2.50e+01 1.24e+00
  ... (remaining 1702 not shown)

  Planarity restraints: 938
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C 122 "    0.036 2.00e-02 2.50e+03   1.63e-02 7.31e+00
        pdb=" N9    A C 122 "   -0.038 2.00e-02 2.50e+03
        pdb=" C8    A C 122 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    A C 122 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    A C 122 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    A C 122 "    0.005 2.00e-02 2.50e+03
        pdb=" N6    A C 122 "    0.007 2.00e-02 2.50e+03
        pdb=" N1    A C 122 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    A C 122 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    A C 122 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4    A C 122 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C  91 "   -0.032 2.00e-02 2.50e+03   1.40e-02 5.86e+00
        pdb=" N9    G C  91 "    0.034 2.00e-02 2.50e+03
        pdb=" C8    G C  91 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    G C  91 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G C  91 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    G C  91 "   -0.002 2.00e-02 2.50e+03
        pdb=" O6    G C  91 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1    G C  91 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    G C  91 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G C  91 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G C  91 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    G C  91 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C C 127 "   -0.030 2.00e-02 2.50e+03   1.56e-02 5.47e+00
        pdb=" N1    C C 127 "    0.034 2.00e-02 2.50e+03
        pdb=" C2    C C 127 "    0.002 2.00e-02 2.50e+03
        pdb=" O2    C C 127 "    0.004 2.00e-02 2.50e+03
        pdb=" N3    C C 127 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    C C 127 "   -0.003 2.00e-02 2.50e+03
        pdb=" N4    C C 127 "   -0.010 2.00e-02 2.50e+03
        pdb=" C5    C C 127 "    0.004 2.00e-02 2.50e+03
        pdb=" C6    C C 127 "    0.003 2.00e-02 2.50e+03
  ... (remaining 935 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 61
        2.55 -     3.14: 6562
        3.14 -     3.72: 16549
        3.72 -     4.31: 23135
        4.31 -     4.90: 32429
  Nonbonded interactions: 78736
  Sorted by model distance:
  nonbonded pdb=" ND1 HIS D 245 "
            pdb="MG    MG D 501 "
     model   vdw
     1.962 2.250
  nonbonded pdb=" NE2 HIS D 269 "
            pdb="MG    MG D 501 "
     model   vdw
     2.018 2.250
  nonbonded pdb=" OP2  DC E 111 "
            pdb="MG    MG D 502 "
     model   vdw
     2.021 2.170
  nonbonded pdb=" ND1 HIS D 273 "
            pdb="MG    MG D 501 "
     model   vdw
     2.071 2.250
  nonbonded pdb=" O2'   U C 180 "
            pdb=" OP1   C C 181 "
     model   vdw
     2.127 3.040
  ... (remaining 78731 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:             1.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     12.900
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
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      :  0.006   0.340   9622  Z= 0.281
  Angle     :  0.672   7.704  14102  Z= 0.385
  Chirality :  0.040   0.309   1705
  Planarity :  0.004   0.053    938
  Dihedral  : 23.812 174.610   4922
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.97 (0.37), residues: 492
  helix:  0.82 (0.42), residues: 152
  sheet: -1.55 (0.65), residues: 65
  loop : -1.27 (0.35), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 363 
 TYR   0.011   0.002   TYR D 340 
 PHE   0.007   0.001   PHE D 453 
 TRP   0.008   0.002   TRP D 478 
 HIS   0.007   0.001   HIS D 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 ( 9620)
  covalent geometry    : angle       0.67154 (14102)
  hydrogen bonds       : bond        0.12252 (  364)
  hydrogen bonds       : angle       5.85488 (  817)
  metal coordination   : bond        0.24074 (    2)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.224 
Fit side-chains
REVERT: D  353 ASP cc_start: 0.7944 (m-30) cc_final: 0.7581 (p0)
REVERT: D  403 ASP cc_start: 0.7861 (m-30) cc_final: 0.7354 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.1519
  time to fit residues: 7.0727
Evaluate side-chains
  27 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   overall best weight:    4.1788

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

Flipped N/Q/H residues before XYZ refinement:
** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.079547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.057186 restraints weight = 24543.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.2901 rms_B_bonded: 1.78
r_work: 0.2783 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2674 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8778
moved from start:          0.0948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.059   9622  Z= 0.400
  Angle     :  0.746  12.287  14102  Z= 0.396
  Chirality :  0.044   0.326   1705
  Planarity :  0.005   0.045    938
  Dihedral  : 24.895 179.838   3920
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  6.12 %
    Favored  : 93.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.01 (0.37), residues: 492
  helix:  0.76 (0.42), residues: 152
  sheet: -1.50 (0.63), residues: 65
  loop : -1.30 (0.36), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 375 
 TYR   0.012   0.002   TYR D   5 
 PHE   0.012   0.002   PHE D 453 
 TRP   0.009   0.002   TRP D 161 
 HIS   0.007   0.002   HIS D 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00829 ( 9620)
  covalent geometry    : angle       0.74595 (14102)
  hydrogen bonds       : bond        0.06207 (  364)
  hydrogen bonds       : angle       4.06965 (  817)
  metal coordination   : bond        0.00694 (    2)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.176 
Fit side-chains
REVERT: D  353 ASP cc_start: 0.8640 (m-30) cc_final: 0.7911 (p0)
  outliers start: 3
  outliers final: 1
  residues processed: 29
  average time/residue: 0.1457
  time to fit residues: 5.4482
Evaluate side-chains
  27 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  426 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 49 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    1.5388

-------------------------------------------------------------------------------
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 = 0.3427 r_free = 0.3427 target = 0.081507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.059562 restraints weight = 23928.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.2923 rms_B_bonded: 1.62
r_work: 0.2806 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2697 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.1112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9622  Z= 0.181
  Angle     :  0.596   9.762  14102  Z= 0.320
  Chirality :  0.036   0.219   1705
  Planarity :  0.004   0.045    938
  Dihedral  : 24.676 177.194   3920
  Min Nonbonded Distance : 1.708

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  7.53 %
    Favored  : 91.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.55 (0.37), residues: 492
  helix:  1.23 (0.42), residues: 154
  sheet: -1.17 (0.67), residues: 55
  loop : -1.13 (0.35), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 155 
 TYR   0.011   0.001   TYR D   5 
 PHE   0.008   0.001   PHE D  79 
 TRP   0.007   0.001   TRP D 478 
 HIS   0.004   0.001   HIS D 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 9620)
  covalent geometry    : angle       0.59556 (14102)
  hydrogen bonds       : bond        0.04445 (  364)
  hydrogen bonds       : angle       3.68235 (  817)
  metal coordination   : bond        0.00143 (    2)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.211 
Fit side-chains
REVERT: D  353 ASP cc_start: 0.8663 (m-30) cc_final: 0.7991 (p0)
  outliers start: 4
  outliers final: 3
  residues processed: 39
  average time/residue: 0.1429
  time to fit residues: 7.2037
Evaluate side-chains
  31 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  273 HIS
Chi-restraints excluded: chain D residue  396 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 57 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 67 optimal weight:   10.0000
   chunk 27 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 54 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 29 optimal weight:    5.9990
   chunk 2 optimal weight:    0.5980
   overall best weight:    3.9188

-------------------------------------------------------------------------------
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 = 0.3365 r_free = 0.3365 target = 0.078583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.056425 restraints weight = 24611.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 1.80
r_work: 0.2729 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2620 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8736
moved from start:          0.1200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.043   9622  Z= 0.376
  Angle     :  0.707  11.234  14102  Z= 0.376
  Chirality :  0.042   0.317   1705
  Planarity :  0.005   0.041    938
  Dihedral  : 24.736 177.219   3920
  Min Nonbonded Distance : 1.548

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  :  9.41 %
    Favored  : 88.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.89 (0.37), residues: 492
  helix:  0.94 (0.42), residues: 152
  sheet: -1.34 (0.60), residues: 65
  loop : -1.31 (0.36), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 101 
 TYR   0.012   0.002   TYR D   5 
 PHE   0.012   0.002   PHE D 453 
 TRP   0.008   0.001   TRP D 161 
 HIS   0.005   0.002   HIS D 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00779 ( 9620)
  covalent geometry    : angle       0.70704 (14102)
  hydrogen bonds       : bond        0.05777 (  364)
  hydrogen bonds       : angle       3.84310 (  817)
  metal coordination   : bond        0.00261 (    2)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 27
  time to evaluate  : 0.220 
Fit side-chains
REVERT: D  208 ARG cc_start: 0.7530 (mpp80) cc_final: 0.6568 (mtp180)
REVERT: D  353 ASP cc_start: 0.8670 (m-30) cc_final: 0.7806 (p0)
  outliers start: 8
  outliers final: 6
  residues processed: 35
  average time/residue: 0.1066
  time to fit residues: 5.1227
Evaluate side-chains
  33 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 27
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue  239 HIS
Chi-restraints excluded: chain D residue  273 HIS
Chi-restraints excluded: chain D residue  396 THR
Chi-restraints excluded: chain D residue  426 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 60 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 20 optimal weight:    6.9990
   chunk 28 optimal weight:    9.9990
   chunk 32 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    1.9188

-------------------------------------------------------------------------------
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 = 0.3408 r_free = 0.3408 target = 0.080667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.058577 restraints weight = 24220.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.2899 rms_B_bonded: 1.62
r_work: 0.2782 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2674 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8695
moved from start:          0.1287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   9622  Z= 0.211
  Angle     :  0.609   9.760  14102  Z= 0.325
  Chirality :  0.037   0.242   1705
  Planarity :  0.004   0.041    938
  Dihedral  : 24.600 178.499   3920
  Min Nonbonded Distance : 1.603

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 10.82 %
    Favored  : 87.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.56 (0.37), residues: 492
  helix:  1.25 (0.42), residues: 152
  sheet: -1.23 (0.66), residues: 55
  loop : -1.13 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 155 
 TYR   0.011   0.001   TYR D   5 
 PHE   0.008   0.001   PHE D  79 
 TRP   0.007   0.001   TRP D 478 
 HIS   0.003   0.001   HIS D 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 9620)
  covalent geometry    : angle       0.60858 (14102)
  hydrogen bonds       : bond        0.04570 (  364)
  hydrogen bonds       : angle       3.66911 (  817)
  metal coordination   : bond        0.00111 (    2)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.212 
Fit side-chains
REVERT: D  201 MET cc_start: 0.8604 (mtm) cc_final: 0.8157 (ttp)
REVERT: D  208 ARG cc_start: 0.7377 (mpp80) cc_final: 0.6368 (mtp180)
REVERT: D  353 ASP cc_start: 0.8708 (m-30) cc_final: 0.7870 (p0)
  outliers start: 6
  outliers final: 6
  residues processed: 34
  average time/residue: 0.1296
  time to fit residues: 5.8906
Evaluate side-chains
  33 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 27
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue  239 HIS
Chi-restraints excluded: chain D residue  273 HIS
Chi-restraints excluded: chain D residue  396 THR
Chi-restraints excluded: chain D residue  426 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 28 optimal weight:   10.0000
   chunk 67 optimal weight:   10.0000
   chunk 46 optimal weight:    3.9990
   chunk 62 optimal weight:    8.9990
   chunk 35 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
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 = 0.3367 r_free = 0.3367 target = 0.078685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.056573 restraints weight = 24289.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.2850 rms_B_bonded: 1.76
r_work: 0.2733 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2625 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8734
moved from start:          0.1361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.041   9622  Z= 0.350
  Angle     :  0.687  10.735  14102  Z= 0.366
  Chirality :  0.041   0.311   1705
  Planarity :  0.005   0.042    938
  Dihedral  : 24.656 179.171   3920
  Min Nonbonded Distance : 1.554

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 10.59 %
    Favored  : 87.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.37), residues: 492
  helix:  0.99 (0.42), residues: 152
  sheet: -1.26 (0.61), residues: 65
  loop : -1.35 (0.36), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 115 
 TYR   0.012   0.002   TYR D   5 
 PHE   0.011   0.001   PHE D 453 
 TRP   0.007   0.001   TRP D 161 
 HIS   0.005   0.001   HIS D 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00726 ( 9620)
  covalent geometry    : angle       0.68745 (14102)
  hydrogen bonds       : bond        0.05512 (  364)
  hydrogen bonds       : angle       3.81638 (  817)
  metal coordination   : bond        0.00235 (    2)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 29
  time to evaluate  : 0.232 
Fit side-chains
REVERT: D  201 MET cc_start: 0.8718 (mtm) cc_final: 0.8284 (ttp)
REVERT: D  208 ARG cc_start: 0.7495 (mpp80) cc_final: 0.6537 (mtp180)
REVERT: D  353 ASP cc_start: 0.8727 (m-30) cc_final: 0.7927 (p0)
  outliers start: 8
  outliers final: 7
  residues processed: 36
  average time/residue: 0.1153
  time to fit residues: 5.6305
Evaluate side-chains
  34 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 27
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue  237 CYS
Chi-restraints excluded: chain D residue  239 HIS
Chi-restraints excluded: chain D residue  273 HIS
Chi-restraints excluded: chain D residue  396 THR
Chi-restraints excluded: chain D residue  426 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
D 273 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.082436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.060494 restraints weight = 24142.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 1.63
r_work: 0.2830 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2719 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9622  Z= 0.137
  Angle     :  0.570  11.778  14102  Z= 0.304
  Chirality :  0.034   0.194   1705
  Planarity :  0.004   0.041    938
  Dihedral  : 24.472 179.503   3920
  Min Nonbonded Distance : 1.657

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 11.53 %
    Favored  : 86.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.37), residues: 492
  helix:  1.40 (0.42), residues: 154
  sheet: -1.22 (0.67), residues: 56
  loop : -1.06 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 155 
 TYR   0.011   0.001   TYR D 484 
 PHE   0.008   0.001   PHE D  79 
 TRP   0.008   0.001   TRP D 478 
 HIS   0.003   0.001   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9620)
  covalent geometry    : angle       0.56998 (14102)
  hydrogen bonds       : bond        0.03977 (  364)
  hydrogen bonds       : angle       3.55262 (  817)
  metal coordination   : bond        0.00068 (    2)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.215 
Fit side-chains
REVERT: D  201 MET cc_start: 0.8548 (mtm) cc_final: 0.8217 (ttp)
REVERT: D  353 ASP cc_start: 0.8682 (m-30) cc_final: 0.7980 (p0)
REVERT: D  389 MET cc_start: 0.8249 (tpp) cc_final: 0.7999 (tpp)
  outliers start: 7
  outliers final: 5
  residues processed: 34
  average time/residue: 0.1165
  time to fit residues: 5.3774
Evaluate side-chains
  31 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 26
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  237 CYS
Chi-restraints excluded: chain D residue  239 HIS
Chi-restraints excluded: chain D residue  396 THR
Chi-restraints excluded: chain D residue  452 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 49 optimal weight:    6.9990
   chunk 42 optimal weight:    0.0970
   chunk 56 optimal weight:    8.9990
   chunk 13 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 20 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 62 optimal weight:    8.9990
   overall best weight:    1.3382

-------------------------------------------------------------------------------
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 = 0.3433 r_free = 0.3433 target = 0.082094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.060105 restraints weight = 24109.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 1.64
r_work: 0.2820 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2710 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9622  Z= 0.164
  Angle     :  0.563   9.391  14102  Z= 0.301
  Chirality :  0.034   0.191   1705
  Planarity :  0.004   0.040    938
  Dihedral  : 24.397 178.291   3920
  Min Nonbonded Distance : 1.616

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 12.00 %
    Favored  : 86.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.38), residues: 492
  helix:  1.56 (0.43), residues: 154
  sheet: -1.12 (0.68), residues: 56
  loop : -1.03 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 195 
 TYR   0.010   0.001   TYR D   5 
 PHE   0.007   0.001   PHE D 453 
 TRP   0.006   0.001   TRP D 478 
 HIS   0.003   0.001   HIS D 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 9620)
  covalent geometry    : angle       0.56299 (14102)
  hydrogen bonds       : bond        0.03997 (  364)
  hydrogen bonds       : angle       3.52197 (  817)
  metal coordination   : bond        0.00093 (    2)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 27
  time to evaluate  : 0.218 
Fit side-chains
REVERT: D  201 MET cc_start: 0.8653 (mtm) cc_final: 0.8265 (ttp)
REVERT: D  353 ASP cc_start: 0.8704 (m-30) cc_final: 0.7917 (p0)
REVERT: D  389 MET cc_start: 0.8312 (tpp) cc_final: 0.8030 (tpp)
  outliers start: 8
  outliers final: 7
  residues processed: 34
  average time/residue: 0.1427
  time to fit residues: 6.3366
Evaluate side-chains
  34 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 27
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  237 CYS
Chi-restraints excluded: chain D residue  239 HIS
Chi-restraints excluded: chain D residue  375 ARG
Chi-restraints excluded: chain D residue  396 THR
Chi-restraints excluded: chain D residue  426 VAL
Chi-restraints excluded: chain D residue  452 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 42 optimal weight:    0.0050
   chunk 26 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 48 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 55 optimal weight:    8.9990
   chunk 0 optimal weight:    7.9990
   chunk 58 optimal weight:    4.9990
   chunk 56 optimal weight:    6.9990
   overall best weight:    2.7600

-------------------------------------------------------------------------------
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 = 0.3389 r_free = 0.3389 target = 0.079869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.057684 restraints weight = 24360.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.2877 rms_B_bonded: 1.74
r_work: 0.2759 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2651 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
moved from start:          0.1616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   9622  Z= 0.280
  Angle     :  0.633   8.166  14102  Z= 0.337
  Chirality :  0.038   0.270   1705
  Planarity :  0.004   0.038    938
  Dihedral  : 24.432 178.465   3920
  Min Nonbonded Distance : 1.570

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 11.53 %
    Favored  : 86.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.37), residues: 492
  helix:  1.35 (0.43), residues: 152
  sheet: -0.92 (0.62), residues: 65
  loop : -1.21 (0.36), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 155 
 TYR   0.014   0.002   TYR D   5 
 PHE   0.009   0.001   PHE D 453 
 TRP   0.005   0.001   TRP D 161 
 HIS   0.004   0.001   HIS D 273 

Details of bonding type rmsd
  covalent geometry    : bond        0.00581 ( 9620)
  covalent geometry    : angle       0.63288 (14102)
  hydrogen bonds       : bond        0.04909 (  364)
  hydrogen bonds       : angle       3.68223 (  817)
  metal coordination   : bond        0.00203 (    2)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 29
  time to evaluate  : 0.224 
Fit side-chains
REVERT: D  201 MET cc_start: 0.8674 (mtm) cc_final: 0.8330 (ttp)
REVERT: D  208 ARG cc_start: 0.7417 (mpp80) cc_final: 0.6472 (mtp180)
REVERT: D  353 ASP cc_start: 0.8706 (m-30) cc_final: 0.7924 (p0)
  outliers start: 10
  outliers final: 9
  residues processed: 36
  average time/residue: 0.1548
  time to fit residues: 7.2324
Evaluate side-chains
  37 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   68 MET
Chi-restraints excluded: chain D residue  228 MET
Chi-restraints excluded: chain D residue  237 CYS
Chi-restraints excluded: chain D residue  239 HIS
Chi-restraints excluded: chain D residue  375 ARG
Chi-restraints excluded: chain D residue  396 THR
Chi-restraints excluded: chain D residue  426 VAL
Chi-restraints excluded: chain D residue  452 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   chunk 55 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 24 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.3431 r_free = 0.3431 target = 0.082262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.060310 restraints weight = 23872.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.2938 rms_B_bonded: 1.63
r_work: 0.2820 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2707 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9622  Z= 0.146
  Angle     :  0.552   8.154  14102  Z= 0.295
  Chirality :  0.033   0.194   1705
  Planarity :  0.004   0.039    938
  Dihedral  : 24.327 178.210   3920
  Min Nonbonded Distance : 1.651

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 11.76 %
    Favored  : 86.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.38), residues: 492
  helix:  1.57 (0.43), residues: 154
  sheet: -1.12 (0.67), residues: 56
  loop : -0.97 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 363 
 TYR   0.010   0.001   TYR D 484 
 PHE   0.007   0.001   PHE D  79 
 TRP   0.008   0.001   TRP D 478 
 HIS   0.003   0.001   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9620)
  covalent geometry    : angle       0.55228 (14102)
  hydrogen bonds       : bond        0.03857 (  364)
  hydrogen bonds       : angle       3.50930 (  817)
  metal coordination   : bond        0.00082 (    2)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 27
  time to evaluate  : 0.164 
Fit side-chains
REVERT: D  201 MET cc_start: 0.8602 (mtm) cc_final: 0.8306 (ttp)
REVERT: D  353 ASP cc_start: 0.8713 (m-30) cc_final: 0.8001 (p0)
REVERT: D  361 LYS cc_start: 0.8876 (tppt) cc_final: 0.8515 (mptt)
  outliers start: 9
  outliers final: 8
  residues processed: 33
  average time/residue: 0.1472
  time to fit residues: 6.2337
Evaluate side-chains
  35 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 27
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   68 MET
Chi-restraints excluded: chain D residue  228 MET
Chi-restraints excluded: chain D residue  237 CYS
Chi-restraints excluded: chain D residue  239 HIS
Chi-restraints excluded: chain D residue  375 ARG
Chi-restraints excluded: chain D residue  396 THR
Chi-restraints excluded: chain D residue  452 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   chunk 62 optimal weight:    8.9990
   chunk 44 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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 = 0.3411 r_free = 0.3411 target = 0.081277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.059201 restraints weight = 23605.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.2912 rms_B_bonded: 1.68
r_work: 0.2793 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2682 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8665
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9622  Z= 0.193
  Angle     :  0.571   7.998  14102  Z= 0.305
  Chirality :  0.034   0.204   1705
  Planarity :  0.004   0.039    938
  Dihedral  : 24.328 177.697   3920
  Min Nonbonded Distance : 1.598

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 11.06 %
    Favored  : 86.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.38), residues: 492
  helix:  1.53 (0.42), residues: 154
  sheet: -1.01 (0.69), residues: 55
  loop : -1.02 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 155 
 TYR   0.011   0.001   TYR D   5 
 PHE   0.007   0.001   PHE D  79 
 TRP   0.005   0.001   TRP D 278 
 HIS   0.003   0.001   HIS D 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 9620)
  covalent geometry    : angle       0.57145 (14102)
  hydrogen bonds       : bond        0.04176 (  364)
  hydrogen bonds       : angle       3.54002 (  817)
  metal coordination   : bond        0.00140 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2237.40 seconds
wall clock time: 39 minutes 0.76 seconds (2340.76 seconds total)