Starting phenix.real_space_refine
on Thu Mar  6 09:34:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8exa_28656/03_2025/8exa_28656.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8exa_28656/03_2025/8exa_28656.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8exa_28656/03_2025/8exa_28656.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8exa_28656/03_2025/8exa_28656.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8exa_28656/03_2025/8exa_28656.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8exa_28656/03_2025/8exa_28656.cif"
  }
  resolution = 3.14
  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=   0.000 sd=   1.000
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: 5
    Type Number    sf(0)   Gaussians
     P     139      5.49       5
     S       2      5.16       5
     C    2984      2.51       5
     N    1029      2.21       5
     O    1385      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5539
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2610
          Classifications: {'peptide': 341}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 9, 'TRANS': 331}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 161
          Unresolved non-hydrogen angles: 191
          Unresolved non-hydrogen dihedrals: 137
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 101
    Chain: "B"
      Number of atoms: 2163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 2163
          Classifications: {'RNA': 101}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 49, 'rna3p_pyr': 42}
          Link IDs: {'rna2p': 10, 'rna3p': 90}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 252
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 252
          Classifications: {'DNA': 13}
          Link IDs: {'rna3p': 12}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {' DC:plan2': 1, ' DC:plan': 1, ' DT:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "D"
      Number of atoms: 514
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 514
          Classifications: {'DNA': 25}
          Link IDs: {'rna3p': 24}
  Time building chain proxies: 4.23, per 1000 atoms: 0.76
  Number of scatterers: 5539
  At special positions: 0
  Unit cell: (81.4, 86.9, 97.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     P     139     15.00
     O    1385      8.00
     N    1029      7.00
     C    2984      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: 1.63
  Conformation dependent library (CDL) restraints added in 596.0 milliseconds
  

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  636

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 2 sheets defined
      53.7% alpha, 15.2% beta
      56 base pairs and 82 stacking pairs defined.
    Time for finding SS restraints: 2.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 46
    Processing helix  chain 'A' and resid 51 through 65
    Processing helix  chain 'A' and resid 68 through 72
    Processing helix  chain 'A' and resid 75 through 96
      removed outlier: 3.714A  pdb=" N   LEU A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   THR A  96 " --> pdb=" O   ASN A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 218
    Processing helix  chain 'A' and resid 218 through 231
    Processing helix  chain 'A' and resid 236 through 271
    Processing helix  chain 'A' and resid 281 through 286
    Processing helix  chain 'A' and resid 288 through 299
      removed outlier: 4.628A  pdb=" N   LEU A 293 " --> pdb=" O   ARG A 289 " (cutoff:3.500A)
      removed outlier: 5.735A  pdb=" N   SER A 294 " --> pdb=" O   ARG A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 314
    Processing helix  chain 'A' and resid 360 through 377
    Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 121
      removed outlier: 7.383A  pdb=" N   ILE A 154 " --> pdb=" O   GLU A 174 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   GLU A 174 " --> pdb=" O   ILE A 154 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ASN A 156 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   TYR A 167 " --> pdb=" O   LEU A  11 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 209
      removed outlier: 4.215A  pdb=" N   VAL A 200 " --> pdb=" O   LYS A 207 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   PHE A 186 " --> pdb=" O   TYR A 272 " (cutoff:3.500A)
      removed outlier: 4.817A  pdb=" N   GLU A 278 " --> pdb=" O   VAL A 190 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   VAL A 192 " --> pdb=" O   GLU A 278 " (cutoff:3.500A)
      removed outlier: 7.385A  pdb=" N   VAL A 321 " --> pdb=" O   ILE A 275 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   THR A 277 " --> pdb=" O   VAL A 321 " (cutoff:3.500A)

    169 hydrogen bonds defined for protein.
    489 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      141 hydrogen bonds
      238 hydrogen bond angles
      0 basepair planarities
      56 basepair parallelities
      82 stacking parallelities
  Total time for adding SS restraints: 2.36

  Time building geometry restraints manager: 1.86 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: 923
        1.33 -     1.45: 2154
        1.45 -     1.57: 2579
        1.57 -     1.69: 273
        1.69 -     1.80: 3
  Bond restraints: 5932
  Sorted by residual:
  bond pdb=" N   GLN A  80 "
       pdb=" CA  GLN A  80 "
    ideal  model  delta    sigma   weight residual
    1.459  1.482 -0.023 1.23e-02 6.61e+03 3.44e+00
  bond pdb=" CB  TRP A 313 "
       pdb=" CG  TRP A 313 "
    ideal  model  delta    sigma   weight residual
    1.498  1.469  0.029 3.10e-02 1.04e+03 8.46e-01
  bond pdb=" C3'  DC C   3 "
       pdb=" O3'  DC C   3 "
    ideal  model  delta    sigma   weight residual
    1.422  1.448 -0.026 3.00e-02 1.11e+03 7.34e-01
  bond pdb=" C4'  DT C   0 "
       pdb=" O4'  DT C   0 "
    ideal  model  delta    sigma   weight residual
    1.450  1.433  0.017 2.00e-02 2.50e+03 6.97e-01
  bond pdb=" CA  GLN A  80 "
       pdb=" C   GLN A  80 "
    ideal  model  delta    sigma   weight residual
    1.524  1.534 -0.010 1.29e-02 6.01e+03 6.52e-01
  ... (remaining 5927 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.99: 8117
        0.99 -     1.97: 448
        1.97 -     2.96: 87
        2.96 -     3.94: 15
        3.94 -     4.93: 6
  Bond angle restraints: 8673
  Sorted by residual:
  angle pdb=" CA  TYR A 309 "
        pdb=" CB  TYR A 309 "
        pdb=" CG  TYR A 309 "
      ideal   model   delta    sigma   weight residual
     113.90  118.72   -4.82 1.80e+00 3.09e-01 7.18e+00
  angle pdb=" C2'   G B   3 "
        pdb=" C1'   G B   3 "
        pdb=" N9    G B   3 "
      ideal   model   delta    sigma   weight residual
     112.00  115.28   -3.28 1.50e+00 4.44e-01 4.79e+00
  angle pdb=" N   ILE A 275 "
        pdb=" CA  ILE A 275 "
        pdb=" C   ILE A 275 "
      ideal   model   delta    sigma   weight residual
     106.53  109.29   -2.76 1.41e+00 5.03e-01 3.83e+00
  angle pdb=" C2'   U B   9 "
        pdb=" C1'   U B   9 "
        pdb=" N1    U B   9 "
      ideal   model   delta    sigma   weight residual
     114.00  111.36    2.64 1.50e+00 4.44e-01 3.10e+00
  angle pdb=" C4'  DG C  -5 "
        pdb=" O4'  DG C  -5 "
        pdb=" C1'  DG C  -5 "
      ideal   model   delta    sigma   weight residual
     109.70  107.08    2.62 1.50e+00 4.44e-01 3.05e+00
  ... (remaining 8668 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.56: 3069
       28.56 -    57.13: 370
       57.13 -    85.69: 148
       85.69 -   114.25: 1
      114.25 -   142.82: 1
  Dihedral angle restraints: 3589
    sinusoidal: 2600
      harmonic: 989
  Sorted by residual:
  dihedral pdb=" C4'  DC C   3 "
           pdb=" C3'  DC C   3 "
           pdb=" O3'  DC C   3 "
           pdb=" P    DA C   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   77.18  142.82     1      3.50e+01 8.16e-04 1.41e+01
  dihedral pdb=" O4'   U B -89 "
           pdb=" C1'   U B -89 "
           pdb=" N1    U B -89 "
           pdb=" C2    U B -89 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00 -119.23  -40.77     1      1.50e+01 4.44e-03 1.04e+01
  dihedral pdb=" CA  LEU A 136 "
           pdb=" C   LEU A 136 "
           pdb=" N   PRO A 137 "
           pdb=" CA  PRO A 137 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.05  -15.95     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 3586 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 769
       0.030 -    0.060: 213
       0.060 -    0.090: 47
       0.090 -    0.119: 26
       0.119 -    0.149: 7
  Chirality restraints: 1062
  Sorted by residual:
  chirality pdb=" CA  PHE A  35 "
            pdb=" N   PHE A  35 "
            pdb=" C   PHE A  35 "
            pdb=" CB  PHE A  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.56e-01
  chirality pdb=" C1'   A B   2 "
            pdb=" O4'   A B   2 "
            pdb=" C2'   A B   2 "
            pdb=" N9    A B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.33    0.13 2.00e-01 2.50e+01 4.17e-01
  chirality pdb=" CA  PRO A 137 "
            pdb=" N   PRO A 137 "
            pdb=" C   PRO A 137 "
            pdb=" CB  PRO A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.77e-01
  ... (remaining 1059 not shown)

  Planarity restraints: 596
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B   3 "   -0.031 2.00e-02 2.50e+03   1.28e-02 4.95e+00
        pdb=" N9    G B   3 "    0.028 2.00e-02 2.50e+03
        pdb=" C8    G B   3 "    0.006 2.00e-02 2.50e+03
        pdb=" N7    G B   3 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G B   3 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G B   3 "   -0.006 2.00e-02 2.50e+03
        pdb=" O6    G B   3 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    G B   3 "   -0.006 2.00e-02 2.50e+03
        pdb=" C2    G B   3 "    0.007 2.00e-02 2.50e+03
        pdb=" N2    G B   3 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G B   3 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    G B   3 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B   9 "    0.026 2.00e-02 2.50e+03   1.39e-02 4.35e+00
        pdb=" N1    U B   9 "   -0.031 2.00e-02 2.50e+03
        pdb=" C2    U B   9 "    0.001 2.00e-02 2.50e+03
        pdb=" O2    U B   9 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3    U B   9 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    U B   9 "    0.005 2.00e-02 2.50e+03
        pdb=" O4    U B   9 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    U B   9 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    U B   9 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B   2 "   -0.023 2.00e-02 2.50e+03   1.03e-02 2.92e+00
        pdb=" N9    A B   2 "    0.023 2.00e-02 2.50e+03
        pdb=" C8    A B   2 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    A B   2 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    A B   2 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    A B   2 "   -0.001 2.00e-02 2.50e+03
        pdb=" N6    A B   2 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    A B   2 "    0.000 2.00e-02 2.50e+03
        pdb=" C2    A B   2 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A B   2 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    A B   2 "    0.003 2.00e-02 2.50e+03
  ... (remaining 593 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 899
        2.76 -     3.29: 5072
        3.29 -     3.83: 11101
        3.83 -     4.36: 12729
        4.36 -     4.90: 18341
  Nonbonded interactions: 48142
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 117 "
            pdb=" OP1   U B   4 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O2    C B-107 "
            pdb=" N2    G B  -6 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" NH1 ARG A  39 "
            pdb=" OE1 GLU A  87 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" N2    G B-114 "
            pdb=" O4    U B -89 "
     model   vdw
     2.301 3.120
  nonbonded pdb=" NH1 ARG A 110 "
            pdb=" OP1   C B   5 "
     model   vdw
     2.319 3.120
  ... (remaining 48137 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.550
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     20.310
  Find NCS groups from input model:        0.040
  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:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6776
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   0.029   5932  Z= 0.219
  Angle     :  0.538   4.927   8673  Z= 0.286
  Chirality :  0.033   0.149   1062
  Planarity :  0.003   0.023    596
  Dihedral  : 22.737 142.816   2953
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  8.50 %
    Favored  : 91.09 %
  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:  0.27 (0.47), residues: 337
  helix:  1.86 (0.40), residues: 175
  sheet: -1.83 (0.63), residues: 65
  loop : -1.41 (0.60), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 300 
 HIS   0.002   0.001   HIS A 166 
 PHE   0.018   0.002   PHE A  35 
 TYR   0.024   0.002   TYR A 309 
 ARG   0.002   0.000   ARG A  39 

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 LEU cc_start: 0.9058 (mt) cc_final: 0.8835 (mt)
REVERT: A   95 ARG cc_start: 0.7416 (mtm-85) cc_final: 0.7187 (mtm110)
  outliers start: 1
  outliers final: 1
  residues processed: 47
  average time/residue: 0.2184
  time to fit residues: 13.1176
Evaluate side-chains
  39 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 39 optimal weight:    7.9990
   chunk 35 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 12 optimal weight:    0.4980
   chunk 24 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 128 GLN
A 227 GLN
A 250 HIS
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.196863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.157172 restraints weight = 7391.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3935 rms_B_bonded: 1.67
r_work: 0.3800 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6658
moved from start:          0.0977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5932  Z= 0.173
  Angle     :  0.499   5.111   8673  Z= 0.264
  Chirality :  0.031   0.126   1062
  Planarity :  0.003   0.020    596
  Dihedral  : 23.801 142.230   2371
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  :  9.31 %
    Favored  : 87.45 %
  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:  0.98 (0.48), residues: 337
  helix:  2.63 (0.40), residues: 169
  sheet: -1.68 (0.65), residues: 65
  loop : -1.12 (0.60), residues: 103

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 300 
 HIS   0.002   0.001   HIS A 166 
 PHE   0.022   0.002   PHE A  35 
 TYR   0.021   0.002   TYR A 309 
 ARG   0.003   0.000   ARG A 110 

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.469 
Fit side-chains
REVERT: A   61 LEU cc_start: 0.8884 (mt) cc_final: 0.8643 (mt)
REVERT: A  143 LYS cc_start: 0.7276 (tttt) cc_final: 0.6483 (mtmt)
REVERT: A  255 ASN cc_start: 0.7358 (m110) cc_final: 0.6997 (m110)
REVERT: A  264 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.7050 (tt)
  outliers start: 8
  outliers final: 4
  residues processed: 48
  average time/residue: 0.1980
  time to fit residues: 12.2967
Evaluate side-chains
  40 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  309 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 38 optimal weight:    8.9990
   chunk 25 optimal weight:    0.8980
   chunk 34 optimal weight:    7.9990
   chunk 4 optimal weight:    7.9990
   chunk 36 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A 255 ASN ** 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 = 0.4399 r_free = 0.4399 target = 0.197257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.157317 restraints weight = 7357.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3981 rms_B_bonded: 1.58
r_work: 0.3844 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6765
moved from start:          0.1083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5932  Z= 0.202
  Angle     :  0.514   5.619   8673  Z= 0.269
  Chirality :  0.032   0.122   1062
  Planarity :  0.003   0.021    596
  Dihedral  : 23.771 142.241   2371
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 10.93 %
    Favored  : 86.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.48), residues: 337
  helix:  2.65 (0.39), residues: 167
  sheet: -1.63 (0.67), residues: 66
  loop : -0.99 (0.61), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 300 
 HIS   0.002   0.001   HIS A 166 
 PHE   0.022   0.002   PHE A  35 
 TYR   0.021   0.002   TYR A 309 
 ARG   0.004   0.000   ARG A  95 

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.386 
Fit side-chains
REVERT: A   61 LEU cc_start: 0.8910 (mt) cc_final: 0.8706 (mt)
REVERT: A  143 LYS cc_start: 0.7148 (tttt) cc_final: 0.6466 (mtmt)
REVERT: A  255 ASN cc_start: 0.7431 (m110) cc_final: 0.7065 (m110)
  outliers start: 7
  outliers final: 4
  residues processed: 43
  average time/residue: 0.2345
  time to fit residues: 12.6263
Evaluate side-chains
  42 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  275 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 13 optimal weight:    0.3980
   chunk 41 optimal weight:   10.0000
   chunk 14 optimal weight:    0.3980
   chunk 39 optimal weight:    7.9990
   chunk 28 optimal weight:    0.4980
   chunk 17 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4438 r_free = 0.4438 target = 0.201162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.161597 restraints weight = 7497.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.4032 rms_B_bonded: 1.63
r_work: 0.3897 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6679
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5932  Z= 0.141
  Angle     :  0.470   7.769   8673  Z= 0.246
  Chirality :  0.030   0.121   1062
  Planarity :  0.003   0.029    596
  Dihedral  : 23.682 142.054   2371
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 11.74 %
    Favored  : 86.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.49), residues: 337
  helix:  2.90 (0.39), residues: 170
  sheet: -1.55 (0.67), residues: 66
  loop : -1.06 (0.61), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 300 
 HIS   0.002   0.001   HIS A 166 
 PHE   0.017   0.002   PHE A  35 
 TYR   0.019   0.002   TYR A 309 
 ARG   0.005   0.000   ARG A  95 

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A  143 LYS cc_start: 0.7169 (tttt) cc_final: 0.6500 (mtmt)
REVERT: A  252 ARG cc_start: 0.7841 (mtp-110) cc_final: 0.7511 (mtp-110)
  outliers start: 5
  outliers final: 3
  residues processed: 43
  average time/residue: 0.2535
  time to fit residues: 13.3540
Evaluate side-chains
  34 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  275 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 43 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 27 optimal weight:    9.9990
   chunk 13 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 40 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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 = 0.4346 r_free = 0.4346 target = 0.195897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.155740 restraints weight = 7447.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3925 rms_B_bonded: 1.68
r_work: 0.3788 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6692
moved from start:          0.1357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5932  Z= 0.240
  Angle     :  0.536   5.997   8673  Z= 0.279
  Chirality :  0.033   0.121   1062
  Planarity :  0.004   0.030    596
  Dihedral  : 23.669 142.758   2371
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 11.74 %
    Favored  : 85.43 %
  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:  0.73 (0.48), residues: 337
  helix:  2.15 (0.38), residues: 177
  sheet: -1.61 (0.68), residues: 66
  loop : -1.11 (0.63), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 300 
 HIS   0.002   0.001   HIS A 262 
 PHE   0.025   0.002   PHE A  35 
 TYR   0.022   0.002   TYR A 309 
 ARG   0.005   0.000   ARG A  95 

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A  143 LYS cc_start: 0.7236 (tttt) cc_final: 0.6512 (mtmt)
  outliers start: 7
  outliers final: 4
  residues processed: 42
  average time/residue: 0.2900
  time to fit residues: 14.7819
Evaluate side-chains
  37 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  275 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 32 optimal weight:   10.0000
   chunk 15 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 37 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 27 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 0 optimal weight:    0.5980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4374 r_free = 0.4374 target = 0.198726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.159094 restraints weight = 7380.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3961 rms_B_bonded: 1.68
r_work: 0.3825 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6618
moved from start:          0.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5932  Z= 0.166
  Angle     :  0.484   4.858   8673  Z= 0.254
  Chirality :  0.030   0.121   1062
  Planarity :  0.003   0.030    596
  Dihedral  : 23.636 142.515   2371
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 12.55 %
    Favored  : 84.62 %
  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:  0.89 (0.48), residues: 337
  helix:  2.32 (0.38), residues: 177
  sheet: -1.55 (0.68), residues: 66
  loop : -1.11 (0.62), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 300 
 HIS   0.003   0.001   HIS A  34 
 PHE   0.019   0.002   PHE A  35 
 TYR   0.020   0.002   TYR A 214 
 ARG   0.003   0.000   ARG A  95 

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 34
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
REVERT: A  143 LYS cc_start: 0.7250 (tttt) cc_final: 0.6488 (mtmt)
  outliers start: 7
  outliers final: 3
  residues processed: 37
  average time/residue: 0.2563
  time to fit residues: 11.7761
Evaluate side-chains
  37 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  275 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 29 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 40 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 23 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.4366 r_free = 0.4366 target = 0.197879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.157997 restraints weight = 7436.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3952 rms_B_bonded: 1.69
r_work: 0.3813 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6663
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   0.027   5932  Z= 0.190
  Angle     :  0.498   5.362   8673  Z= 0.262
  Chirality :  0.031   0.138   1062
  Planarity :  0.004   0.033    596
  Dihedral  : 23.625 142.563   2371
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 13.77 %
    Favored  : 83.40 %
  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:  0.87 (0.48), residues: 337
  helix:  2.33 (0.38), residues: 176
  sheet: -1.64 (0.67), residues: 67
  loop : -1.05 (0.62), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 300 
 HIS   0.003   0.001   HIS A  34 
 PHE   0.015   0.002   PHE A  94 
 TYR   0.021   0.002   TYR A 309 
 ARG   0.006   0.000   ARG A  95 

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: A  143 LYS cc_start: 0.7185 (tttt) cc_final: 0.6477 (mtmt)
REVERT: A  289 ARG cc_start: 0.3920 (tmt170) cc_final: 0.3520 (mtp-110)
  outliers start: 7
  outliers final: 4
  residues processed: 39
  average time/residue: 0.2755
  time to fit residues: 13.2688
Evaluate side-chains
  38 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  275 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 8 optimal weight:    0.6980
   chunk 42 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 39 optimal weight:    7.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.195556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.155630 restraints weight = 7476.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.3922 rms_B_bonded: 1.69
r_work: 0.3789 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6669
moved from start:          0.1581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5932  Z= 0.233
  Angle     :  0.538   5.902   8673  Z= 0.282
  Chirality :  0.033   0.132   1062
  Planarity :  0.004   0.030    596
  Dihedral  : 23.659 142.872   2371
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.17 %
    Favored  : 83.40 %
  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:  0.67 (0.47), residues: 337
  helix:  2.14 (0.38), residues: 176
  sheet: -1.71 (0.67), residues: 67
  loop : -1.11 (0.61), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 300 
 HIS   0.003   0.001   HIS A  34 
 PHE   0.012   0.002   PHE A  94 
 TYR   0.023   0.002   TYR A 309 
 ARG   0.006   0.001   ARG A  95 

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
REVERT: A  143 LYS cc_start: 0.7201 (tttt) cc_final: 0.6473 (mtmt)
REVERT: A  255 ASN cc_start: 0.7311 (m110) cc_final: 0.6954 (m110)
  outliers start: 6
  outliers final: 4
  residues processed: 40
  average time/residue: 0.3739
  time to fit residues: 18.5531
Evaluate side-chains
  39 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  275 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 12 optimal weight:    0.2980
   chunk 42 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 3 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.4366 r_free = 0.4366 target = 0.197790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.158091 restraints weight = 7495.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3953 rms_B_bonded: 1.69
r_work: 0.3815 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6653
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5932  Z= 0.183
  Angle     :  0.498   5.181   8673  Z= 0.263
  Chirality :  0.031   0.137   1062
  Planarity :  0.004   0.041    596
  Dihedral  : 23.638 143.076   2371
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 14.98 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.48), residues: 337
  helix:  2.28 (0.38), residues: 176
  sheet: -1.69 (0.67), residues: 67
  loop : -1.10 (0.61), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 300 
 HIS   0.003   0.001   HIS A  34 
 PHE   0.018   0.002   PHE A  94 
 TYR   0.022   0.002   TYR A 309 
 ARG   0.007   0.000   ARG A  95 

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: A  143 LYS cc_start: 0.7216 (tttt) cc_final: 0.6489 (mtmt)
  outliers start: 5
  outliers final: 4
  residues processed: 38
  average time/residue: 0.3291
  time to fit residues: 14.8899
Evaluate side-chains
  37 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  275 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 44 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 34 optimal weight:    7.9990
   chunk 8 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 41 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 3 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4385 r_free = 0.4385 target = 0.199642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.159954 restraints weight = 7514.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3973 rms_B_bonded: 1.73
r_work: 0.3840 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6602
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5932  Z= 0.151
  Angle     :  0.478   5.010   8673  Z= 0.255
  Chirality :  0.031   0.196   1062
  Planarity :  0.003   0.029    596
  Dihedral  : 23.624 142.738   2371
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 14.98 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.48), residues: 337
  helix:  2.49 (0.39), residues: 176
  sheet: -1.58 (0.67), residues: 66
  loop : -1.11 (0.61), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 300 
 HIS   0.002   0.001   HIS A  34 
 PHE   0.013   0.002   PHE A  94 
 TYR   0.020   0.002   TYR A 309 
 ARG   0.007   0.001   ARG A  95 

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
REVERT: A  143 LYS cc_start: 0.7196 (tttt) cc_final: 0.6460 (mtmt)
REVERT: A  250 HIS cc_start: 0.7253 (OUTLIER) cc_final: 0.6738 (m90)
REVERT: A  289 ARG cc_start: 0.5844 (mtp-110) cc_final: 0.5562 (tpt-90)
  outliers start: 5
  outliers final: 4
  residues processed: 38
  average time/residue: 0.2737
  time to fit residues: 12.6769
Evaluate side-chains
  36 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  275 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 6 optimal weight:    0.1980
   chunk 24 optimal weight:    0.6980
   chunk 37 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.7784

-------------------------------------------------------------------------------
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 = 0.4381 r_free = 0.4381 target = 0.199275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.159681 restraints weight = 7558.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3974 rms_B_bonded: 1.71
r_work: 0.3837 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6603
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5932  Z= 0.165
  Angle     :  0.480   4.903   8673  Z= 0.255
  Chirality :  0.031   0.167   1062
  Planarity :  0.003   0.033    596
  Dihedral  : 23.608 142.558   2371
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.98 %
    Favored  : 82.59 %
  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:  0.98 (0.48), residues: 337
  helix:  2.44 (0.38), residues: 177
  sheet: -1.61 (0.66), residues: 67
  loop : -1.08 (0.62), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 300 
 HIS   0.003   0.001   HIS A  34 
 PHE   0.015   0.002   PHE A  94 
 TYR   0.021   0.002   TYR A 309 
 ARG   0.008   0.000   ARG A  95 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2836.73 seconds
wall clock time: 50 minutes 19.31 seconds (3019.31 seconds total)