Starting phenix.real_space_refine
on Wed Mar 12 06:21:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c0i_45085/03_2025/9c0i_45085.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c0i_45085/03_2025/9c0i_45085.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c0i_45085/03_2025/9c0i_45085.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c0i_45085/03_2025/9c0i_45085.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c0i_45085/03_2025/9c0i_45085.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c0i_45085/03_2025/9c0i_45085.cif"
  }
  resolution = 2.91
  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=   0.004
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
     K       1      8.98       5
     P     197      5.49       5
     Mg      1      5.21       5
     S      13      5.16       5
     C    4108      2.51       5
     N    1355      2.21       5
     O    2001      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7676
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3481
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 425, 3481
          Classifications: {'peptide': 425}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 13, 'TRANS': 411}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "P"
      Number of atoms: 104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 104
          Classifications: {'DNA': 5}
          Link IDs: {'rna3p': 4}
    Chain: "R"
      Number of atoms: 4089
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 4089
          Classifications: {'RNA': 192}
          Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 12, 'rna3p_pur': 81, 'rna3p_pyr': 81}
          Link IDs: {'rna2p': 30, 'rna3p': 161}
          Chain breaks: 7
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'  K': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.12, per 1000 atoms: 0.67
  Number of scatterers: 7676
  At special positions: 0
  Unit cell: (130.832, 125.528, 83.096, 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)
     K       1     19.00
     S      13     16.00
     P     197     15.00
     Mg      1     11.99
     O    2001      8.00
     N    1355      7.00
     C    4108      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: 1.98
  Conformation dependent library (CDL) restraints added in 398.9 milliseconds
  

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  814

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 4 sheets defined
      54.4% alpha, 17.6% beta
      71 base pairs and 116 stacking pairs defined.
    Time for finding SS restraints: 3.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 6
      removed outlier: 3.521A  pdb=" N   ASP A   5 " --> pdb=" O   ASN A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 31
      removed outlier: 3.598A  pdb=" N   SER A  31 " --> pdb=" O   VAL A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 38
    Processing helix  chain 'A' and resid 76 through 101
      removed outlier: 3.986A  pdb=" N   GLY A  92 " --> pdb=" O   GLU A  88 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   HIS A  93 " --> pdb=" O   TYR A  89 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU A  96 " --> pdb=" O   GLY A  92 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LEU A  97 " --> pdb=" O   HIS A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 132
    Processing helix  chain 'A' and resid 149 through 162
    Processing helix  chain 'A' and resid 167 through 179
    Processing helix  chain 'A' and resid 185 through 193
    Processing helix  chain 'A' and resid 208 through 216
    Processing helix  chain 'A' and resid 237 through 246
      removed outlier: 3.744A  pdb=" N   MET A 246 " --> pdb=" O   SER A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 260
      removed outlier: 3.746A  pdb=" N   ARG A 260 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 280
    Processing helix  chain 'A' and resid 282 through 291
    Processing helix  chain 'A' and resid 300 through 303
      removed outlier: 3.855A  pdb=" N   THR A 303 " --> pdb=" O   THR A 300 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 300 through 303'
    Processing helix  chain 'A' and resid 336 through 368
      removed outlier: 3.765A  pdb=" N   LEU A 340 " --> pdb=" O   ARG A 336 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE A 364 " --> pdb=" O   SER A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 385
    Processing helix  chain 'A' and resid 391 through 404
      removed outlier: 3.522A  pdb=" N   TYR A 395 " --> pdb=" O   ASN A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 413
      removed outlier: 3.850A  pdb=" N   LYS A 409 " --> pdb=" O   SER A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 425
    Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 74
      removed outlier: 6.259A  pdb=" N   PHE A  44 " --> pdb=" O   VAL A 183 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 267
      removed outlier: 4.837A  pdb=" N   GLU A 297 " --> pdb=" O   SER A 142 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 267
      removed outlier: 3.569A  pdb=" N   CYS A 134 " --> pdb=" O   PHE A 308 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 323

    197 hydrogen bonds defined for protein.
    558 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      172 hydrogen bonds
      304 hydrogen bond angles
      0 basepair planarities
      71 basepair parallelities
      116 stacking parallelities
  Total time for adding SS restraints: 2.88

  Time building geometry restraints manager: 2.34 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 853
        1.31 -     1.44: 3375
        1.44 -     1.56: 3600
        1.56 -     1.68: 385
        1.68 -     1.81: 22
  Bond restraints: 8235
  Sorted by residual:
  bond pdb=" CA  SER A  22 "
       pdb=" CB  SER A  22 "
    ideal  model  delta    sigma   weight residual
    1.532  1.465  0.067 1.59e-02 3.96e+03 1.77e+01
  bond pdb=" CA  ALA A  26 "
       pdb=" CB  ALA A  26 "
    ideal  model  delta    sigma   weight residual
    1.529  1.469  0.060 1.55e-02 4.16e+03 1.51e+01
  bond pdb=" C   PRO A  20 "
       pdb=" O   PRO A  20 "
    ideal  model  delta    sigma   weight residual
    1.233  1.186  0.047 1.24e-02 6.50e+03 1.45e+01
  bond pdb=" C   PRO A 199 "
       pdb=" O   PRO A 199 "
    ideal  model  delta    sigma   weight residual
    1.235  1.186  0.049 1.30e-02 5.92e+03 1.40e+01
  bond pdb=" CA  SER A  80 "
       pdb=" CB  SER A  80 "
    ideal  model  delta    sigma   weight residual
    1.528  1.475  0.054 1.66e-02 3.63e+03 1.05e+01
  ... (remaining 8230 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.63: 11683
        2.63 -     5.26: 315
        5.26 -     7.89: 40
        7.89 -    10.51: 4
       10.51 -    13.14: 2
  Bond angle restraints: 12044
  Sorted by residual:
  angle pdb=" C3'   A R  24 "
        pdb=" O3'   A R  24 "
        pdb=" P     U R  25 "
      ideal   model   delta    sigma   weight residual
     120.20  107.06   13.14 1.50e+00 4.44e-01 7.68e+01
  angle pdb=" C3'   U R  23 "
        pdb=" O3'   U R  23 "
        pdb=" P     A R  24 "
      ideal   model   delta    sigma   weight residual
     120.20  110.80    9.40 1.50e+00 4.44e-01 3.92e+01
  angle pdb=" N   ILE A 291 "
        pdb=" CA  ILE A 291 "
        pdb=" C   ILE A 291 "
      ideal   model   delta    sigma   weight residual
     112.90  107.57    5.33 9.60e-01 1.09e+00 3.08e+01
  angle pdb=" N   ILE A 128 "
        pdb=" CA  ILE A 128 "
        pdb=" C   ILE A 128 "
      ideal   model   delta    sigma   weight residual
     110.72  105.57    5.15 1.01e+00 9.80e-01 2.60e+01
  angle pdb=" O3'   A R 210 "
        pdb=" C3'   A R 210 "
        pdb=" C2'   A R 210 "
      ideal   model   delta    sigma   weight residual
     113.70  121.17   -7.47 1.50e+00 4.44e-01 2.48e+01
  ... (remaining 12039 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.22: 4669
       33.22 -    66.44: 471
       66.44 -    99.66: 49
       99.66 -   132.87: 2
      132.87 -   166.09: 1
  Dihedral angle restraints: 5192
    sinusoidal: 3929
      harmonic: 1263
  Sorted by residual:
  dihedral pdb=" O4'   A R 123 "
           pdb=" C1'   A R 123 "
           pdb=" N9    A R 123 "
           pdb=" C4    A R 123 "
      ideal   model   delta sinusoidal    sigma   weight residual
      68.00  151.57  -83.57     1      1.70e+01 3.46e-03 2.95e+01
  dihedral pdb=" O4'   U R 205 "
           pdb=" C1'   U R 205 "
           pdb=" N1    U R 205 "
           pdb=" C2    U R 205 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -88.78  -71.22     1      1.50e+01 4.44e-03 2.89e+01
  dihedral pdb=" CA  THR A 282 "
           pdb=" C   THR A 282 "
           pdb=" N   LEU A 283 "
           pdb=" CA  LEU A 283 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.25  -26.75     0      5.00e+00 4.00e-02 2.86e+01
  ... (remaining 5189 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 1355
       0.090 -    0.181: 117
       0.181 -    0.271: 10
       0.271 -    0.362: 5
       0.362 -    0.452: 3
  Chirality restraints: 1490
  Sorted by residual:
  chirality pdb=" P    DG P   1 "
            pdb=" OP1  DG P   1 "
            pdb=" OP2  DG P   1 "
            pdb=" O5'  DG P   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35    2.80   -0.45 2.00e-01 2.50e+01 5.12e+00
  chirality pdb=" P    DT P   5 "
            pdb=" OP1  DT P   5 "
            pdb=" OP2  DT P   5 "
            pdb=" O5'  DT P   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.73   -0.39 2.00e-01 2.50e+01 3.76e+00
  chirality pdb=" P    DA P   2 "
            pdb=" OP1  DA P   2 "
            pdb=" OP2  DA P   2 "
            pdb=" O5'  DA P   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.71   -0.37 2.00e-01 2.50e+01 3.34e+00
  ... (remaining 1487 not shown)

  Planarity restraints: 803
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G R  33 "   -0.030 2.00e-02 2.50e+03   1.41e-02 5.97e+00
        pdb=" N9    G R  33 "    0.035 2.00e-02 2.50e+03
        pdb=" C8    G R  33 "    0.009 2.00e-02 2.50e+03
        pdb=" N7    G R  33 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    G R  33 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6    G R  33 "   -0.003 2.00e-02 2.50e+03
        pdb=" O6    G R  33 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    G R  33 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    G R  33 "    0.007 2.00e-02 2.50e+03
        pdb=" N2    G R  33 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G R  33 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    G R  33 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 404 "   -0.011 2.00e-02 2.50e+03   2.29e-02 5.25e+00
        pdb=" C   ASN A 404 "    0.040 2.00e-02 2.50e+03
        pdb=" O   ASN A 404 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   SER A 405 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 383 "    0.186 9.50e-02 1.11e+02   8.38e-02 5.06e+00
        pdb=" NE  ARG A 383 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 383 "    0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 383 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 383 "    0.002 2.00e-02 2.50e+03
  ... (remaining 800 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.70: 412
        2.70 -     3.31: 6858
        3.31 -     3.92: 17454
        3.92 -     4.53: 22336
        4.53 -     5.14: 29347
  Nonbonded interactions: 76407
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 140 "
            pdb="MG    MG A 501 "
     model   vdw
     2.090 2.170
  nonbonded pdb=" O   LYS A  55 "
            pdb=" OG  SER A  64 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" OG1 THR A 208 "
            pdb=" OD2 ASP A 211 "
     model   vdw
     2.393 3.040
  nonbonded pdb=" OG  SER A 195 "
            pdb=" OP2   C R 218 "
     model   vdw
     2.404 3.040
  nonbonded pdb=" NH2 ARG A 217 "
            pdb=" O6    G R  22 "
     model   vdw
     2.407 3.120
  ... (remaining 76402 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:             0.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     22.880
  Find NCS groups from input model:        0.060
  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:13.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
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   0.069   8235  Z= 0.344
  Angle     :  1.031  13.142  12044  Z= 0.563
  Chirality :  0.057   0.452   1490
  Planarity :  0.008   0.084    803
  Dihedral  : 21.515 166.093   4378
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 1.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  8.31 %
    Favored  : 90.88 %
  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: -0.39 (0.37), residues: 423
  helix: -0.44 (0.31), residues: 205
  sheet:  1.13 (0.68), residues: 57
  loop : -0.29 (0.48), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A   8 
 HIS   0.008   0.002   HIS A 263 
 PHE   0.021   0.004   PHE A 328 
 TYR   0.023   0.003   TYR A  83 
 ARG   0.015   0.002   ARG A 383 

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.500 
Fit side-chains
REVERT: A  390 ARG cc_start: 0.8246 (mtm180) cc_final: 0.8028 (mtp180)
  outliers start: 3
  outliers final: 3
  residues processed: 43
  average time/residue: 1.4655
  time to fit residues: 66.3454
Evaluate side-chains
  35 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 32
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  294 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 46 optimal weight:   30.0000
   chunk 25 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9980
   chunk 47 optimal weight:   20.0000
   chunk 18 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 55 optimal weight:    9.9990
   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 = 0.3898 r_free = 0.3898 target = 0.169421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.110337 restraints weight = 8279.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 1.23
r_work: 0.2753 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work: 0.2620 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8777
moved from start:          0.1260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8235  Z= 0.153
  Angle     :  0.531   6.070  12044  Z= 0.279
  Chirality :  0.035   0.219   1490
  Planarity :  0.004   0.045    803
  Dihedral  : 22.038 178.165   3495
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  9.38 %
    Favored  : 89.54 %
  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:  1.09 (0.40), residues: 423
  helix:  1.17 (0.35), residues: 212
  sheet:  1.27 (0.69), residues: 57
  loop :  0.02 (0.50), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 157 
 HIS   0.002   0.001   HIS A 263 
 PHE   0.011   0.001   PHE A 328 
 TYR   0.010   0.001   TYR A 245 
 ARG   0.003   0.000   ARG A 290 

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 0.513 
Fit side-chains
REVERT: A  250 ASP cc_start: 0.8548 (m-30) cc_final: 0.8276 (m-30)
  outliers start: 4
  outliers final: 2
  residues processed: 41
  average time/residue: 1.6271
  time to fit residues: 69.9860
Evaluate side-chains
  33 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 31
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LYS
Chi-restraints excluded: chain A residue  130 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 19 optimal weight:    0.0670
   chunk 41 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 49 optimal weight:    7.9990
   chunk 4 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 45 optimal weight:   20.0000
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.9724

-------------------------------------------------------------------------------
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 = 0.3925 r_free = 0.3925 target = 0.171149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.110305 restraints weight = 8492.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 1.45
r_work: 0.2770 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8235  Z= 0.120
  Angle     :  0.462   5.545  12044  Z= 0.243
  Chirality :  0.031   0.219   1490
  Planarity :  0.004   0.041    803
  Dihedral  : 21.776 175.742   3491
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 11.26 %
    Favored  : 88.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.41), residues: 423
  helix:  1.85 (0.36), residues: 212
  sheet:  1.57 (0.68), residues: 55
  loop :  0.09 (0.49), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 157 
 HIS   0.003   0.001   HIS A 263 
 PHE   0.009   0.001   PHE A 328 
 TYR   0.010   0.001   TYR A  86 
 ARG   0.002   0.000   ARG A 266 

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 34
  time to evaluate  : 0.502 
Fit side-chains
REVERT: A   68 LYS cc_start: 0.7781 (tttm) cc_final: 0.7329 (mtpt)
REVERT: A  305 ILE cc_start: 0.9052 (mt) cc_final: 0.8800 (mm)
  outliers start: 2
  outliers final: 1
  residues processed: 35
  average time/residue: 1.7585
  time to fit residues: 64.4537
Evaluate side-chains
  29 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 43 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 50 optimal weight:   10.0000
   chunk 10 optimal weight:    0.0370
   chunk 60 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 40 optimal weight:    0.2980
   overall best weight:    0.9660

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

Flipped N/Q/H residues before XYZ refinement:
A 293 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.172551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.113135 restraints weight = 8295.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 1.05
r_work: 0.2810 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2674 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8744
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8235  Z= 0.119
  Angle     :  0.444   5.012  12044  Z= 0.232
  Chirality :  0.030   0.215   1490
  Planarity :  0.004   0.040    803
  Dihedral  : 21.366 161.482   3491
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 12.06 %
    Favored  : 86.60 %
  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:  2.03 (0.41), residues: 423
  helix:  2.11 (0.37), residues: 212
  sheet:  2.37 (0.70), residues: 47
  loop :  0.06 (0.47), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 157 
 HIS   0.003   0.001   HIS A 263 
 PHE   0.008   0.001   PHE A 328 
 TYR   0.010   0.001   TYR A  86 
 ARG   0.003   0.000   ARG A 204 

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.505 
Fit side-chains
REVERT: A   68 LYS cc_start: 0.7700 (tttm) cc_final: 0.7223 (mtpt)
REVERT: A  122 LYS cc_start: 0.8506 (tttt) cc_final: 0.7941 (tptt)
  outliers start: 5
  outliers final: 3
  residues processed: 36
  average time/residue: 1.5748
  time to fit residues: 59.6308
Evaluate side-chains
  34 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   38 LYS
Chi-restraints excluded: chain A residue  191 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9990
   chunk 47 optimal weight:   30.0000
   chunk 44 optimal weight:   10.0000
   chunk 53 optimal weight:   10.0000
   chunk 60 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 14 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 40 optimal weight:    0.2980
   overall best weight:    3.2588

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

Flipped N/Q/H residues before XYZ refinement:
A 293 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.167142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.106236 restraints weight = 8219.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 1.15
r_work: 0.2694 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work: 0.2566 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8831
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   8235  Z= 0.286
  Angle     :  0.573   6.800  12044  Z= 0.296
  Chirality :  0.036   0.224   1490
  Planarity :  0.005   0.045    803
  Dihedral  : 21.430 160.570   3491
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 13.14 %
    Favored  : 85.52 %
  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:  1.41 (0.41), residues: 423
  helix:  1.71 (0.37), residues: 211
  sheet:  1.20 (0.67), residues: 57
  loop : -0.18 (0.49), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 157 
 HIS   0.003   0.001   HIS A 170 
 PHE   0.014   0.002   PHE A 328 
 TYR   0.012   0.002   TYR A  86 
 ARG   0.003   0.001   ARG A 336 

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.504 
Fit side-chains
REVERT: A   68 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7485 (tttm)
REVERT: A  417 LYS cc_start: 0.8671 (mttt) cc_final: 0.8456 (mttm)
  outliers start: 5
  outliers final: 2
  residues processed: 36
  average time/residue: 1.4974
  time to fit residues: 56.8064
Evaluate side-chains
  36 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   38 LYS
Chi-restraints excluded: chain A residue   68 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0980
   chunk 11 optimal weight:    0.9980
   chunk 46 optimal weight:   30.0000
   chunk 21 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 44 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 15 optimal weight:    0.7980
   chunk 52 optimal weight:   40.0000
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 293 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.169804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.108064 restraints weight = 8192.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 1.17
r_work: 0.2742 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work: 0.2612 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8775
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8235  Z= 0.110
  Angle     :  0.479   5.310  12044  Z= 0.253
  Chirality :  0.031   0.225   1490
  Planarity :  0.004   0.042    803
  Dihedral  : 21.386 161.309   3491
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 12.60 %
    Favored  : 86.06 %
  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:  1.82 (0.41), residues: 423
  helix:  2.02 (0.37), residues: 212
  sheet:  1.42 (0.68), residues: 55
  loop :  0.05 (0.50), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 157 
 HIS   0.002   0.000   HIS A  77 
 PHE   0.009   0.001   PHE A 328 
 TYR   0.010   0.001   TYR A  14 
 ARG   0.003   0.000   ARG A 204 

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.558 
Fit side-chains
REVERT: A   68 LYS cc_start: 0.7761 (tttm) cc_final: 0.7191 (mtpt)
REVERT: A  250 ASP cc_start: 0.8597 (m-30) cc_final: 0.8318 (m-30)
REVERT: A  301 LYS cc_start: 0.8791 (mttm) cc_final: 0.8532 (mtmt)
REVERT: A  417 LYS cc_start: 0.8590 (mttt) cc_final: 0.8362 (mttm)
  outliers start: 5
  outliers final: 3
  residues processed: 40
  average time/residue: 1.4687
  time to fit residues: 61.9308
Evaluate side-chains
  37 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   38 LYS
Chi-restraints excluded: chain A residue  191 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 4 optimal weight:    9.9990
   chunk 30 optimal weight:    9.9990
   chunk 47 optimal weight:   30.0000
   chunk 2 optimal weight:    0.5980
   chunk 19 optimal weight:    0.3980
   chunk 42 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 17 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
A 293 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.170243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.108715 restraints weight = 8234.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 1.16
r_work: 0.2771 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2641 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8775
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8235  Z= 0.126
  Angle     :  0.456   5.036  12044  Z= 0.240
  Chirality :  0.031   0.217   1490
  Planarity :  0.004   0.041    803
  Dihedral  : 21.279 161.071   3491
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 12.87 %
    Favored  : 86.06 %
  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:  1.99 (0.42), residues: 423
  helix:  2.13 (0.37), residues: 212
  sheet:  1.41 (0.69), residues: 54
  loop :  0.23 (0.50), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 157 
 HIS   0.002   0.001   HIS A 263 
 PHE   0.008   0.001   PHE A  44 
 TYR   0.010   0.001   TYR A  86 
 ARG   0.003   0.000   ARG A 204 

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.567 
Fit side-chains
REVERT: A   68 LYS cc_start: 0.7731 (tttm) cc_final: 0.7261 (mtpt)
REVERT: A  250 ASP cc_start: 0.8582 (m-30) cc_final: 0.8331 (m-30)
REVERT: A  417 LYS cc_start: 0.8612 (mttt) cc_final: 0.8377 (mttm)
  outliers start: 4
  outliers final: 2
  residues processed: 38
  average time/residue: 1.5719
  time to fit residues: 62.8647
Evaluate side-chains
  37 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 35
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   38 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 14 optimal weight:    7.9990
   chunk 42 optimal weight:   10.0000
   chunk 49 optimal weight:    8.9990
   chunk 8 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   chunk 17 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 44 optimal weight:    8.9990
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 293 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.169010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.107570 restraints weight = 8259.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 1.23
r_work: 0.2721 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work: 0.2590 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8810
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8235  Z= 0.182
  Angle     :  0.487   5.218  12044  Z= 0.254
  Chirality :  0.032   0.219   1490
  Planarity :  0.004   0.043    803
  Dihedral  : 21.269 161.443   3491
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 13.14 %
    Favored  : 85.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.41), residues: 423
  helix:  2.06 (0.37), residues: 211
  sheet:  1.47 (0.67), residues: 55
  loop :  0.03 (0.49), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 157 
 HIS   0.002   0.001   HIS A 263 
 PHE   0.010   0.001   PHE A 328 
 TYR   0.011   0.001   TYR A  86 
 ARG   0.003   0.000   ARG A 204 

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.532 
Fit side-chains
REVERT: A   68 LYS cc_start: 0.7741 (tttm) cc_final: 0.7250 (mtpt)
REVERT: A  250 ASP cc_start: 0.8645 (m-30) cc_final: 0.8377 (m-30)
REVERT: A  417 LYS cc_start: 0.8611 (mttt) cc_final: 0.8389 (mttm)
  outliers start: 4
  outliers final: 2
  residues processed: 37
  average time/residue: 1.4607
  time to fit residues: 56.9869
Evaluate side-chains
  35 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 33
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   38 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 49 optimal weight:    8.9990
   chunk 3 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 55 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 44 optimal weight:   10.0000
   chunk 32 optimal weight:    0.7980
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
A  81 HIS
A 293 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.168119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.105020 restraints weight = 8287.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 1.23
r_work: 0.2714 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2584 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8795
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8235  Z= 0.213
  Angle     :  0.516   5.366  12044  Z= 0.269
  Chirality :  0.034   0.220   1490
  Planarity :  0.004   0.043    803
  Dihedral  : 21.291 162.716   3491
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 14.21 %
    Favored  : 84.99 %
  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:  1.70 (0.41), residues: 423
  helix:  1.93 (0.36), residues: 211
  sheet:  1.44 (0.67), residues: 55
  loop : -0.03 (0.49), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 157 
 HIS   0.002   0.001   HIS A 263 
 PHE   0.012   0.002   PHE A 328 
 TYR   0.012   0.002   TYR A 245 
 ARG   0.003   0.000   ARG A 204 

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.496 
Fit side-chains
REVERT: A  417 LYS cc_start: 0.8595 (mttt) cc_final: 0.8355 (mttm)
  outliers start: 3
  outliers final: 2
  residues processed: 35
  average time/residue: 1.4435
  time to fit residues: 53.2820
Evaluate side-chains
  36 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 34
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   38 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 43 optimal weight:   10.0000
   chunk 29 optimal weight:    2.9990
   chunk 60 optimal weight:   10.0000
   chunk 57 optimal weight:   10.0000
   chunk 9 optimal weight:    3.9990
   chunk 49 optimal weight:    8.9990
   chunk 59 optimal weight:   10.0000
   chunk 6 optimal weight:    0.0030
   chunk 22 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   chunk 54 optimal weight:   10.0000
   overall best weight:    3.7998

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

Flipped N/Q/H residues before XYZ refinement:
A 293 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.166229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.104639 restraints weight = 8253.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 1.29
r_work: 0.2682 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work: 0.2553 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8833
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   8235  Z= 0.330
  Angle     :  0.600   6.266  12044  Z= 0.311
  Chirality :  0.038   0.224   1490
  Planarity :  0.005   0.047    803
  Dihedral  : 21.497 163.161   3491
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 13.94 %
    Favored  : 84.99 %
  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:  1.31 (0.41), residues: 423
  helix:  1.65 (0.36), residues: 211
  sheet:  0.97 (0.65), residues: 57
  loop : -0.18 (0.49), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 157 
 HIS   0.003   0.001   HIS A 263 
 PHE   0.014   0.002   PHE A 328 
 TYR   0.014   0.002   TYR A 245 
 ARG   0.004   0.001   ARG A 390 

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

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

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  846 Ramachandran restraints generated.
    423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.489 
Fit side-chains
REVERT: A  417 LYS cc_start: 0.8664 (mttt) cc_final: 0.8440 (mttm)
  outliers start: 4
  outliers final: 3
  residues processed: 38
  average time/residue: 1.5025
  time to fit residues: 60.1644
Evaluate side-chains
  37 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   38 LYS
Chi-restraints excluded: chain A residue  191 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 45 optimal weight:   20.0000
   chunk 59 optimal weight:   10.0000
   chunk 24 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0020
   chunk 12 optimal weight:    4.9990
   chunk 54 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    5.9990
   overall best weight:    0.6990

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

Flipped N/Q/H residues before XYZ refinement:
A 293 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.171450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.112752 restraints weight = 8235.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 1.25
r_work: 0.2798 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work: 0.2667 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8745
moved from start:          0.2704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8235  Z= 0.103
  Angle     :  0.432   5.446  12044  Z= 0.227
  Chirality :  0.030   0.214   1490
  Planarity :  0.004   0.040    803
  Dihedral  : 21.179 162.202   3491
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 13.67 %
    Favored  : 85.25 %
  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:  1.99 (0.41), residues: 423
  helix:  2.18 (0.36), residues: 212
  sheet:  1.48 (0.67), residues: 55
  loop :  0.11 (0.50), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 157 
 HIS   0.002   0.000   HIS A 263 
 PHE   0.007   0.001   PHE A 328 
 TYR   0.009   0.001   TYR A  86 
 ARG   0.003   0.000   ARG A 336 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5160.58 seconds
wall clock time: 88 minutes 45.05 seconds (5325.05 seconds total)