Starting phenix.real_space_refine
on Fri Aug 22 12:39:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6yj5_10816/08_2025/6yj5_10816_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6yj5_10816/08_2025/6yj5_10816.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6yj5_10816/08_2025/6yj5_10816.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6yj5_10816/08_2025/6yj5_10816.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6yj5_10816/08_2025/6yj5_10816_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6yj5_10816/08_2025/6yj5_10816_neut.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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: 4
    Type Number    sf(0)   Gaussians
     S       5      5.16       5
     C    1308      2.51       5
     N     352      2.21       5
     O     396      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2061
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "q"
      Number of atoms: 2061
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2061
          Classifications: {'peptide': 306}
          Incomplete info: {'truncation_to_alanine': 93}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 280}
          Unresolved chain link angles: 9
          Unresolved non-hydrogen bonds: 336
          Unresolved non-hydrogen angles: 425
          Unresolved non-hydrogen dihedrals: 288
          Unresolved non-hydrogen chiralities: 25
          Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 6, 'PHE:plan': 3, 'HIS:plan': 3, 'TRP:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 10, 'ARG:plan': 5, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 168
  Time building chain proxies: 0.96, per 1000 atoms: 0.47
  Number of scatterers: 2061
  At special positions: 0
  Unit cell: (55.915, 72.795, 61.19, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       5     16.00
     O     396      8.00
     N     352      7.00
     C    1308      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.18
  Conformation dependent library (CDL) restraints added in 155.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  608 Ramachandran restraints generated.
    304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  564

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 2 sheets defined
      34.3% alpha, 5.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'q' and resid 6 through 15
      removed outlier: 3.583A  pdb=" N   LEU q  10 " --> pdb=" O   SER q   6 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ALA q  11 " --> pdb=" O   PRO q   7 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   LYS q  12 " --> pdb=" O   ALA q   8 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   SER q  15 " --> pdb=" O   ALA q  11 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 38 through 43
      removed outlier: 3.566A  pdb=" N   MET q  43 " --> pdb=" O   TYR q  39 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 54 through 59
      removed outlier: 3.924A  pdb=" N   ASN q  59 " --> pdb=" O   ILE q  55 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 74 through 79
    Processing helix  chain 'q' and resid 100 through 110
      removed outlier: 3.763A  pdb=" N   VAL q 104 " --> pdb=" O   GLY q 100 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   PHE q 110 " --> pdb=" O   THR q 106 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 120 through 126
      removed outlier: 3.619A  pdb=" N   TYR q 124 " --> pdb=" O   GLY q 120 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 169 through 175
    Processing helix  chain 'q' and resid 176 through 179
    Processing helix  chain 'q' and resid 181 through 185
      removed outlier: 3.547A  pdb=" N   GLY q 184 " --> pdb=" O   ASN q 181 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 186 through 191
      removed outlier: 3.526A  pdb=" N   VAL q 191 " --> pdb=" O   ILE q 187 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 237 through 247
    Processing helix  chain 'q' and resid 260 through 264
      removed outlier: 3.504A  pdb=" N   VAL q 264 " --> pdb=" O   GLY q 261 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 265 through 266
      No H-bonds generated for 'chain 'q' and resid 265 through 266'
    Processing helix  chain 'q' and resid 267 through 277
      removed outlier: 4.961A  pdb=" N   LEU q 273 " --> pdb=" O   ILE q 269 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 290 through 297
    Processing sheet with id=AA1, first strand: chain 'q' and resid 3 through 5
      removed outlier: 3.556A  pdb=" N   LYS q   3 " --> pdb=" O   VAL q 115 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   ILE q  89 " --> pdb=" O   GLN q 116 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   LEU q 118 " --> pdb=" O   ILE q  89 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   VAL q  91 " --> pdb=" O   LEU q 118 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'q' and resid 192 through 193
      removed outlier: 6.281A  pdb=" N   THR q 192 " --> pdb=" O   ILE q 257 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   ILE q 256 " --> pdb=" O   ALA q 285 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2

    44 hydrogen bonds defined for protein.
    120 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.23

  Time building geometry restraints manager: 0.26 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 698
        1.34 -     1.46: 450
        1.46 -     1.57: 950
        1.57 -     1.69: 0
        1.69 -     1.81: 8
  Bond restraints: 2106
  Sorted by residual:
  bond pdb=" CA  GLY q 140 "
       pdb=" C   GLY q 140 "
    ideal  model  delta    sigma   weight residual
    1.516  1.498  0.019 1.31e-02 5.83e+03 2.04e+00
  bond pdb=" C   MET q  43 "
       pdb=" N   LYS q  44 "
    ideal  model  delta    sigma   weight residual
    1.333  1.312  0.020 1.52e-02 4.33e+03 1.81e+00
  bond pdb=" CB  PRO q  69 "
       pdb=" CG  PRO q  69 "
    ideal  model  delta    sigma   weight residual
    1.492  1.428  0.064 5.00e-02 4.00e+02 1.66e+00
  bond pdb=" CG  PRO q  48 "
       pdb=" CD  PRO q  48 "
    ideal  model  delta    sigma   weight residual
    1.503  1.461  0.042 3.40e-02 8.65e+02 1.53e+00
  bond pdb=" CG  LEU q  51 "
       pdb=" CD1 LEU q  51 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.035 3.30e-02 9.18e+02 1.15e+00
  ... (remaining 2101 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.15: 2500
        1.15 -     2.30: 316
        2.30 -     3.45: 55
        3.45 -     4.60: 9
        4.60 -     5.75: 9
  Bond angle restraints: 2889
  Sorted by residual:
  angle pdb=" N   GLY q 140 "
        pdb=" CA  GLY q 140 "
        pdb=" C   GLY q 140 "
      ideal   model   delta    sigma   weight residual
     114.25  110.04    4.21 1.30e+00 5.92e-01 1.05e+01
  angle pdb=" N   PHE q 226 "
        pdb=" CA  PHE q 226 "
        pdb=" CB  PHE q 226 "
      ideal   model   delta    sigma   weight residual
     110.39  107.68    2.71 9.50e-01 1.11e+00 8.15e+00
  angle pdb=" N   LEU q  14 "
        pdb=" CA  LEU q  14 "
        pdb=" C   LEU q  14 "
      ideal   model   delta    sigma   weight residual
     111.36  114.40   -3.04 1.09e+00 8.42e-01 7.78e+00
  angle pdb=" N   ASN q 232 "
        pdb=" CA  ASN q 232 "
        pdb=" C   ASN q 232 "
      ideal   model   delta    sigma   weight residual
     110.80  116.16   -5.36 2.13e+00 2.20e-01 6.33e+00
  angle pdb=" C   GLU q 231 "
        pdb=" N   ASN q 232 "
        pdb=" CA  ASN q 232 "
      ideal   model   delta    sigma   weight residual
     121.54  125.72   -4.18 1.91e+00 2.74e-01 4.80e+00
  ... (remaining 2884 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 1145
       17.95 -    35.91: 74
       35.91 -    53.86: 11
       53.86 -    71.81: 2
       71.81 -    89.77: 1
  Dihedral angle restraints: 1233
    sinusoidal: 355
      harmonic: 878
  Sorted by residual:
  dihedral pdb=" CA  GLN q  72 "
           pdb=" C   GLN q  72 "
           pdb=" N   THR q  73 "
           pdb=" CA  THR q  73 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.20   27.80     0      5.00e+00 4.00e-02 3.09e+01
  dihedral pdb=" CA  ILE q 269 "
           pdb=" C   ILE q 269 "
           pdb=" N   ASP q 270 "
           pdb=" CA  ASP q 270 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.19   23.81     0      5.00e+00 4.00e-02 2.27e+01
  dihedral pdb=" CA  THR q 138 "
           pdb=" C   THR q 138 "
           pdb=" N   TRP q 139 "
           pdb=" CA  TRP q 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.78   21.22     0      5.00e+00 4.00e-02 1.80e+01
  ... (remaining 1230 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 163
       0.030 -    0.060: 107
       0.060 -    0.089: 40
       0.089 -    0.119: 18
       0.119 -    0.148: 6
  Chirality restraints: 334
  Sorted by residual:
  chirality pdb=" CA  ILE q 130 "
            pdb=" N   ILE q 130 "
            pdb=" C   ILE q 130 "
            pdb=" CB  ILE q 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.48e-01
  chirality pdb=" CA  PRO q 101 "
            pdb=" N   PRO q 101 "
            pdb=" C   PRO q 101 "
            pdb=" CB  PRO q 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.82e-01
  chirality pdb=" CA  ILE q 257 "
            pdb=" N   ILE q 257 "
            pdb=" C   ILE q 257 "
            pdb=" CB  ILE q 257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.44e-01
  ... (remaining 331 not shown)

  Planarity restraints: 387
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG q 197 "    0.029 5.00e-02 4.00e+02   4.29e-02 2.95e+00
        pdb=" N   PRO q 198 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO q 198 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO q 198 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY q 100 "    0.026 5.00e-02 4.00e+02   4.00e-02 2.56e+00
        pdb=" N   PRO q 101 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO q 101 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO q 101 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE q  74 "   -0.013 2.00e-02 2.50e+03   1.09e-02 2.07e+00
        pdb=" CG  PHE q  74 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 PHE q  74 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE q  74 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE q  74 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE q  74 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE q  74 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 384 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 168
        2.73 -     3.27: 2199
        3.27 -     3.81: 3086
        3.81 -     4.36: 3655
        4.36 -     4.90: 6026
  Nonbonded interactions: 15134
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS q 108 "
            pdb=" OE2 GLU q 274 "
     model   vdw
     2.183 3.120
  nonbonded pdb=" N   SER q   2 "
            pdb=" OE1 GLU q 274 "
     model   vdw
     2.206 3.120
  nonbonded pdb=" O   ARG q 102 "
            pdb=" OG1 THR q 106 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" NH2 ARG q 102 "
            pdb=" OD2 ASP q 288 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" N   GLU q   9 "
            pdb=" OE1 GLU q   9 "
     model   vdw
     2.321 3.120
  ... (remaining 15129 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 group one per residue
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:             6.230
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.830
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5928
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      :  0.007   0.064   2106  Z= 0.324
  Angle     :  0.874   5.754   2889  Z= 0.505
  Chirality :  0.048   0.148    334
  Planarity :  0.005   0.043    387
  Dihedral  : 13.190  89.768    669
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.50 %
    Favored  : 87.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.13 (0.38), residues: 304
  helix: -4.08 (0.28), residues: 88
  sheet: -2.97 (0.77), residues: 28
  loop : -3.29 (0.40), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG q 163 
 TYR   0.008   0.002   TYR q 124 
 PHE   0.024   0.002   PHE q  74 
 TRP   0.007   0.001   TRP q 142 
 HIS   0.001   0.001   HIS q 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00738 ( 2106)
  covalent geometry    : angle       0.87398 ( 2889)
  hydrogen bonds       : bond        0.22481 (   44)
  hydrogen bonds       : angle       8.83394 (  120)

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

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

  608 Ramachandran restraints generated.
    304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  608 Ramachandran restraints generated.
    304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.078 
Fit side-chains
   revert: symmetry clash
REVERT: q    4 LEU cc_start: 0.6754 (pp) cc_final: 0.6549 (pp)
REVERT: q    6 SER cc_start: 0.7911 (m) cc_final: 0.7182 (p)
REVERT: q   89 ILE cc_start: 0.8145 (pt) cc_final: 0.7855 (mt)
REVERT: q  114 ASN cc_start: 0.6728 (m110) cc_final: 0.6156 (m110)
REVERT: q  117 PHE cc_start: 0.8105 (t80) cc_final: 0.7728 (t80)
REVERT: q  163 ARG cc_start: 0.6876 (ptp90) cc_final: 0.6622 (ptp90)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.0771
  time to fit residues: 3.8445
Evaluate side-chains
  32 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 28 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0570
   chunk 15 optimal weight:    0.0370
   chunk 29 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    0.5376

-------------------------------------------------------------------------------
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 = 0.4118 r_free = 0.4118 target = 0.190824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.177705 restraints weight = 2856.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.178980 restraints weight = 2074.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.180047 restraints weight = 1637.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.180459 restraints weight = 1387.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.180462 restraints weight = 1265.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6741
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2106  Z= 0.122
  Angle     :  0.609   4.760   2889  Z= 0.325
  Chirality :  0.050   0.142    334
  Planarity :  0.005   0.046    387
  Dihedral  :  5.493  19.028    320
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.21 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  7.98 %
    Favored  : 90.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.57 (0.43), residues: 304
  helix: -2.63 (0.42), residues: 91
  sheet: -1.95 (0.76), residues: 32
  loop : -2.37 (0.46), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG q  46 
 TYR   0.016   0.001   TYR q  52 
 PHE   0.012   0.001   PHE q  74 
 TRP   0.010   0.001   TRP q 291 
 HIS   0.002   0.001   HIS q 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 2106)
  covalent geometry    : angle       0.60936 ( 2889)
  hydrogen bonds       : bond        0.02423 (   44)
  hydrogen bonds       : angle       5.63044 (  120)

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

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

  608 Ramachandran restraints generated.
    304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  608 Ramachandran restraints generated.
    304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.094 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 38
  average time/residue: 0.0599
  time to fit residues: 2.7454
Evaluate side-chains
  27 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue  259 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 19 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 29 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   chunk 16 optimal weight:    0.4980
   chunk 3 optimal weight:    0.2980
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.6382

-------------------------------------------------------------------------------
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 = 0.4059 r_free = 0.4059 target = 0.185643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.174012 restraints weight = 3143.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.174948 restraints weight = 2487.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.175267 restraints weight = 2089.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.175595 restraints weight = 1921.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.175606 restraints weight = 1774.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6841
moved from start:          0.3266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2106  Z= 0.121
  Angle     :  0.571   4.660   2889  Z= 0.304
  Chirality :  0.048   0.126    334
  Planarity :  0.005   0.049    387
  Dihedral  :  5.091  18.587    320
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.21 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 12.27 %
    Favored  : 86.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.95 (0.46), residues: 304
  helix: -2.22 (0.45), residues: 94
  sheet: -1.22 (0.83), residues: 32
  loop : -1.97 (0.49), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG q  46 
 TYR   0.007   0.001   TYR q 157 
 PHE   0.011   0.001   PHE q  74 
 TRP   0.008   0.001   TRP q 105 
 HIS   0.004   0.002   HIS q 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 2106)
  covalent geometry    : angle       0.57116 ( 2889)
  hydrogen bonds       : bond        0.02381 (   44)
  hydrogen bonds       : angle       4.93836 (  120)

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

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

  608 Ramachandran restraints generated.
    304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  608 Ramachandran restraints generated.
    304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.075 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 36
  average time/residue: 0.0440
  time to fit residues: 2.0157
Evaluate side-chains
  23 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue  259 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 20 optimal weight:    0.0020
   chunk 16 optimal weight:    0.7980
   chunk 29 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0470
   chunk 5 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.4286

-------------------------------------------------------------------------------
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 = 0.4058 r_free = 0.4058 target = 0.185450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.172229 restraints weight = 2932.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.173075 restraints weight = 2297.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.173075 restraints weight = 1938.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.173075 restraints weight = 1938.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.173075 restraints weight = 1938.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6855
moved from start:          0.3903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   2106  Z= 0.098
  Angle     :  0.548   5.573   2889  Z= 0.285
  Chirality :  0.048   0.128    334
  Planarity :  0.005   0.050    387
  Dihedral  :  4.642  17.773    320
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 16.56 %
    Favored  : 82.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.45 (0.47), residues: 304
  helix: -1.62 (0.51), residues: 88
  sheet: -0.65 (0.89), residues: 32
  loop : -1.86 (0.47), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG q  46 
 TYR   0.006   0.001   TYR q 157 
 PHE   0.013   0.001   PHE q  74 
 TRP   0.008   0.001   TRP q 291 
 HIS   0.003   0.002   HIS q 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 2106)
  covalent geometry    : angle       0.54849 ( 2889)
  hydrogen bonds       : bond        0.01994 (   44)
  hydrogen bonds       : angle       4.43426 (  120)

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

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

  608 Ramachandran restraints generated.
    304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  608 Ramachandran restraints generated.
    304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 29
  time to evaluate  : 0.085 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 30
  average time/residue: 0.0570
  time to fit residues: 2.0886
Evaluate side-chains
  28 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 18 optimal weight:    9.9990
   chunk 1 optimal weight:    0.0020
   chunk 14 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 17 optimal weight:    6.9990
   chunk 7 optimal weight:    0.0170
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.5226

-------------------------------------------------------------------------------
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 = 0.4035 r_free = 0.4035 target = 0.182129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.168261 restraints weight = 2988.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.169231 restraints weight = 2330.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.169581 restraints weight = 1959.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.170570 restraints weight = 1809.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.170604 restraints weight = 1617.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6883
moved from start:          0.4253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2106  Z= 0.105
  Angle     :  0.546   6.809   2889  Z= 0.279
  Chirality :  0.048   0.127    334
  Planarity :  0.005   0.050    387
  Dihedral  :  4.527  18.238    320
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 17.79 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.29 (0.46), residues: 304
  helix: -1.41 (0.52), residues: 88
  sheet: -0.67 (0.87), residues: 32
  loop : -1.78 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG q 133 
 TYR   0.006   0.001   TYR q 157 
 PHE   0.011   0.001   PHE q  74 
 TRP   0.008   0.001   TRP q 291 
 HIS   0.003   0.002   HIS q 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 2106)
  covalent geometry    : angle       0.54567 ( 2889)
  hydrogen bonds       : bond        0.02064 (   44)
  hydrogen bonds       : angle       4.40369 (  120)

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

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

  608 Ramachandran restraints generated.
    304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  608 Ramachandran restraints generated.
    304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 33
  time to evaluate  : 0.076 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 34
  average time/residue: 0.0324
  time to fit residues: 1.5207
Evaluate side-chains
  28 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 27
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue   73 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 27 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 24 optimal weight:    0.3980
   chunk 6 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 29 optimal weight:    6.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4009 r_free = 0.4009 target = 0.179517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.165647 restraints weight = 2962.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.166776 restraints weight = 2315.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.167391 restraints weight = 1929.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.167631 restraints weight = 1730.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.168164 restraints weight = 1634.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
moved from start:          0.4754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2106  Z= 0.123
  Angle     :  0.569   7.505   2889  Z= 0.290
  Chirality :  0.048   0.121    334
  Planarity :  0.005   0.052    387
  Dihedral  :  4.760  19.819    320
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 19.02 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.30 (0.46), residues: 304
  helix: -1.47 (0.50), residues: 93
  sheet: -0.31 (0.93), residues: 28
  loop : -1.80 (0.45), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG q 133 
 TYR   0.005   0.001   TYR q 157 
 PHE   0.011   0.001   PHE q  74 
 TRP   0.009   0.001   TRP q 291 
 HIS   0.003   0.002   HIS q 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 2106)
  covalent geometry    : angle       0.56883 ( 2889)
  hydrogen bonds       : bond        0.02184 (   44)
  hydrogen bonds       : angle       4.45179 (  120)

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

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

  608 Ramachandran restraints generated.
    304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  608 Ramachandran restraints generated.
    304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.074 
Fit side-chains
REVERT: q   28 LEU cc_start: 0.7735 (mt) cc_final: 0.7487 (mt)
  outliers start: 3
  outliers final: 2
  residues processed: 29
  average time/residue: 0.0423
  time to fit residues: 1.6002
Evaluate side-chains
  29 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 27
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue   73 THR
Chi-restraints excluded: chain q residue   79 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   chunk 16 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 13 optimal weight:    0.2980
   chunk 18 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4003 r_free = 0.4003 target = 0.179242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.165111 restraints weight = 2968.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.166109 restraints weight = 2336.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.167014 restraints weight = 1965.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.167273 restraints weight = 1711.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.167273 restraints weight = 1606.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6964
moved from start:          0.5048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2106  Z= 0.110
  Angle     :  0.537   4.812   2889  Z= 0.275
  Chirality :  0.047   0.120    334
  Planarity :  0.005   0.056    387
  Dihedral  :  4.583  19.155    320
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 20.25 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.14 (0.46), residues: 304
  helix: -1.46 (0.50), residues: 93
  sheet: -0.10 (0.99), residues: 28
  loop : -1.65 (0.46), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG q 133 
 TYR   0.005   0.001   TYR q 157 
 PHE   0.012   0.001   PHE q  74 
 TRP   0.011   0.001   TRP q 291 
 HIS   0.004   0.002   HIS q 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 2106)
  covalent geometry    : angle       0.53689 ( 2889)
  hydrogen bonds       : bond        0.02039 (   44)
  hydrogen bonds       : angle       4.32054 (  120)

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

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

  608 Ramachandran restraints generated.
    304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  608 Ramachandran restraints generated.
    304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 29
  time to evaluate  : 0.083 
Fit side-chains
REVERT: q   28 LEU cc_start: 0.7729 (mt) cc_final: 0.7514 (mt)
  outliers start: 3
  outliers final: 2
  residues processed: 30
  average time/residue: 0.0404
  time to fit residues: 1.6013
Evaluate side-chains
  30 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 28
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue   47 ILE
Chi-restraints excluded: chain q residue   79 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 6 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0570
   chunk 20 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0670
   chunk 8 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.5836

-------------------------------------------------------------------------------
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 = 0.4004 r_free = 0.4004 target = 0.179150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.164769 restraints weight = 3008.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.165673 restraints weight = 2348.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.166598 restraints weight = 1966.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.166970 restraints weight = 1730.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.167242 restraints weight = 1600.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6960
moved from start:          0.5234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   2106  Z= 0.105
  Angle     :  0.538   5.357   2889  Z= 0.278
  Chirality :  0.048   0.136    334
  Planarity :  0.005   0.053    387
  Dihedral  :  4.554  19.180    320
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.54 %
    Favored  : 90.46 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 17.18 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.06 (0.47), residues: 304
  helix: -1.42 (0.50), residues: 93
  sheet: -0.27 (1.05), residues: 28
  loop : -1.55 (0.46), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG q  13 
 TYR   0.005   0.001   TYR q 157 
 PHE   0.011   0.001   PHE q  74 
 TRP   0.010   0.001   TRP q 291 
 HIS   0.003   0.002   HIS q 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 2106)
  covalent geometry    : angle       0.53761 ( 2889)
  hydrogen bonds       : bond        0.01987 (   44)
  hydrogen bonds       : angle       4.24755 (  120)

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

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

  608 Ramachandran restraints generated.
    304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  608 Ramachandran restraints generated.
    304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 27
  time to evaluate  : 0.065 
Fit side-chains
REVERT: q   28 LEU cc_start: 0.7668 (mt) cc_final: 0.7442 (mt)
REVERT: q   39 TYR cc_start: 0.8281 (t80) cc_final: 0.8069 (t80)
  outliers start: 5
  outliers final: 2
  residues processed: 29
  average time/residue: 0.0399
  time to fit residues: 1.4838
Evaluate side-chains
  29 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 27
  time to evaluate  : 0.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue    4 LEU
Chi-restraints excluded: chain q residue   47 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 4 optimal weight:    0.4980
   chunk 13 optimal weight:    0.0870
   chunk 7 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0570
   chunk 3 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0020
   overall best weight:    0.2484

-------------------------------------------------------------------------------
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 = 0.4042 r_free = 0.4042 target = 0.182799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.168579 restraints weight = 2960.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.169697 restraints weight = 2263.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.170314 restraints weight = 1872.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.170927 restraints weight = 1668.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.171041 restraints weight = 1534.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6890
moved from start:          0.5395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2106  Z= 0.089
  Angle     :  0.514   4.926   2889  Z= 0.266
  Chirality :  0.047   0.142    334
  Planarity :  0.005   0.055    387
  Dihedral  :  4.211  18.343    320
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 19.63 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.76 (0.48), residues: 304
  helix: -0.94 (0.55), residues: 83
  sheet: -0.27 (1.03), residues: 28
  loop : -1.45 (0.45), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG q  46 
 TYR   0.004   0.001   TYR q  52 
 PHE   0.010   0.001   PHE q  74 
 TRP   0.011   0.001   TRP q 291 
 HIS   0.001   0.001   HIS q 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00199 ( 2106)
  covalent geometry    : angle       0.51356 ( 2889)
  hydrogen bonds       : bond        0.01719 (   44)
  hydrogen bonds       : angle       3.96037 (  120)

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

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

  608 Ramachandran restraints generated.
    304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  608 Ramachandran restraints generated.
    304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 32
  time to evaluate  : 0.079 
Fit side-chains
REVERT: q   28 LEU cc_start: 0.7582 (mt) cc_final: 0.7348 (mt)
REVERT: q   39 TYR cc_start: 0.8219 (t80) cc_final: 0.8019 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 32
  average time/residue: 0.0589
  time to fit residues: 2.3042
Evaluate side-chains
  29 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue    4 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 1 optimal weight:    0.0870
   chunk 5 optimal weight:    0.5980
   chunk 17 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 16 optimal weight:    7.9990
   chunk 15 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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 = 0.4015 r_free = 0.4015 target = 0.180082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.165415 restraints weight = 3044.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.166395 restraints weight = 2358.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.167196 restraints weight = 1988.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.167196 restraints weight = 1764.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.167196 restraints weight = 1764.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6948
moved from start:          0.5433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2106  Z= 0.110
  Angle     :  0.553   5.229   2889  Z= 0.289
  Chirality :  0.048   0.170    334
  Planarity :  0.005   0.052    387
  Dihedral  :  4.359  18.671    320
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 18.40 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.78 (0.48), residues: 304
  helix: -1.07 (0.54), residues: 87
  sheet: -0.37 (1.02), residues: 28
  loop : -1.39 (0.46), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG q 133 
 TYR   0.005   0.001   TYR q  92 
 PHE   0.011   0.001   PHE q 107 
 TRP   0.010   0.001   TRP q 291 
 HIS   0.003   0.002   HIS q 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 2106)
  covalent geometry    : angle       0.55333 ( 2889)
  hydrogen bonds       : bond        0.01994 (   44)
  hydrogen bonds       : angle       4.04374 (  120)

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

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

  608 Ramachandran restraints generated.
    304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  608 Ramachandran restraints generated.
    304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.079 
Fit side-chains
REVERT: q   28 LEU cc_start: 0.7580 (mt) cc_final: 0.7346 (mt)
REVERT: q   39 TYR cc_start: 0.8244 (t80) cc_final: 0.8032 (t80)
  outliers start: 3
  outliers final: 3
  residues processed: 30
  average time/residue: 0.0376
  time to fit residues: 1.4834
Evaluate side-chains
  31 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain q residue    4 LEU
Chi-restraints excluded: chain q residue   51 LEU
Chi-restraints excluded: chain q residue  269 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    0.0470
   chunk 9 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 29 optimal weight:    7.9990
   chunk 10 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 18 optimal weight:    9.9990
   overall best weight:    0.6482

-------------------------------------------------------------------------------
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 = 0.3999 r_free = 0.3999 target = 0.178045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.163658 restraints weight = 3049.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.164724 restraints weight = 2334.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.165579 restraints weight = 1923.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.165818 restraints weight = 1687.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.166178 restraints weight = 1585.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6950
moved from start:          0.5465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2106  Z= 0.114
  Angle     :  0.543   5.133   2889  Z= 0.284
  Chirality :  0.048   0.181    334
  Planarity :  0.005   0.053    387
  Dihedral  :  4.483  19.004    320
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.21 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 19.02 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.75 (0.48), residues: 304
  helix: -1.10 (0.53), residues: 87
  sheet: -0.44 (1.03), residues: 28
  loop : -1.32 (0.47), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG q 133 
 TYR   0.005   0.001   TYR q  92 
 PHE   0.013   0.002   PHE q  74 
 TRP   0.011   0.001   TRP q 291 
 HIS   0.004   0.002   HIS q 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 2106)
  covalent geometry    : angle       0.54295 ( 2889)
  hydrogen bonds       : bond        0.02090 (   44)
  hydrogen bonds       : angle       4.10182 (  120)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 782.28 seconds
wall clock time: 14 minutes 3.45 seconds (843.45 seconds total)