Starting phenix.real_space_refine
on Thu Oct 22 17:58:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/26qm_80829/10_2026/26qm_80829_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/26qm_80829/10_2026/26qm_80829.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/26qm_80829/10_2026/26qm_80829_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/26qm_80829/10_2026/26qm_80829_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/26qm_80829/10_2026/26qm_80829.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/26qm_80829/10_2026/26qm_80829.map"
  }
  resolution = 3.07
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.083
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      28      5.16       5
     C    2038      2.51       5
     N     496      2.21       5
     O     547      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3112
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3022
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 380, 3022
          Classifications: {'peptide': 380}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 14, 'TRANS': 365}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "A"
      Number of atoms: 90
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 90
          Unusual residues: {'UPG': 1}
          Classifications: {'peptide': 1, 'undetermined': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 1.03, per 1000 atoms: 0.33
  Number of scatterers: 3112
  At special positions: 0
  Unit cell: (69.35, 59.13, 82.49, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      28     16.00
     P       3     15.00
     O     547      8.00
     N     496      7.00
     C    2038      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 296 " - pdb=" SG  CYS A 323 " distance=2.04

  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: 0.19
  Conformation dependent library (CDL) restraints added in 105.8 milliseconds
  

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  708

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 2 sheets defined
      58.7% alpha, 12.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 36
    Processing helix  chain 'A' and resid 65 through 75
    Processing helix  chain 'A' and resid 93 through 101
      removed outlier: 3.515A  pdb=" N   VAL A  97 " --> pdb=" O   PRO A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 134
      Proline residue:  A 130  - end of helix
    Processing helix  chain 'A' and resid 153 through 160
    Processing helix  chain 'A' and resid 179 through 192
      removed outlier: 3.511A  pdb=" N   THR A 183 " --> pdb=" O   GLY A 179 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   SER A 192 " --> pdb=" O   TYR A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 203
    Processing helix  chain 'A' and resid 217 through 223
      removed outlier: 3.560A  pdb=" N   ALA A 223 " --> pdb=" O   VAL A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 230
    Processing helix  chain 'A' and resid 234 through 246
      removed outlier: 3.577A  pdb=" N   PHE A 238 " --> pdb=" O   ALA A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 284
    Processing helix  chain 'A' and resid 285 through 290
    Processing helix  chain 'A' and resid 291 through 295
      removed outlier: 3.755A  pdb=" N   GLU A 295 " --> pdb=" O   PRO A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 311
      removed outlier: 3.515A  pdb=" N   LEU A 301 " --> pdb=" O   PHE A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 339
    Processing helix  chain 'A' and resid 345 through 368
    Processing sheet with id=AA1, first strand: chain 'A' and resid 110 through 114
      removed outlier: 3.860A  pdb=" N   ARG A 111 " --> pdb=" O   VAL A  83 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU A  85 " --> pdb=" O   ARG A 111 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   CYS A 143 " --> pdb=" O   LEU A  56 " (cutoff:3.500A)
      removed outlier: 5.951A  pdb=" N   SER A 212 " --> pdb=" O   GLY A 170 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   GLY A 170 " --> pdb=" O   SER A 212 " (cutoff:3.500A)
      removed outlier: 8.450A  pdb=" N   GLY A 166 " --> pdb=" O   ARG A 216 " (cutoff:3.500A)
      removed outlier: 9.049A  pdb=" N   VAL A 165 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
      removed outlier: 12.071A  pdb=" N   SER A 253 " --> pdb=" O   VAL A 165 " (cutoff:3.500A)
      removed outlier: 12.841A  pdb=" N   LEU A 167 " --> pdb=" O   SER A 253 " (cutoff:3.500A)
      removed outlier: 12.682A  pdb=" N   GLN A 255 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 8.526A  pdb=" N   HIS A 169 " --> pdb=" O   GLN A 255 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   ALA A 257 " --> pdb=" O   HIS A 169 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   LEU A 171 " --> pdb=" O   ALA A 257 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   GLN A 259 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   TYR A 173 " --> pdb=" O   GLN A 259 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   MET A 258 " --> pdb=" O   ARG A 148 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 381 through 382

    173 hydrogen bonds defined for protein.
    498 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: 0.44

  Time building geometry restraints manager: 0.27 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 477
        1.29 -     1.42: 864
        1.42 -     1.55: 1799
        1.55 -     1.68: 8
        1.68 -     1.81: 45
  Bond restraints: 3193
  Sorted by residual:
  bond pdb=" C2C UPG A 401 "
       pdb=" C3C UPG A 401 "
    ideal  model  delta    sigma   weight residual
    1.531  1.259  0.272 2.00e-02 2.50e+03 1.85e+02
  bond pdb=" C46 P5S A 402 "
       pdb=" C48 P5S A 402 "
    ideal  model  delta    sigma   weight residual
    1.533  1.320  0.213 2.00e-02 2.50e+03 1.13e+02
  bond pdb=" C4C UPG A 401 "
       pdb=" C5C UPG A 401 "
    ideal  model  delta    sigma   weight residual
    1.514  1.355  0.159 2.00e-02 2.50e+03 6.31e+01
  bond pdb=" C2  UPG A 401 "
       pdb=" N3  UPG A 401 "
    ideal  model  delta    sigma   weight residual
    1.371  1.522 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" C1C UPG A 401 "
       pdb=" O4C UPG A 401 "
    ideal  model  delta    sigma   weight residual
    1.399  1.269  0.130 2.00e-02 2.50e+03 4.25e+01
  ... (remaining 3188 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.96: 4240
        2.96 -     5.92: 56
        5.92 -     8.87: 21
        8.87 -    11.83: 5
       11.83 -    14.79: 3
  Bond angle restraints: 4325
  Sorted by residual:
  angle pdb=" O1B UPG A 401 "
        pdb=" PB  UPG A 401 "
        pdb=" O2B UPG A 401 "
      ideal   model   delta    sigma   weight residual
     122.19  107.40   14.79 3.00e+00 1.11e-01 2.43e+01
  angle pdb=" O1A UPG A 401 "
        pdb=" PA  UPG A 401 "
        pdb=" O2A UPG A 401 "
      ideal   model   delta    sigma   weight residual
     121.98  108.69   13.29 3.00e+00 1.11e-01 1.96e+01
  angle pdb=" O13 P5S A 402 "
        pdb=" P12 P5S A 402 "
        pdb=" O15 P5S A 402 "
      ideal   model   delta    sigma   weight residual
     121.25  109.18   12.07 3.00e+00 1.11e-01 1.62e+01
  angle pdb=" N   GLN A 270 "
        pdb=" CA  GLN A 270 "
        pdb=" C   GLN A 270 "
      ideal   model   delta    sigma   weight residual
     111.07  106.78    4.29 1.07e+00 8.73e-01 1.61e+01
  angle pdb=" N   MET A 211 "
        pdb=" CA  MET A 211 "
        pdb=" C   MET A 211 "
      ideal   model   delta    sigma   weight residual
     113.50  108.61    4.89 1.23e+00 6.61e-01 1.58e+01
  ... (remaining 4320 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.36: 1843
       35.36 -    70.72: 52
       70.72 -   106.09: 15
      106.09 -   141.45: 11
      141.45 -   176.81: 5
  Dihedral angle restraints: 1926
    sinusoidal: 823
      harmonic: 1103
  Sorted by residual:
  dihedral pdb=" CB  CYS A 296 "
           pdb=" SG  CYS A 296 "
           pdb=" SG  CYS A 323 "
           pdb=" CB  CYS A 323 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -11.06  -74.94     1      1.00e+01 1.00e-02 7.11e+01
  dihedral pdb=" CB  P5S A 402 "
           pdb=" OG  P5S A 402 "
           pdb=" P12 P5S A 402 "
           pdb=" O13 P5S A 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.21 -135.98 -176.81     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C40 P5S A 402 "
           pdb=" C38 P5S A 402 "
           pdb=" C39 P5S A 402 "
           pdb=" O47 P5S A 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -33.56  134.94 -168.50     1      3.00e+01 1.11e-03 2.11e+01
  ... (remaining 1923 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 424
       0.069 -    0.138: 51
       0.138 -    0.207: 1
       0.207 -    0.276: 1
       0.276 -    0.345: 1
  Chirality restraints: 478
  Sorted by residual:
  chirality pdb=" C3C UPG A 401 "
            pdb=" C2C UPG A 401 "
            pdb=" C4C UPG A 401 "
            pdb=" O3C UPG A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.39   -0.35 2.00e-01 2.50e+01 2.98e+00
  chirality pdb=" C4C UPG A 401 "
            pdb=" C3C UPG A 401 "
            pdb=" C5C UPG A 401 "
            pdb=" O4C UPG A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.43   -2.70    0.27 2.00e-01 2.50e+01 1.78e+00
  chirality pdb=" CA  P5S A 402 "
            pdb=" N   P5S A 402 "
            pdb=" C   P5S A 402 "
            pdb=" CB  P5S A 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.59   -0.19 2.00e-01 2.50e+01 8.66e-01
  ... (remaining 475 not shown)

  Planarity restraints: 525
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 201 "   -0.014 2.00e-02 2.50e+03   2.87e-02 8.26e+00
        pdb=" C   ASN A 201 "    0.050 2.00e-02 2.50e+03
        pdb=" O   ASN A 201 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   VAL A 202 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 269 "    0.011 2.00e-02 2.50e+03   2.24e-02 5.00e+00
        pdb=" C   PHE A 269 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   PHE A 269 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLN A 270 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 323 "    0.007 2.00e-02 2.50e+03   1.48e-02 2.19e+00
        pdb=" C   CYS A 323 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   CYS A 323 "    0.010 2.00e-02 2.50e+03
        pdb=" N   LEU A 324 "    0.009 2.00e-02 2.50e+03
  ... (remaining 522 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 987
        2.83 -     3.34: 2933
        3.34 -     3.86: 5256
        3.86 -     4.38: 5904
        4.38 -     4.90: 10269
  Nonbonded interactions: 25349
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 278 "
            pdb=" O   ASP A 370 "
     model   vdw
     2.307 3.120
  nonbonded pdb=" O   ASN A  69 "
            pdb=" OG1 THR A  72 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" O2C UPG A 401 "
            pdb=" O3C UPG A 401 "
     model   vdw
     2.367 2.432
  nonbonded pdb=" OG  SER A 145 "
            pdb=" O3C UPG A 401 "
     model   vdw
     2.383 3.040
  nonbonded pdb=" C4' UPG A 401 "
            pdb=" O6' UPG A 401 "
     model   vdw
     2.384 2.776
  ... (remaining 25344 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.050
  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:                    0.000
  Process input model:                     4.560
  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:0.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
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      :  0.010   0.272   3194  Z= 0.527
  Angle     :  0.983  14.788   4327  Z= 0.440
  Chirality :  0.045   0.345    478
  Planarity :  0.004   0.029    525
  Dihedral  : 23.174 176.811   1215
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  :  6.23 %
    Favored  : 92.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.79 (0.39), residues: 376
  helix: -0.05 (0.32), residues: 213
  sheet: -2.28 (0.77), residues: 37
  loop : -2.76 (0.46), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 356 
 TYR   0.003   0.001   TYR A 237 
 PHE   0.012   0.001   PHE A  19 
 TRP   0.005   0.000   TRP A 326 
 HIS   0.001   0.000   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01017 /  0.53 ( 3193)
  covalent geometry    : angle       0.98056 /  0.44 ( 4325)
  SS BOND              : bond        0.01331 /  0.70 (    1)
  SS BOND              : angle       3.59165 /  2.02 (    2)
  hydrogen bonds       : bond        0.13618 /  9.91 (  173)
  hydrogen bonds       : angle       5.34133 /  4.09 (  498)

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

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

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A   34 ARG cc_start: 0.7823 (mtt-85) cc_final: 0.6121 (tmm160)
REVERT: A   50 LEU cc_start: 0.7469 (mp) cc_final: 0.7220 (mt)
REVERT: A  121 ILE cc_start: 0.7754 (pp) cc_final: 0.7510 (pp)
REVERT: A  129 MET cc_start: 0.7632 (mmm) cc_final: 0.7427 (mmm)
REVERT: A  284 LEU cc_start: 0.6876 (tm) cc_final: 0.6467 (tm)
  outliers start: 5
  outliers final: 1
  residues processed: 70
  average time/residue: 0.0792
  time to fit residues: 6.5657
Evaluate side-chains
  50 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  372 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 37]
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    0.4980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.8184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  88 GLN
A 186 GLN
A 270 GLN
** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.185086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.155100 restraints weight = 3646.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3769 rms_B_bonded: 2.12
r_work: 0.3658 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3515 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3194  Z= 0.164
  Angle     :  0.625  11.112   4327  Z= 0.307
  Chirality :  0.043   0.152    478
  Planarity :  0.004   0.031    525
  Dihedral  : 23.095 167.962    524
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 11.84 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -0.23 (0.43), residues: 376
  helix:  1.27 (0.35), residues: 214
  sheet: -2.06 (0.76), residues: 37
  loop : -2.06 (0.49), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 148 
 TYR   0.010   0.001   TYR A 349 
 PHE   0.019   0.002   PHE A 327 
 TRP   0.015   0.001   TRP A  23 
 HIS   0.003   0.001   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00358 /  0.16 ( 3193)
  covalent geometry    : angle       0.62326 /  0.31 ( 4325)
  SS BOND              : bond        0.01562 /  0.82 (    1)
  SS BOND              : angle       2.52205 /  1.46 (    2)
  hydrogen bonds       : bond        0.04244 /  2.82 (  173)
  hydrogen bonds       : angle       3.95023 /  2.93 (  498)

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

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

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A   75 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7940 (tm-30)
REVERT: A   80 LYS cc_start: 0.7715 (ptmt) cc_final: 0.7514 (ptmm)
REVERT: A  111 ARG cc_start: 0.7510 (ptm160) cc_final: 0.6935 (ttp-110)
REVERT: A  113 PHE cc_start: 0.6865 (m-80) cc_final: 0.6303 (m-80)
REVERT: A  121 ILE cc_start: 0.7764 (pp) cc_final: 0.7558 (pp)
REVERT: A  129 MET cc_start: 0.7928 (mmm) cc_final: 0.7728 (mmm)
REVERT: A  205 PHE cc_start: 0.7546 (m-80) cc_final: 0.6994 (m-80)
REVERT: A  233 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.6983 (mp)
REVERT: A  284 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6433 (tm)
  outliers start: 12
  outliers final: 5
  residues processed: 56
  average time/residue: 0.0578
  time to fit residues: 4.0898
Evaluate side-chains
  52 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LEU
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  296 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks: [5, 36, 30, 18, 17, 16, 13, 25, 0, 3, 33]
   chunk 5 optimal weight:   10.0000
   chunk 36 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 282 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.179467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.149086 restraints weight = 3658.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 2.00
r_work: 0.3540 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3398 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.3509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3194  Z= 0.137
  Angle     :  0.574   8.647   4327  Z= 0.283
  Chirality :  0.043   0.170    478
  Planarity :  0.003   0.031    525
  Dihedral  : 20.428 160.709    523
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 14.95 %
    Favored  : 82.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.34 (0.43), residues: 376
  helix:  1.75 (0.36), residues: 213
  sheet: -1.67 (0.79), residues: 37
  loop : -1.90 (0.48), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 148 
 TYR   0.006   0.001   TYR A 349 
 PHE   0.014   0.002   PHE A 327 
 TRP   0.014   0.001   TRP A  23 
 HIS   0.003   0.001   HIS A  26 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.14 ( 3193)
  covalent geometry    : angle       0.57140 /  0.28 ( 4325)
  SS BOND              : bond        0.00063 /  0.03 (    1)
  SS BOND              : angle       2.50829 /  1.44 (    2)
  hydrogen bonds       : bond        0.04227 /  2.79 (  173)
  hydrogen bonds       : angle       3.78942 /  2.81 (  498)

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

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

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A    1 MET cc_start: 0.4771 (mmp) cc_final: 0.4544 (mmp)
REVERT: A   75 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7706 (tm-30)
REVERT: A   78 TYR cc_start: 0.8735 (t80) cc_final: 0.8121 (t80)
REVERT: A  111 ARG cc_start: 0.7616 (ptm160) cc_final: 0.7141 (ttp-110)
REVERT: A  113 PHE cc_start: 0.6903 (m-80) cc_final: 0.6632 (m-80)
REVERT: A  284 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6514 (tm)
  outliers start: 9
  outliers final: 4
  residues processed: 64
  average time/residue: 0.0568
  time to fit residues: 4.5984
Evaluate side-chains
  59 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LEU
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  296 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks: [16, 24, 10, 8, 34, 31, 7, 15, 22, 36, 17]
   chunk 16 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 8 optimal weight:    7.9990
   chunk 34 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0670
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.5918

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 159 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.179244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.148168 restraints weight = 3663.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 2.09
r_work: 0.3572 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3432 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.3886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3194  Z= 0.121
  Angle     :  0.532   8.903   4327  Z= 0.268
  Chirality :  0.042   0.165    478
  Planarity :  0.004   0.061    525
  Dihedral  : 18.700 150.607    523
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 16.51 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.54 (0.44), residues: 376
  helix:  1.87 (0.36), residues: 215
  sheet: -1.52 (0.80), residues: 37
  loop : -1.81 (0.50), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 148 
 TYR   0.006   0.001   TYR A 349 
 PHE   0.016   0.002   PHE A 327 
 TRP   0.010   0.001   TRP A  23 
 HIS   0.002   0.001   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.12 ( 3193)
  covalent geometry    : angle       0.52986 /  0.27 ( 4325)
  SS BOND              : bond        0.01530 /  0.81 (    1)
  SS BOND              : angle       2.27879 /  1.34 (    2)
  hydrogen bonds       : bond        0.04108 /  2.71 (  173)
  hydrogen bonds       : angle       3.76688 /  2.81 (  498)

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

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

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A   16 PHE cc_start: 0.7087 (m-80) cc_final: 0.6809 (m-80)
REVERT: A  111 ARG cc_start: 0.7616 (ptm160) cc_final: 0.7145 (ttp-110)
REVERT: A  113 PHE cc_start: 0.6784 (m-80) cc_final: 0.6519 (m-80)
REVERT: A  162 THR cc_start: 0.6741 (OUTLIER) cc_final: 0.6362 (p)
REVERT: A  284 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6365 (tm)
  outliers start: 9
  outliers final: 4
  residues processed: 63
  average time/residue: 0.0574
  time to fit residues: 4.5675
Evaluate side-chains
  55 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LEU
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  296 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks: [10, 2, 20, 21, 18, 12, 31, 8, 35, 13, 23]
   chunk 10 optimal weight:    7.9990
   chunk 2 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 12 optimal weight:    5.9990
   chunk 31 optimal weight:    0.5980
   chunk 8 optimal weight:    6.9990
   chunk 35 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 23 optimal weight:    4.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 159 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.177473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.146445 restraints weight = 3628.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 2.02
r_work: 0.3540 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3399 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.4242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3194  Z= 0.132
  Angle     :  0.553   9.382   4327  Z= 0.278
  Chirality :  0.042   0.180    478
  Planarity :  0.004   0.054    525
  Dihedral  : 17.401 149.760    523
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 15.89 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.52 (0.44), residues: 376
  helix:  1.84 (0.36), residues: 216
  sheet: -1.39 (0.80), residues: 37
  loop : -1.87 (0.51), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 148 
 TYR   0.007   0.001   TYR A 349 
 PHE   0.018   0.002   PHE A 327 
 TRP   0.011   0.001   TRP A  23 
 HIS   0.002   0.001   HIS A  26 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.13 ( 3193)
  covalent geometry    : angle       0.54976 /  0.28 ( 4325)
  SS BOND              : bond        0.01322 /  0.70 (    1)
  SS BOND              : angle       2.70302 /  1.58 (    2)
  hydrogen bonds       : bond        0.04231 /  2.77 (  173)
  hydrogen bonds       : angle       3.76745 /  2.82 (  498)

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

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

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.069 
Fit side-chains
REVERT: A   16 PHE cc_start: 0.7055 (m-80) cc_final: 0.6758 (m-80)
REVERT: A   78 TYR cc_start: 0.8750 (t80) cc_final: 0.8140 (t80)
REVERT: A  111 ARG cc_start: 0.7600 (ptm160) cc_final: 0.7081 (ttp-110)
REVERT: A  113 PHE cc_start: 0.6773 (m-80) cc_final: 0.6518 (m-80)
REVERT: A  162 THR cc_start: 0.6654 (OUTLIER) cc_final: 0.6238 (p)
REVERT: A  260 ASN cc_start: 0.8716 (t0) cc_final: 0.8144 (t0)
REVERT: A  284 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6404 (tm)
  outliers start: 14
  outliers final: 5
  residues processed: 68
  average time/residue: 0.0520
  time to fit residues: 4.4709
Evaluate side-chains
  60 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LEU
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  296 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks: [10, 8, 24, 9, 14, 7, 12, 31, 23, 36, 6]
   chunk 10 optimal weight:    6.9990
   chunk 8 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 159 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.176689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.145515 restraints weight = 3612.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 2.01
r_work: 0.3524 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3383 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.4502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3194  Z= 0.141
  Angle     :  0.581   9.828   4327  Z= 0.294
  Chirality :  0.042   0.182    478
  Planarity :  0.004   0.047    525
  Dihedral  : 16.508 143.739    523
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 17.76 %
    Favored  : 78.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.65 (0.44), residues: 376
  helix:  1.96 (0.36), residues: 213
  sheet: -1.35 (0.81), residues: 37
  loop : -1.76 (0.52), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 148 
 TYR   0.007   0.001   TYR A 349 
 PHE   0.022   0.002   PHE A 311 
 TRP   0.010   0.001   TRP A  23 
 HIS   0.002   0.001   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.14 ( 3193)
  covalent geometry    : angle       0.57737 /  0.29 ( 4325)
  SS BOND              : bond        0.01016 /  0.53 (    1)
  SS BOND              : angle       2.86972 /  1.68 (    2)
  hydrogen bonds       : bond        0.04391 /  2.89 (  173)
  hydrogen bonds       : angle       3.83860 /  2.84 (  498)

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

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

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A   16 PHE cc_start: 0.7043 (m-80) cc_final: 0.6793 (m-80)
REVERT: A   78 TYR cc_start: 0.8770 (t80) cc_final: 0.8142 (t80)
REVERT: A  111 ARG cc_start: 0.7643 (ptm160) cc_final: 0.7121 (ttp-110)
REVERT: A  113 PHE cc_start: 0.6746 (m-80) cc_final: 0.6350 (m-80)
REVERT: A  260 ASN cc_start: 0.8728 (t0) cc_final: 0.8135 (t0)
REVERT: A  284 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6456 (tm)
  outliers start: 12
  outliers final: 6
  residues processed: 66
  average time/residue: 0.0479
  time to fit residues: 4.1235
Evaluate side-chains
  61 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 LEU
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  296 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks: [3, 18, 33, 24, 29, 21, 26, 7, 30, 13, 0]
   chunk 3 optimal weight:    2.9990
   chunk 18 optimal weight:    0.4980
   chunk 33 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0980
   chunk 30 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 159 ASN
A 222 GLN
A 309 HIS
A 333 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.177940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.146591 restraints weight = 3695.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 2.06
r_work: 0.3548 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3408 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.4588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3194  Z= 0.124
  Angle     :  0.555   9.607   4327  Z= 0.282
  Chirality :  0.042   0.179    478
  Planarity :  0.004   0.043    525
  Dihedral  : 15.825 138.020    523
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 18.38 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.77 (0.44), residues: 376
  helix:  1.98 (0.36), residues: 215
  sheet: -1.26 (0.80), residues: 37
  loop : -1.60 (0.54), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 356 
 TYR   0.007   0.001   TYR A 349 
 PHE   0.019   0.001   PHE A 327 
 TRP   0.009   0.001   TRP A 326 
 HIS   0.002   0.001   HIS A  26 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.12 ( 3193)
  covalent geometry    : angle       0.55108 /  0.28 ( 4325)
  SS BOND              : bond        0.01158 /  0.61 (    1)
  SS BOND              : angle       3.09561 /  1.82 (    2)
  hydrogen bonds       : bond        0.04271 /  2.80 (  173)
  hydrogen bonds       : angle       3.83580 /  2.86 (  498)

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

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

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A   75 GLU cc_start: 0.7708 (tp30) cc_final: 0.7469 (tp30)
REVERT: A  111 ARG cc_start: 0.7629 (ptm160) cc_final: 0.7106 (ttp-110)
REVERT: A  113 PHE cc_start: 0.6700 (m-80) cc_final: 0.6300 (m-80)
REVERT: A  260 ASN cc_start: 0.8733 (t0) cc_final: 0.8149 (t0)
REVERT: A  284 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6429 (tm)
  outliers start: 7
  outliers final: 4
  residues processed: 61
  average time/residue: 0.0459
  time to fit residues: 3.6340
Evaluate side-chains
  60 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  296 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks: [17, 24, 9, 34, 3, 11, 8, 25, 0, 15, 28]
   chunk 17 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0980
   chunk 9 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 15 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 159 ASN
A 222 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.177658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.146287 restraints weight = 3748.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 2.07
r_work: 0.3565 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3426 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.4694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3194  Z= 0.125
  Angle     :  0.556  10.005   4327  Z= 0.283
  Chirality :  0.042   0.189    478
  Planarity :  0.004   0.042    525
  Dihedral  : 15.186 126.837    523
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 19.94 %
    Favored  : 78.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.88 (0.44), residues: 376
  helix:  2.06 (0.36), residues: 213
  sheet: -1.20 (0.80), residues: 37
  loop : -1.48 (0.54), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 356 
 TYR   0.008   0.001   TYR A 349 
 PHE   0.025   0.002   PHE A 311 
 TRP   0.009   0.001   TRP A  23 
 HIS   0.002   0.001   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.12 ( 3193)
  covalent geometry    : angle       0.55233 /  0.28 ( 4325)
  SS BOND              : bond        0.01106 /  0.58 (    1)
  SS BOND              : angle       3.05842 /  1.80 (    2)
  hydrogen bonds       : bond        0.04318 /  2.84 (  173)
  hydrogen bonds       : angle       3.86021 /  2.87 (  498)

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

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

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A   75 GLU cc_start: 0.7765 (tp30) cc_final: 0.7530 (tp30)
REVERT: A  111 ARG cc_start: 0.7588 (ptm160) cc_final: 0.7087 (ttp-110)
REVERT: A  113 PHE cc_start: 0.6644 (m-80) cc_final: 0.6334 (m-80)
REVERT: A  260 ASN cc_start: 0.8753 (t0) cc_final: 0.8166 (t0)
REVERT: A  284 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6442 (tm)
  outliers start: 6
  outliers final: 4
  residues processed: 59
  average time/residue: 0.0502
  time to fit residues: 3.8218
Evaluate side-chains
  60 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  296 CYS
Chi-restraints excluded: chain A residue  380 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks: [9, 3, 23, 30, 5, 24, 25, 2, 29, 35, 4]
   chunk 9 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.8786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 159 ASN
A 222 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.175106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.143310 restraints weight = 3775.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 2.10
r_work: 0.3508 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3368 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.4953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3194  Z= 0.154
  Angle     :  0.588  10.389   4327  Z= 0.301
  Chirality :  0.043   0.196    478
  Planarity :  0.004   0.043    525
  Dihedral  : 14.438 104.474    523
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 19.63 %
    Favored  : 78.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.64 (0.44), residues: 376
  helix:  1.87 (0.35), residues: 215
  sheet: -0.69 (0.88), residues: 35
  loop : -1.87 (0.51), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 148 
 TYR   0.009   0.001   TYR A 349 
 PHE   0.021   0.002   PHE A 327 
 TRP   0.011   0.001   TRP A  23 
 HIS   0.002   0.001   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.15 ( 3193)
  covalent geometry    : angle       0.58421 /  0.30 ( 4325)
  SS BOND              : bond        0.01518 /  0.80 (    1)
  SS BOND              : angle       3.08015 /  1.81 (    2)
  hydrogen bonds       : bond        0.04749 /  3.12 (  173)
  hydrogen bonds       : angle       3.96244 /  2.93 (  498)

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

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

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.083 
Fit side-chains
REVERT: A   16 PHE cc_start: 0.7158 (m-80) cc_final: 0.6938 (m-80)
REVERT: A   75 GLU cc_start: 0.7825 (tp30) cc_final: 0.7577 (tp30)
REVERT: A  111 ARG cc_start: 0.7572 (ptm160) cc_final: 0.7089 (ttp-110)
REVERT: A  113 PHE cc_start: 0.6801 (m-80) cc_final: 0.6491 (m-80)
REVERT: A  174 VAL cc_start: 0.8992 (t) cc_final: 0.8673 (p)
REVERT: A  284 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6537 (tm)
  outliers start: 6
  outliers final: 3
  residues processed: 61
  average time/residue: 0.0539
  time to fit residues: 4.1876
Evaluate side-chains
  61 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  296 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks: [14, 36, 17, 19, 37, 35, 9, 6, 3, 5, 22]
   chunk 14 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0670
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.7520

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 159 ASN
A 222 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.175958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.144939 restraints weight = 3701.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 2.05
r_work: 0.3514 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3374 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.4976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3194  Z= 0.140
  Angle     :  0.573  10.372   4327  Z= 0.292
  Chirality :  0.042   0.198    478
  Planarity :  0.004   0.042    525
  Dihedral  : 13.218 105.126    523
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 20.25 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.44), residues: 376
  helix:  1.92 (0.35), residues: 215
  sheet: -0.52 (0.88), residues: 35
  loop : -1.83 (0.51), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 148 
 TYR   0.008   0.001   TYR A 349 
 PHE   0.027   0.002   PHE A 311 
 TRP   0.009   0.001   TRP A 305 
 HIS   0.003   0.001   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.14 ( 3193)
  covalent geometry    : angle       0.56913 /  0.29 ( 4325)
  SS BOND              : bond        0.01100 /  0.58 (    1)
  SS BOND              : angle       3.20710 /  1.89 (    2)
  hydrogen bonds       : bond        0.04524 /  2.97 (  173)
  hydrogen bonds       : angle       3.91949 /  2.91 (  498)

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

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

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  752 Ramachandran restraints generated.
    376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A   16 PHE cc_start: 0.7131 (m-80) cc_final: 0.6887 (m-80)
REVERT: A   75 GLU cc_start: 0.7811 (tp30) cc_final: 0.7545 (tp30)
REVERT: A  111 ARG cc_start: 0.7596 (ptm160) cc_final: 0.7106 (ttp-110)
REVERT: A  113 PHE cc_start: 0.6753 (m-80) cc_final: 0.6463 (m-80)
REVERT: A  284 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6458 (tm)
  outliers start: 6
  outliers final: 4
  residues processed: 61
  average time/residue: 0.0528
  time to fit residues: 4.1486
Evaluate side-chains
  60 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  296 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks: [30, 6, 4, 33, 25, 22, 11, 32, 31, 2, 23]
   chunk 30 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 159 ASN
A 222 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.165714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.133356 restraints weight = 3738.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 2.07
r_work: 0.3479 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3338 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.5040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3194  Z= 0.140
  Angle     :  0.577  10.403   4327  Z= 0.295
  Chirality :  0.043   0.197    478
  Planarity :  0.004   0.042    525
  Dihedral  : 12.732 107.678    523
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 18.69 %
    Favored  : 78.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.83 (0.44), residues: 376
  helix:  1.98 (0.35), residues: 214
  sheet: -1.05 (0.80), residues: 37
  loop : -1.52 (0.54), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 280 
 TYR   0.008   0.001   TYR A 349 
 PHE   0.020   0.002   PHE A 327 
 TRP   0.009   0.001   TRP A  23 
 HIS   0.002   0.001   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.14 ( 3193)
  covalent geometry    : angle       0.57294 /  0.29 ( 4325)
  SS BOND              : bond        0.01303 /  0.69 (    1)
  SS BOND              : angle       3.19989 /  1.88 (    2)
  hydrogen bonds       : bond        0.04559 /  2.99 (  173)
  hydrogen bonds       : angle       3.92523 /  2.91 (  498)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1065.15 seconds
wall clock time: 18 minutes 55.66 seconds (1135.66 seconds total)