Starting phenix.real_space_refine
on Wed Mar  5 16:36:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wll_37623/03_2025/8wll_37623.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wll_37623/03_2025/8wll_37623.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wll_37623/03_2025/8wll_37623.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wll_37623/03_2025/8wll_37623.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wll_37623/03_2025/8wll_37623.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wll_37623/03_2025/8wll_37623.cif"
  }
  resolution = 3.74
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.079
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      28      5.16       5
     C    1875      2.51       5
     N     433      2.21       5
     O     479      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 2815
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2771
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 389, 2771
          Classifications: {'peptide': 389}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 22, 'TRANS': 366}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 157
          Unresolved non-hydrogen angles: 194
          Unresolved non-hydrogen dihedrals: 131
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 108
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'YHR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.65, per 1000 atoms: 0.94
  Number of scatterers: 2815
  At special positions: 0
  Unit cell: (73.216, 53.248, 64.064, 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      28     16.00
     O     479      8.00
     N     433      7.00
     C    1875      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: 0.90
  Conformation dependent library (CDL) restraints added in 380.8 milliseconds
  

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  702

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 0 sheets defined
      89.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 40
      removed outlier: 3.847A  pdb=" N   ILE A  22 " --> pdb=" O   SER A  18 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 54
      removed outlier: 3.625A  pdb=" N   GLU A  54 " --> pdb=" O   SER A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 156
      removed outlier: 4.112A  pdb=" N   LYS A 138 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   ALA A 139 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      Proline residue:  A 147  - end of helix
    Processing helix  chain 'A' and resid 158 through 178
      removed outlier: 3.942A  pdb=" N   ILE A 162 " --> pdb=" O   TYR A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 211
      removed outlier: 3.822A  pdb=" N   ILE A 194 " --> pdb=" O   SER A 190 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLY A 195 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   MET A 204 " --> pdb=" O   SER A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 246
      removed outlier: 4.161A  pdb=" N   VAL A 232 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LEU A 233 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
      Proline residue:  A 236  - end of helix
      removed outlier: 3.540A  pdb=" N   VAL A 246 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 270
      removed outlier: 3.518A  pdb=" N   LEU A 270 " --> pdb=" O   GLN A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 291
    Processing helix  chain 'A' and resid 291 through 321
      removed outlier: 3.784A  pdb=" N   ALA A 297 " --> pdb=" O   TYR A 293 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   ILE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      Proline residue:  A 313  - end of helix
      Proline residue:  A 316  - end of helix
    Processing helix  chain 'A' and resid 328 through 349
      removed outlier: 4.544A  pdb=" N   VAL A 332 " --> pdb=" O   TRP A 328 " (cutoff:3.500A)
      Proline residue:  A 336  - end of helix
    Processing helix  chain 'A' and resid 351 through 356
    Processing helix  chain 'A' and resid 356 through 375
    Processing helix  chain 'A' and resid 376 through 378
      No H-bonds generated for 'chain 'A' and resid 376 through 378'
    Processing helix  chain 'A' and resid 384 through 414
      Proline residue:  A 404  - end of helix
      removed outlier: 3.998A  pdb=" N   GLY A 407 " --> pdb=" O   MET A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 447
      Proline residue:  A 437  - end of helix
      removed outlier: 4.142A  pdb=" N   ALA A 446 " --> pdb=" O   ALA A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 464
    Processing helix  chain 'A' and resid 465 through 471

    243 hydrogen bonds defined for protein.
    717 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: 0.73

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        0.63 -     0.87: 2
        0.87 -     1.10: 0
        1.10 -     1.34: 842
        1.34 -     1.58: 1987
        1.58 -     1.82: 52
  Bond restraints: 2883
  Sorted by residual:
  bond pdb=" C6  YHR A 501 "
       pdb=" C7  YHR A 501 "
    ideal  model  delta    sigma   weight residual
    1.521  0.629  0.892 2.00e-02 2.50e+03 1.99e+03
  bond pdb=" C13 YHR A 501 "
       pdb=" C14 YHR A 501 "
    ideal  model  delta    sigma   weight residual
    1.527  0.839  0.688 2.00e-02 2.50e+03 1.18e+03
  bond pdb=" C5  YHR A 501 "
       pdb=" C6  YHR A 501 "
    ideal  model  delta    sigma   weight residual
    1.527  1.276  0.251 2.00e-02 2.50e+03 1.57e+02
  bond pdb=" C12 YHR A 501 "
       pdb=" C13 YHR A 501 "
    ideal  model  delta    sigma   weight residual
    1.503  1.745 -0.242 2.00e-02 2.50e+03 1.46e+02
  bond pdb=" C16 YHR A 501 "
       pdb=" C3  YHR A 501 "
    ideal  model  delta    sigma   weight residual
    1.531  1.299  0.232 2.00e-02 2.50e+03 1.34e+02
  ... (remaining 2878 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 3768
        2.20 -     4.40: 119
        4.40 -     6.60: 41
        6.60 -     8.80: 10
        8.80 -    11.00: 5
  Bond angle restraints: 3943
  Sorted by residual:
  angle pdb=" CB  MET A 397 "
        pdb=" CG  MET A 397 "
        pdb=" SD  MET A 397 "
      ideal   model   delta    sigma   weight residual
     112.70  123.70  -11.00 3.00e+00 1.11e-01 1.35e+01
  angle pdb=" C7  YHR A 501 "
        pdb=" N8  YHR A 501 "
        pdb=" C9  YHR A 501 "
      ideal   model   delta    sigma   weight residual
     111.89  122.57  -10.68 3.00e+00 1.11e-01 1.27e+01
  angle pdb=" C33 YHR A 501 "
        pdb=" C31 YHR A 501 "
        pdb=" O30 YHR A 501 "
      ideal   model   delta    sigma   weight residual
     112.77  122.76   -9.99 3.00e+00 1.11e-01 1.11e+01
  angle pdb=" N   GLY A 235 "
        pdb=" CA  GLY A 235 "
        pdb=" C   GLY A 235 "
      ideal   model   delta    sigma   weight residual
     112.34  118.82   -6.48 2.04e+00 2.40e-01 1.01e+01
  angle pdb=" CB  MET A 403 "
        pdb=" CG  MET A 403 "
        pdb=" SD  MET A 403 "
      ideal   model   delta    sigma   weight residual
     112.70  121.92   -9.22 3.00e+00 1.11e-01 9.45e+00
  ... (remaining 3938 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.56: 1468
       11.56 -    23.11: 147
       23.11 -    34.66: 72
       34.66 -    46.22: 27
       46.22 -    57.77: 5
  Dihedral angle restraints: 1719
    sinusoidal: 619
      harmonic: 1100
  Sorted by residual:
  dihedral pdb=" CA  ARG A 326 "
           pdb=" C   ARG A 326 "
           pdb=" N   LYS A 327 "
           pdb=" CA  LYS A 327 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.96   19.04     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  GLY A 235 "
           pdb=" C   GLY A 235 "
           pdb=" N   PRO A 236 "
           pdb=" CA  PRO A 236 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.87  -18.13     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CG  ARG A 357 "
           pdb=" CD  ARG A 357 "
           pdb=" NE  ARG A 357 "
           pdb=" CZ  ARG A 357 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  130.81  -40.81     2      1.50e+01 4.44e-03 9.11e+00
  ... (remaining 1716 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.348: 483
       0.348 -    0.695: 1
       0.695 -    1.043: 1
       1.043 -    1.391: 0
       1.391 -    1.738: 1
  Chirality restraints: 486
  Sorted by residual:
  chirality pdb=" C6  YHR A 501 "
            pdb=" C15 YHR A 501 "
            pdb=" C5  YHR A 501 "
            pdb=" C7  YHR A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    0.79    1.74 2.00e-01 2.50e+01 7.55e+01
  chirality pdb=" C13 YHR A 501 "
            pdb=" C12 YHR A 501 "
            pdb=" C14 YHR A 501 "
            pdb=" N8  YHR A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.29   -1.46   -0.83 2.00e-01 2.50e+01 1.71e+01
  chirality pdb=" C3  YHR A 501 "
            pdb=" C16 YHR A 501 "
            pdb=" C4  YHR A 501 "
            pdb=" O2  YHR A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.58    2.11    0.47 2.00e-01 2.50e+01 5.64e+00
  ... (remaining 483 not shown)

  Planarity restraints: 479
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 291 "   -0.055 5.00e-02 4.00e+02   8.32e-02 1.11e+01
        pdb=" N   PRO A 292 "    0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO A 292 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 292 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 250 "   -0.045 5.00e-02 4.00e+02   6.63e-02 7.04e+00
        pdb=" N   PRO A 251 "    0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A 251 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 251 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 375 "   -0.033 5.00e-02 4.00e+02   5.02e-02 4.03e+00
        pdb=" N   PRO A 376 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A 376 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 376 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 476 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 552
        2.77 -     3.30: 3075
        3.30 -     3.84: 4819
        3.84 -     4.37: 5149
        4.37 -     4.90: 9055
  Nonbonded interactions: 22650
  Sorted by model distance:
  nonbonded pdb=" C15 YHR A 501 "
            pdb=" N8  YHR A 501 "
     model   vdw
     2.238 2.840
  nonbonded pdb=" OG  SER A 137 "
            pdb=" OG  SER A 190 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   PHE A 170 "
            pdb=" OG1 THR A 173 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   ALA A 297 "
            pdb=" OG  SER A 300 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" OG  SER A 325 "
            pdb=" OE1 GLN A 329 "
     model   vdw
     2.314 3.040
  ... (remaining 22645 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:             1.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.720
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
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      :  0.024   0.892   2883  Z= 1.747
  Angle     :  1.058  11.003   3943  Z= 0.473
  Chirality :  0.102   1.738    486
  Planarity :  0.007   0.083    479
  Dihedral  : 13.070  57.774   1017
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.44), residues: 385
  helix:  0.87 (0.30), residues: 323
  sheet:  None (None), residues: 0
  loop : -1.89 (0.79), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 451 
 HIS   0.002   0.001   HIS A 414 
 PHE   0.020   0.002   PHE A 166 
 TYR   0.016   0.002   TYR A  47 
 ARG   0.003   0.001   ARG A  19 

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A  144 ILE cc_start: 0.8518 (mm) cc_final: 0.8285 (mm)
REVERT: A  287 THR cc_start: 0.7984 (p) cc_final: 0.7783 (p)
REVERT: A  408 TYR cc_start: 0.8277 (t80) cc_final: 0.7731 (t80)
REVERT: A  453 MET cc_start: 0.7950 (mmm) cc_final: 0.7587 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.1097
  time to fit residues: 19.7135
Evaluate side-chains
  111 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 192 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.146816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.128187 restraints weight = 5235.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.131601 restraints weight = 3199.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.134181 restraints weight = 2194.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   2883  Z= 0.254
  Angle     :  0.808   8.596   3943  Z= 0.382
  Chirality :  0.045   0.188    486
  Planarity :  0.006   0.054    479
  Dihedral  :  7.041  52.654    467
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 19.42 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.44), residues: 385
  helix:  1.09 (0.29), residues: 332
  sheet:  None (None), residues: 0
  loop : -2.98 (0.76), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 451 
 HIS   0.002   0.001   HIS A 353 
 PHE   0.019   0.002   PHE A  27 
 TYR   0.022   0.002   TYR A 341 
 ARG   0.002   0.000   ARG A 326 

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 146
  time to evaluate  : 0.310 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7688 (tt) cc_final: 0.6936 (mp)
REVERT: A  133 LEU cc_start: 0.8402 (mm) cc_final: 0.8068 (mm)
REVERT: A  355 MET cc_start: 0.7988 (ppp) cc_final: 0.7783 (ppp)
REVERT: A  388 ASN cc_start: 0.8740 (m-40) cc_final: 0.8504 (m110)
REVERT: A  402 MET cc_start: 0.8247 (mmp) cc_final: 0.8039 (mmp)
REVERT: A  408 TYR cc_start: 0.8326 (t80) cc_final: 0.7760 (t80)
  outliers start: 9
  outliers final: 7
  residues processed: 148
  average time/residue: 0.1024
  time to fit residues: 19.1552
Evaluate side-chains
  121 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  350 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9990
   chunk 9 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0060
   chunk 13 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    1.0004

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

Flipped N/Q/H residues before XYZ refinement:
** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.144238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.125336 restraints weight = 5212.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.128920 restraints weight = 3141.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.131393 restraints weight = 2108.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.1986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   2883  Z= 0.270
  Angle     :  0.785   7.520   3943  Z= 0.376
  Chirality :  0.045   0.199    486
  Planarity :  0.005   0.041    479
  Dihedral  :  6.251  52.979    467
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 26.62 %
    Favored  : 69.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.44), residues: 385
  helix:  1.17 (0.29), residues: 332
  sheet:  None (None), residues: 0
  loop : -2.97 (0.81), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 451 
 HIS   0.002   0.001   HIS A 353 
 PHE   0.020   0.001   PHE A  27 
 TYR   0.013   0.002   TYR A 341 
 ARG   0.001   0.000   ARG A 326 

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 142
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7782 (tt) cc_final: 0.7113 (mp)
REVERT: A  133 LEU cc_start: 0.8444 (mm) cc_final: 0.8095 (mm)
REVERT: A  330 LEU cc_start: 0.7406 (mt) cc_final: 0.6798 (mt)
REVERT: A  355 MET cc_start: 0.7959 (ppp) cc_final: 0.7753 (tmm)
REVERT: A  388 ASN cc_start: 0.8779 (m-40) cc_final: 0.8485 (m110)
REVERT: A  408 TYR cc_start: 0.8311 (t80) cc_final: 0.7825 (t80)
  outliers start: 11
  outliers final: 7
  residues processed: 144
  average time/residue: 0.0998
  time to fit residues: 18.1695
Evaluate side-chains
  141 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 134
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  375 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 192 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.143936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.125477 restraints weight = 5275.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.128963 restraints weight = 3132.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.131265 restraints weight = 2102.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   2883  Z= 0.263
  Angle     :  0.795   7.261   3943  Z= 0.379
  Chirality :  0.045   0.176    486
  Planarity :  0.005   0.038    479
  Dihedral  :  5.977  52.258    467
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 27.34 %
    Favored  : 67.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.44), residues: 385
  helix:  1.24 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -2.93 (0.82), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 451 
 HIS   0.002   0.000   HIS A 353 
 PHE   0.020   0.001   PHE A  27 
 TYR   0.013   0.002   TYR A 341 
 ARG   0.001   0.000   ARG A 326 

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 139
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A   49 TYR cc_start: 0.8162 (t80) cc_final: 0.7759 (t80)
REVERT: A  124 LEU cc_start: 0.7795 (tt) cc_final: 0.7105 (mp)
REVERT: A  133 LEU cc_start: 0.8433 (mm) cc_final: 0.8074 (mm)
REVERT: A  191 LEU cc_start: 0.7949 (tt) cc_final: 0.7621 (tt)
REVERT: A  230 MET cc_start: 0.8402 (ppp) cc_final: 0.8027 (tmm)
REVERT: A  330 LEU cc_start: 0.7417 (mt) cc_final: 0.6868 (mt)
REVERT: A  388 ASN cc_start: 0.8792 (m-40) cc_final: 0.8474 (m110)
REVERT: A  408 TYR cc_start: 0.8327 (t80) cc_final: 0.7808 (t80)
REVERT: A  453 MET cc_start: 0.8357 (mmm) cc_final: 0.7878 (mmm)
  outliers start: 13
  outliers final: 10
  residues processed: 144
  average time/residue: 0.0988
  time to fit residues: 18.1211
Evaluate side-chains
  137 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 127
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  451 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 23 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 3 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0670
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
A 192 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.143935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.126362 restraints weight = 5250.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.130087 restraints weight = 3046.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.132631 restraints weight = 1984.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   2883  Z= 0.247
  Angle     :  0.824   7.997   3943  Z= 0.387
  Chirality :  0.045   0.189    486
  Planarity :  0.005   0.039    479
  Dihedral  :  5.858  51.983    467
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 30.94 %
    Favored  : 64.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.44), residues: 385
  helix:  1.24 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -2.92 (0.83), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 451 
 HIS   0.005   0.001   HIS A  53 
 PHE   0.019   0.001   PHE A  27 
 TYR   0.019   0.002   TYR A 211 
 ARG   0.002   0.000   ARG A  19 

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A   49 TYR cc_start: 0.8116 (t80) cc_final: 0.7769 (t80)
REVERT: A  191 LEU cc_start: 0.7973 (tt) cc_final: 0.7654 (tt)
REVERT: A  315 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8340 (mp)
REVERT: A  330 LEU cc_start: 0.7309 (mt) cc_final: 0.7042 (mt)
REVERT: A  408 TYR cc_start: 0.8308 (t80) cc_final: 0.7781 (t80)
REVERT: A  453 MET cc_start: 0.8315 (mmm) cc_final: 0.7893 (mmm)
  outliers start: 12
  outliers final: 10
  residues processed: 132
  average time/residue: 0.0989
  time to fit residues: 16.7084
Evaluate side-chains
  137 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 126
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  451 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 36 optimal weight:    0.3980
   chunk 21 optimal weight:    3.9990
   chunk 18 optimal weight:    0.4980
   chunk 35 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3831 r_free = 0.3831 target = 0.144475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.126655 restraints weight = 5399.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.130342 restraints weight = 3094.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.133004 restraints weight = 2019.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   2883  Z= 0.253
  Angle     :  0.830   9.589   3943  Z= 0.393
  Chirality :  0.045   0.166    486
  Planarity :  0.005   0.039    479
  Dihedral  :  5.852  51.240    467
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 32.73 %
    Favored  : 61.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.44), residues: 385
  helix:  1.20 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -2.92 (0.84), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 451 
 HIS   0.007   0.002   HIS A  53 
 PHE   0.018   0.001   PHE A  27 
 TYR   0.014   0.001   TYR A 211 
 ARG   0.001   0.000   ARG A  19 

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A  191 LEU cc_start: 0.8040 (tt) cc_final: 0.7703 (tt)
REVERT: A  315 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8351 (mp)
REVERT: A  330 LEU cc_start: 0.7247 (mt) cc_final: 0.6974 (mt)
REVERT: A  388 ASN cc_start: 0.8741 (m-40) cc_final: 0.8492 (m110)
REVERT: A  408 TYR cc_start: 0.8308 (t80) cc_final: 0.7777 (t80)
REVERT: A  453 MET cc_start: 0.8318 (mmm) cc_final: 0.7897 (mmm)
  outliers start: 17
  outliers final: 9
  residues processed: 134
  average time/residue: 0.1154
  time to fit residues: 19.7776
Evaluate side-chains
  136 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  451 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 5 optimal weight:    0.4980
   chunk 6 optimal weight:    0.6980
   chunk 33 optimal weight:    8.9990
   chunk 19 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 23 optimal weight:    0.4980
   chunk 37 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 305 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.143886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.126249 restraints weight = 5340.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.129807 restraints weight = 3094.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.132331 restraints weight = 2044.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   2883  Z= 0.259
  Angle     :  0.837   9.518   3943  Z= 0.397
  Chirality :  0.045   0.144    486
  Planarity :  0.005   0.038    479
  Dihedral  :  5.807  51.202    467
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 33.81 %
    Favored  : 60.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.44), residues: 385
  helix:  1.15 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -2.88 (0.84), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 451 
 HIS   0.005   0.001   HIS A  53 
 PHE   0.019   0.001   PHE A  27 
 TYR   0.013   0.001   TYR A  47 
 ARG   0.001   0.000   ARG A  19 

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A  133 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7869 (tp)
REVERT: A  175 MET cc_start: 0.7808 (mtp) cc_final: 0.7468 (mtp)
REVERT: A  191 LEU cc_start: 0.7986 (tt) cc_final: 0.7634 (tt)
REVERT: A  210 VAL cc_start: 0.8239 (t) cc_final: 0.8017 (t)
REVERT: A  315 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8543 (mp)
REVERT: A  327 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7777 (mtmm)
REVERT: A  330 LEU cc_start: 0.7288 (mt) cc_final: 0.7033 (mt)
REVERT: A  341 TYR cc_start: 0.8073 (t80) cc_final: 0.7689 (t80)
REVERT: A  355 MET cc_start: 0.8054 (tmm) cc_final: 0.7736 (ppp)
REVERT: A  388 ASN cc_start: 0.8741 (m-40) cc_final: 0.8467 (m110)
REVERT: A  408 TYR cc_start: 0.8314 (t80) cc_final: 0.7780 (t80)
REVERT: A  453 MET cc_start: 0.8370 (mmm) cc_final: 0.7958 (mmm)
  outliers start: 16
  outliers final: 10
  residues processed: 136
  average time/residue: 0.1055
  time to fit residues: 18.1083
Evaluate side-chains
  137 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  451 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 10 optimal weight:    7.9990
   chunk 13 optimal weight:    6.9990
   chunk 16 optimal weight:    0.1980
   chunk 19 optimal weight:   20.0000
   chunk 37 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 2 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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 = 0.3837 r_free = 0.3837 target = 0.144292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.126426 restraints weight = 5194.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.130071 restraints weight = 3013.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.132639 restraints weight = 1986.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.2882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   2883  Z= 0.254
  Angle     :  0.834  10.076   3943  Z= 0.399
  Chirality :  0.045   0.149    486
  Planarity :  0.005   0.037    479
  Dihedral  :  5.762  51.639    467
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 34.89 %
    Favored  : 60.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.44), residues: 385
  helix:  1.13 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -2.86 (0.84), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 451 
 HIS   0.004   0.001   HIS A  53 
 PHE   0.019   0.001   PHE A  27 
 TYR   0.013   0.001   TYR A  47 
 ARG   0.001   0.000   ARG A 326 

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A  133 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7879 (tp)
REVERT: A  175 MET cc_start: 0.7874 (mtp) cc_final: 0.7525 (mtp)
REVERT: A  191 LEU cc_start: 0.7964 (tt) cc_final: 0.7621 (tt)
REVERT: A  315 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8528 (mp)
REVERT: A  327 LYS cc_start: 0.8042 (ttmm) cc_final: 0.7743 (mtmm)
REVERT: A  330 LEU cc_start: 0.7258 (mt) cc_final: 0.7008 (mt)
REVERT: A  341 TYR cc_start: 0.8104 (t80) cc_final: 0.7685 (t80)
REVERT: A  388 ASN cc_start: 0.8732 (m-40) cc_final: 0.8433 (m110)
REVERT: A  408 TYR cc_start: 0.8320 (t80) cc_final: 0.7769 (t80)
REVERT: A  453 MET cc_start: 0.8400 (mmm) cc_final: 0.7959 (mmm)
  outliers start: 14
  outliers final: 12
  residues processed: 134
  average time/residue: 0.1008
  time to fit residues: 17.2237
Evaluate side-chains
  139 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  451 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 3 optimal weight:    0.4980
   chunk 23 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3855 r_free = 0.3855 target = 0.145647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.127511 restraints weight = 5206.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.131185 restraints weight = 3028.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.133724 restraints weight = 1999.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.2916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   2883  Z= 0.251
  Angle     :  0.884  14.885   3943  Z= 0.415
  Chirality :  0.046   0.162    486
  Planarity :  0.005   0.035    479
  Dihedral  :  5.743  51.877    467
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 36.69 %
    Favored  : 58.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.44), residues: 385
  helix:  1.11 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -2.89 (0.84), residues: 52

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 328 
 HIS   0.004   0.001   HIS A  53 
 PHE   0.017   0.001   PHE A  27 
 TYR   0.010   0.001   TYR A  47 
 ARG   0.001   0.001   ARG A 326 

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7812 (tt) cc_final: 0.7211 (mp)
REVERT: A  133 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8061 (mm)
REVERT: A  175 MET cc_start: 0.7882 (mtp) cc_final: 0.7550 (mtp)
REVERT: A  191 LEU cc_start: 0.7926 (tt) cc_final: 0.7563 (tt)
REVERT: A  327 LYS cc_start: 0.8003 (ttmm) cc_final: 0.7677 (mtmm)
REVERT: A  341 TYR cc_start: 0.8093 (t80) cc_final: 0.7677 (t80)
REVERT: A  388 ASN cc_start: 0.8708 (m-40) cc_final: 0.8388 (m110)
REVERT: A  408 TYR cc_start: 0.8325 (t80) cc_final: 0.7770 (t80)
REVERT: A  453 MET cc_start: 0.8355 (mmm) cc_final: 0.7943 (mmm)
  outliers start: 14
  outliers final: 11
  residues processed: 141
  average time/residue: 0.0995
  time to fit residues: 17.8175
Evaluate side-chains
  143 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   38 THR
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  451 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 19 optimal weight:    7.9990
   chunk 3 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 5 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.144899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.127019 restraints weight = 5284.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.130732 restraints weight = 3045.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.133189 restraints weight = 1988.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   2883  Z= 0.272
  Angle     :  0.908  15.203   3943  Z= 0.427
  Chirality :  0.048   0.236    486
  Planarity :  0.005   0.036    479
  Dihedral  :  5.741  51.978    467
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 38.13 %
    Favored  : 56.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.44), residues: 385
  helix:  1.06 (0.29), residues: 334
  sheet:  None (None), residues: 0
  loop : -3.03 (0.83), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 328 
 HIS   0.004   0.001   HIS A  53 
 PHE   0.022   0.001   PHE A 303 
 TYR   0.013   0.001   TYR A 341 
 ARG   0.001   0.001   ARG A 326 

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.362 
Fit side-chains
REVERT: A  133 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7902 (tp)
REVERT: A  175 MET cc_start: 0.7896 (mtp) cc_final: 0.7575 (mtp)
REVERT: A  191 LEU cc_start: 0.7962 (tt) cc_final: 0.7591 (tt)
REVERT: A  315 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8544 (mp)
REVERT: A  327 LYS cc_start: 0.8033 (ttmm) cc_final: 0.7693 (mtmm)
REVERT: A  330 LEU cc_start: 0.7244 (mt) cc_final: 0.6813 (mt)
REVERT: A  388 ASN cc_start: 0.8712 (m-40) cc_final: 0.8400 (m110)
REVERT: A  408 TYR cc_start: 0.8330 (t80) cc_final: 0.7760 (t80)
REVERT: A  453 MET cc_start: 0.8430 (mmm) cc_final: 0.7983 (mmm)
  outliers start: 14
  outliers final: 11
  residues processed: 130
  average time/residue: 0.1109
  time to fit residues: 18.6114
Evaluate side-chains
  133 residues out of total 315 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  451 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 4 optimal weight:   10.0000
   chunk 5 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 20 optimal weight:    0.1980
   chunk 3 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 13 optimal weight:    6.9990
   chunk 19 optimal weight:    9.9990
   chunk 27 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   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 = 0.3853 r_free = 0.3853 target = 0.145347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.127098 restraints weight = 5148.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.130820 restraints weight = 3010.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.133410 restraints weight = 1989.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.3095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   2883  Z= 0.262
  Angle     :  0.901  14.881   3943  Z= 0.426
  Chirality :  0.048   0.235    486
  Planarity :  0.005   0.035    479
  Dihedral  :  5.853  52.354    467
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 38.13 %
    Favored  : 57.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.44), residues: 385
  helix:  1.01 (0.29), residues: 334
  sheet:  None (None), residues: 0
  loop : -3.12 (0.82), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 328 
 HIS   0.004   0.001   HIS A  53 
 PHE   0.021   0.001   PHE A 303 
 TYR   0.013   0.001   TYR A 341 
 ARG   0.002   0.001   ARG A  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1257.80 seconds
wall clock time: 22 minutes 42.32 seconds (1362.32 seconds total)