Starting phenix.real_space_refine
on Wed Mar  5 16:37:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wlm_37624/03_2025/8wlm_37624.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wlm_37624/03_2025/8wlm_37624.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wlm_37624/03_2025/8wlm_37624.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wlm_37624/03_2025/8wlm_37624.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wlm_37624/03_2025/8wlm_37624.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wlm_37624/03_2025/8wlm_37624.cif"
  }
  resolution = 3.57
  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=  -0.001 sd=   0.097
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    1860      2.51       5
     N     436      2.21       5
     O     480      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 2804
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 2791
          Classifications: {'peptide': 382}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 23, 'TRANS': 358}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 84
          Unresolved non-hydrogen angles: 105
          Unresolved non-hydrogen dihedrals: 83
          Planarities with less than four sites: {'TYR:plan': 3, 'PHE:plan': 2, 'ARG:plan': 3, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 57
    Chain: "A"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 13
          Unusual residues: {'SRO': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.47, per 1000 atoms: 0.88
  Number of scatterers: 2804
  At special positions: 0
  Unit cell: (68.968, 66.172, 68.968, 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     480      8.00
     N     436      7.00
     C    1860      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: 0.75
  Conformation dependent library (CDL) restraints added in 319.9 milliseconds
  

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  688

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 0 sheets defined
      88.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 50
      removed outlier: 3.606A  pdb=" N   ILE A  22 " --> pdb=" O   SER A  18 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   LEU A  23 " --> pdb=" O   ARG A  19 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 5.020A  pdb=" N   VAL A  41 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      Proline residue:  A  42  - end of helix
      Proline residue:  A  45  - end of helix
    Processing helix  chain 'A' and resid 132 through 156
      Proline residue:  A 147  - end of helix
      removed outlier: 3.882A  pdb=" N   ASN A 154 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 178
      removed outlier: 3.655A  pdb=" N   ILE A 162 " --> pdb=" O   TYR A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 211
    Processing helix  chain 'A' and resid 213 through 246
      removed outlier: 3.895A  pdb=" N   GLY A 227 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   LEU A 228 " --> pdb=" O   ALA A 224 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   ALA A 229 " --> pdb=" O   LEU A 225 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   VAL A 232 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
      Proline residue:  A 236  - end of helix
      removed outlier: 3.822A  pdb=" N   VAL A 246 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 265
      removed outlier: 3.602A  pdb=" N   ILE A 265 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 289
      removed outlier: 3.590A  pdb=" N   LEU A 288 " --> pdb=" O   PRO A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 315
      removed outlier: 3.695A  pdb=" N   ILE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      Proline residue:  A 313  - end of helix
    Processing helix  chain 'A' and resid 315 through 320
      removed outlier: 4.027A  pdb=" N   MET A 320 " --> pdb=" O   PRO A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 356
      removed outlier: 4.574A  pdb=" N   GLY A 331 " --> pdb=" O   LYS A 327 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   VAL A 332 " --> pdb=" O   TRP A 328 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   PHE A 334 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
      Proline residue:  A 336  - end of helix
      removed outlier: 3.881A  pdb=" N   ILE A 339 " --> pdb=" O   LEU A 335 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLY A 349 " --> pdb=" O   THR A 345 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   ILE A 350 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
      removed outlier: 5.286A  pdb=" N   HIS A 353 " --> pdb=" O   GLY A 349 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   LYS A 354 " --> pdb=" O   ILE A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 375
    Processing helix  chain 'A' and resid 381 through 414
      removed outlier: 4.277A  pdb=" N   ALA A 386 " --> pdb=" O   TYR A 382 " (cutoff:3.500A)
      Proline residue:  A 387  - end of helix
      Proline residue:  A 404  - end of helix
      removed outlier: 4.102A  pdb=" N   GLY A 407 " --> pdb=" O   MET A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 436
    Processing helix  chain 'A' and resid 436 through 447
    Processing helix  chain 'A' and resid 448 through 464
    Processing helix  chain 'A' and resid 465 through 472
      removed outlier: 3.625A  pdb=" N   PHE A 469 " --> pdb=" O   LEU A 466 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   SER A 472 " --> pdb=" O   PHE A 469 " (cutoff:3.500A)

    224 hydrogen bonds defined for protein.
    663 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: 0.78

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 827
        1.34 -     1.46: 386
        1.46 -     1.57: 1606
        1.57 -     1.69: 0
        1.69 -     1.81: 48
  Bond restraints: 2867
  Sorted by residual:
  bond pdb=" CA  SRO A 501 "
       pdb=" NZ  SRO A 501 "
    ideal  model  delta    sigma   weight residual
    1.469  1.415  0.054 2.00e-02 2.50e+03 7.38e+00
  bond pdb=" CD2 SRO A 501 "
       pdb=" CE2 SRO A 501 "
    ideal  model  delta    sigma   weight residual
    1.419  1.368  0.051 2.00e-02 2.50e+03 6.55e+00
  bond pdb=" CA  SRO A 501 "
       pdb=" CB  SRO A 501 "
    ideal  model  delta    sigma   weight residual
    1.524  1.569 -0.045 2.00e-02 2.50e+03 5.01e+00
  bond pdb=" CZ3 SRO A 501 "
       pdb=" CH2 SRO A 501 "
    ideal  model  delta    sigma   weight residual
    1.407  1.375  0.032 2.00e-02 2.50e+03 2.55e+00
  bond pdb=" C   VAL A  41 "
       pdb=" N   PRO A  42 "
    ideal  model  delta    sigma   weight residual
    1.337  1.352 -0.016 1.06e-02 8.90e+03 2.17e+00
  ... (remaining 2862 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 3769
        1.81 -     3.62: 102
        3.62 -     5.43: 26
        5.43 -     7.23: 8
        7.23 -     9.04: 2
  Bond angle restraints: 3907
  Sorted by residual:
  angle pdb=" CB  MET A 402 "
        pdb=" CG  MET A 402 "
        pdb=" SD  MET A 402 "
      ideal   model   delta    sigma   weight residual
     112.70  103.66    9.04 3.00e+00 1.11e-01 9.08e+00
  angle pdb=" C   ILE A 265 "
        pdb=" N   GLN A 266 "
        pdb=" CA  GLN A 266 "
      ideal   model   delta    sigma   weight residual
     121.54  126.82   -5.28 1.91e+00 2.74e-01 7.64e+00
  angle pdb=" CA  PRO A 236 "
        pdb=" C   PRO A 236 "
        pdb=" N   PRO A 237 "
      ideal   model   delta    sigma   weight residual
     117.93  121.20   -3.27 1.20e+00 6.94e-01 7.43e+00
  angle pdb=" CA  MET A 402 "
        pdb=" CB  MET A 402 "
        pdb=" CG  MET A 402 "
      ideal   model   delta    sigma   weight residual
     114.10  119.29   -5.19 2.00e+00 2.50e-01 6.72e+00
  angle pdb=" N   PRO A 236 "
        pdb=" CA  PRO A 236 "
        pdb=" C   PRO A 236 "
      ideal   model   delta    sigma   weight residual
     110.70  113.80   -3.10 1.22e+00 6.72e-01 6.45e+00
  ... (remaining 3902 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.32: 1519
       17.32 -    34.65: 119
       34.65 -    51.97: 36
       51.97 -    69.29: 4
       69.29 -    86.61: 4
  Dihedral angle restraints: 1682
    sinusoidal: 604
      harmonic: 1078
  Sorted by residual:
  dihedral pdb=" CA  MET A 402 "
           pdb=" C   MET A 402 "
           pdb=" N   MET A 403 "
           pdb=" CA  MET A 403 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.09   16.91     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CB  GLU A 244 "
           pdb=" CG  GLU A 244 "
           pdb=" CD  GLU A 244 "
           pdb=" OE1 GLU A 244 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.61  -86.61     1      3.00e+01 1.11e-03 1.00e+01
  dihedral pdb=" CB  GLU A 312 "
           pdb=" CG  GLU A 312 "
           pdb=" CD  GLU A 312 "
           pdb=" OE1 GLU A 312 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -77.86   77.86     1      3.00e+01 1.11e-03 8.42e+00
  ... (remaining 1679 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 278
       0.031 -    0.062: 116
       0.062 -    0.093: 49
       0.093 -    0.123: 25
       0.123 -    0.154: 9
  Chirality restraints: 477
  Sorted by residual:
  chirality pdb=" CA  PHE A 348 "
            pdb=" N   PHE A 348 "
            pdb=" C   PHE A 348 "
            pdb=" CB  PHE A 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.95e-01
  chirality pdb=" CA  THR A 322 "
            pdb=" N   THR A 322 "
            pdb=" C   THR A 322 "
            pdb=" CB  THR A 322 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.15 2.00e-01 2.50e+01 5.37e-01
  chirality pdb=" CA  CYS A 430 "
            pdb=" N   CYS A 430 "
            pdb=" C   CYS A 430 "
            pdb=" CB  CYS A 430 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.19e-01
  ... (remaining 474 not shown)

  Planarity restraints: 481
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 348 "    0.007 2.00e-02 2.50e+03   1.48e-02 2.19e+00
        pdb=" C   PHE A 348 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   PHE A 348 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLY A 349 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 449 "    0.024 5.00e-02 4.00e+02   3.58e-02 2.05e+00
        pdb=" N   PRO A 450 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A 450 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 450 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 265 "    0.007 2.00e-02 2.50e+03   1.34e-02 1.79e+00
        pdb=" C   ILE A 265 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   ILE A 265 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLN A 266 "    0.008 2.00e-02 2.50e+03
  ... (remaining 478 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 240
        2.74 -     3.28: 3112
        3.28 -     3.82: 4822
        3.82 -     4.36: 5261
        4.36 -     4.90: 9305
  Nonbonded interactions: 22740
  Sorted by model distance:
  nonbonded pdb=" O   MET A 175 "
            pdb=" OG  SER A 179 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OE2 GLU A 215 "
            pdb=" ND1 HIS A 353 "
     model   vdw
     2.424 3.120
  nonbonded pdb=" O   ILE A 301 "
            pdb=" ND2 ASN A 305 "
     model   vdw
     2.426 3.120
  nonbonded pdb=" OD2 ASP A 291 "
            pdb=" NH1 ARG A 413 "
     model   vdw
     2.464 3.120
  nonbonded pdb=" O   SER A 472 "
            pdb=" OG  SER A 472 "
     model   vdw
     2.501 3.040
  ... (remaining 22735 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:             0.570
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.190
  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:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   2867  Z= 0.279
  Angle     :  0.798   9.042   3907  Z= 0.391
  Chirality :  0.046   0.154    477
  Planarity :  0.005   0.036    481
  Dihedral  : 14.404  86.614    994
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  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:  0.52 (0.43), residues: 378
  helix:  0.86 (0.30), residues: 310
  sheet:  None (None), residues: 0
  loop : -1.79 (0.72), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 358 
 HIS   0.001   0.000   HIS A 414 
 PHE   0.022   0.002   PHE A 463 
 TYR   0.015   0.002   TYR A 422 
 ARG   0.004   0.001   ARG A 155 

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A  166 PHE cc_start: 0.7621 (m-80) cc_final: 0.7236 (m-80)
REVERT: A  194 ILE cc_start: 0.8531 (mm) cc_final: 0.8160 (mm)
REVERT: A  198 CYS cc_start: 0.8432 (p) cc_final: 0.8164 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1243
  time to fit residues: 16.4007
Evaluate side-chains
  93 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 15 optimal weight:    7.9990
   chunk 9 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0020
   chunk 34 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.6188

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

Flipped N/Q/H residues before XYZ refinement:
** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.151436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.131551 restraints weight = 4564.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.135441 restraints weight = 2399.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.138074 restraints weight = 1501.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2867  Z= 0.207
  Angle     :  0.685   7.805   3907  Z= 0.337
  Chirality :  0.042   0.138    477
  Planarity :  0.005   0.034    481
  Dihedral  :  6.402  63.195    401
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 17.01 %
    Favored  : 81.29 %
  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: 378
  helix:  1.06 (0.30), residues: 314
  sheet:  None (None), residues: 0
  loop : -2.08 (0.68), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 318 
 HIS   0.001   0.001   HIS A 353 
 PHE   0.017   0.001   PHE A 348 
 TYR   0.017   0.001   TYR A 422 
 ARG   0.005   0.001   ARG A 155 

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  166 PHE cc_start: 0.7589 (m-80) cc_final: 0.7231 (m-80)
REVERT: A  204 MET cc_start: 0.8736 (mmt) cc_final: 0.8472 (mmt)
REVERT: A  230 MET cc_start: 0.7400 (ttm) cc_final: 0.7089 (ttm)
REVERT: A  286 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8295 (p)
REVERT: A  353 HIS cc_start: 0.8565 (t-170) cc_final: 0.8185 (t-170)
  outliers start: 5
  outliers final: 4
  residues processed: 101
  average time/residue: 0.0881
  time to fit residues: 11.6336
Evaluate side-chains
  97 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  286 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 5 optimal weight:    0.0980
   chunk 14 optimal weight:    0.8980
   chunk 32 optimal weight:    0.3980
   chunk 19 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0020
   chunk 1 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.3588

-------------------------------------------------------------------------------
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**
** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.154525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.134275 restraints weight = 4476.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.138251 restraints weight = 2365.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.140975 restraints weight = 1486.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2867  Z= 0.192
  Angle     :  0.676   8.127   3907  Z= 0.328
  Chirality :  0.042   0.137    477
  Planarity :  0.004   0.036    481
  Dihedral  :  6.040  58.720    401
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 21.77 %
    Favored  : 75.51 %
  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:  0.99 (0.44), residues: 378
  helix:  1.18 (0.30), residues: 312
  sheet:  None (None), residues: 0
  loop : -1.72 (0.72), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 318 
 HIS   0.001   0.000   HIS A 353 
 PHE   0.019   0.001   PHE A 348 
 TYR   0.010   0.001   TYR A 422 
 ARG   0.006   0.001   ARG A 155 

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A  166 PHE cc_start: 0.7445 (m-80) cc_final: 0.7153 (m-80)
REVERT: A  204 MET cc_start: 0.8687 (mmt) cc_final: 0.8406 (mmt)
REVERT: A  230 MET cc_start: 0.7381 (ttm) cc_final: 0.7046 (ttm)
REVERT: A  353 HIS cc_start: 0.8544 (t-170) cc_final: 0.8295 (t70)
REVERT: A  355 MET cc_start: 0.8134 (tmm) cc_final: 0.7619 (tmm)
REVERT: A  468 PHE cc_start: 0.8449 (t80) cc_final: 0.8050 (t80)
  outliers start: 8
  outliers final: 5
  residues processed: 100
  average time/residue: 0.0915
  time to fit residues: 11.8487
Evaluate side-chains
  98 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 93
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  427 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   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 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.158086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.138527 restraints weight = 4459.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.142470 restraints weight = 2287.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.145202 restraints weight = 1420.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2867  Z= 0.204
  Angle     :  0.677   8.337   3907  Z= 0.328
  Chirality :  0.042   0.139    477
  Planarity :  0.004   0.037    481
  Dihedral  :  5.907  56.130    401
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 24.15 %
    Favored  : 72.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.44), residues: 378
  helix:  1.17 (0.30), residues: 314
  sheet:  None (None), residues: 0
  loop : -1.90 (0.72), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 358 
 HIS   0.001   0.001   HIS A 353 
 PHE   0.019   0.001   PHE A 348 
 TYR   0.010   0.001   TYR A 422 
 ARG   0.006   0.001   ARG A 155 

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A  166 PHE cc_start: 0.7451 (m-80) cc_final: 0.7204 (m-80)
REVERT: A  204 MET cc_start: 0.8721 (mmt) cc_final: 0.8411 (mmt)
REVERT: A  230 MET cc_start: 0.7376 (ttm) cc_final: 0.7072 (ttm)
REVERT: A  335 LEU cc_start: 0.8817 (tp) cc_final: 0.8609 (tp)
REVERT: A  346 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.8271 (m110)
REVERT: A  353 HIS cc_start: 0.8611 (t-170) cc_final: 0.8377 (t70)
REVERT: A  355 MET cc_start: 0.8221 (tmm) cc_final: 0.7736 (tmm)
REVERT: A  453 MET cc_start: 0.8911 (mmm) cc_final: 0.8600 (mmm)
  outliers start: 10
  outliers final: 6
  residues processed: 102
  average time/residue: 0.0947
  time to fit residues: 12.5171
Evaluate side-chains
  97 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  346 ASN
Chi-restraints excluded: chain A residue  427 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 9 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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**
A 219 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.159010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.139069 restraints weight = 4448.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.143159 restraints weight = 2259.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.145740 restraints weight = 1387.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   2867  Z= 0.215
  Angle     :  0.688   8.840   3907  Z= 0.333
  Chirality :  0.043   0.155    477
  Planarity :  0.004   0.035    481
  Dihedral  :  5.862  54.736    401
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 25.51 %
    Favored  : 71.43 %
  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:  0.92 (0.44), residues: 378
  helix:  1.09 (0.30), residues: 314
  sheet:  None (None), residues: 0
  loop : -1.57 (0.76), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 358 
 HIS   0.001   0.001   HIS A 353 
 PHE   0.021   0.002   PHE A 463 
 TYR   0.011   0.001   TYR A 422 
 ARG   0.007   0.001   ARG A 155 

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A  166 PHE cc_start: 0.7378 (m-80) cc_final: 0.7127 (m-80)
REVERT: A  204 MET cc_start: 0.8669 (mmt) cc_final: 0.8390 (mmt)
REVERT: A  230 MET cc_start: 0.7383 (ttm) cc_final: 0.7094 (ttm)
REVERT: A  286 THR cc_start: 0.8586 (m) cc_final: 0.8230 (p)
REVERT: A  310 MET cc_start: 0.8533 (mmm) cc_final: 0.8276 (mmm)
REVERT: A  353 HIS cc_start: 0.8604 (t-170) cc_final: 0.8385 (t70)
REVERT: A  355 MET cc_start: 0.8214 (tmm) cc_final: 0.7599 (tmm)
REVERT: A  365 MET cc_start: 0.7789 (mmm) cc_final: 0.7518 (mmm)
REVERT: A  402 MET cc_start: 0.8380 (tpp) cc_final: 0.8089 (mmm)
REVERT: A  453 MET cc_start: 0.8874 (mmm) cc_final: 0.8555 (mmm)
  outliers start: 9
  outliers final: 4
  residues processed: 99
  average time/residue: 0.1018
  time to fit residues: 13.1602
Evaluate side-chains
  96 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  427 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 15 optimal weight:    0.2980
   chunk 10 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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**
A 219 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.157858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.137846 restraints weight = 4538.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.141857 restraints weight = 2306.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.144420 restraints weight = 1430.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2867  Z= 0.219
  Angle     :  0.709   9.910   3907  Z= 0.335
  Chirality :  0.043   0.139    477
  Planarity :  0.004   0.036    481
  Dihedral  :  5.858  54.286    401
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 27.55 %
    Favored  : 70.41 %
  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:  1.05 (0.44), residues: 378
  helix:  1.29 (0.30), residues: 306
  sheet:  None (None), residues: 0
  loop : -1.77 (0.71), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 358 
 HIS   0.003   0.001   HIS A 414 
 PHE   0.022   0.002   PHE A 463 
 TYR   0.012   0.001   TYR A 422 
 ARG   0.007   0.001   ARG A 155 

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A   22 ILE cc_start: 0.8775 (mp) cc_final: 0.8412 (mm)
REVERT: A  166 PHE cc_start: 0.7473 (m-80) cc_final: 0.7255 (m-80)
REVERT: A  189 ARG cc_start: 0.8331 (mmt180) cc_final: 0.8084 (mmt180)
REVERT: A  204 MET cc_start: 0.8699 (mmt) cc_final: 0.8385 (mmt)
REVERT: A  230 MET cc_start: 0.7395 (ttm) cc_final: 0.7110 (ttm)
REVERT: A  286 THR cc_start: 0.8649 (m) cc_final: 0.8301 (p)
REVERT: A  353 HIS cc_start: 0.8583 (t-170) cc_final: 0.8351 (t70)
  outliers start: 6
  outliers final: 5
  residues processed: 97
  average time/residue: 0.1153
  time to fit residues: 14.0854
Evaluate side-chains
  98 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 93
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  427 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 18 optimal weight:    7.9990
   chunk 33 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 36 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 2 optimal weight:    7.9990
   chunk 12 optimal weight:    0.2980
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3827 r_free = 0.3827 target = 0.155156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.134322 restraints weight = 4616.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.138484 restraints weight = 2232.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.141158 restraints weight = 1332.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.2572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2867  Z= 0.210
  Angle     :  0.709   8.954   3907  Z= 0.337
  Chirality :  0.043   0.138    477
  Planarity :  0.004   0.036    481
  Dihedral  :  5.717  46.814    401
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 27.89 %
    Favored  : 69.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.44), residues: 378
  helix:  1.15 (0.30), residues: 312
  sheet:  None (None), residues: 0
  loop : -1.54 (0.77), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 358 
 HIS   0.001   0.001   HIS A 353 
 PHE   0.022   0.002   PHE A 463 
 TYR   0.012   0.001   TYR A 422 
 ARG   0.008   0.001   ARG A 155 

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A  166 PHE cc_start: 0.7573 (m-80) cc_final: 0.7342 (m-80)
REVERT: A  189 ARG cc_start: 0.8302 (mmt180) cc_final: 0.8050 (mmt180)
REVERT: A  204 MET cc_start: 0.8751 (mmt) cc_final: 0.8431 (mmt)
REVERT: A  230 MET cc_start: 0.7414 (ttm) cc_final: 0.7126 (ttm)
REVERT: A  286 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8309 (p)
REVERT: A  355 MET cc_start: 0.8223 (tmm) cc_final: 0.7684 (tmm)
  outliers start: 7
  outliers final: 5
  residues processed: 98
  average time/residue: 0.0947
  time to fit residues: 11.9171
Evaluate side-chains
  97 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  427 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0970
   chunk 14 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0980
   chunk 22 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.4578

-------------------------------------------------------------------------------
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 = 0.3846 r_free = 0.3846 target = 0.157033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.135932 restraints weight = 4497.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.140195 restraints weight = 2189.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.142977 restraints weight = 1320.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2867  Z= 0.190
  Angle     :  0.719   8.987   3907  Z= 0.341
  Chirality :  0.043   0.180    477
  Planarity :  0.004   0.037    481
  Dihedral  :  5.815  47.619    401
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 28.23 %
    Favored  : 69.73 %
  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:  1.10 (0.45), residues: 378
  helix:  1.24 (0.30), residues: 312
  sheet:  None (None), residues: 0
  loop : -1.57 (0.77), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 358 
 HIS   0.004   0.002   HIS A 353 
 PHE   0.022   0.001   PHE A 348 
 TYR   0.010   0.001   TYR A 422 
 ARG   0.007   0.001   ARG A 155 

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A  166 PHE cc_start: 0.7679 (m-80) cc_final: 0.7464 (m-80)
REVERT: A  189 ARG cc_start: 0.8271 (mmt180) cc_final: 0.8008 (mmt180)
REVERT: A  204 MET cc_start: 0.8745 (mmt) cc_final: 0.8468 (mmt)
REVERT: A  230 MET cc_start: 0.7339 (ttm) cc_final: 0.7071 (ttm)
REVERT: A  286 THR cc_start: 0.8644 (m) cc_final: 0.8305 (p)
REVERT: A  355 MET cc_start: 0.8203 (tmm) cc_final: 0.7698 (tmm)
REVERT: A  406 MET cc_start: 0.8072 (mmm) cc_final: 0.7860 (mtp)
  outliers start: 6
  outliers final: 5
  residues processed: 100
  average time/residue: 0.1001
  time to fit residues: 12.8346
Evaluate side-chains
  99 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  427 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0770
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.5538

-------------------------------------------------------------------------------
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**
A 353 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.157575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.136815 restraints weight = 4449.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.141042 restraints weight = 2158.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.143874 restraints weight = 1297.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.2762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2867  Z= 0.200
  Angle     :  0.710   9.282   3907  Z= 0.337
  Chirality :  0.042   0.144    477
  Planarity :  0.004   0.037    481
  Dihedral  :  5.958  50.530    401
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 30.27 %
    Favored  : 67.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.04 (0.45), residues: 378
  helix:  1.21 (0.30), residues: 312
  sheet:  None (None), residues: 0
  loop : -1.63 (0.78), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 358 
 HIS   0.001   0.001   HIS A 414 
 PHE   0.036   0.002   PHE A 463 
 TYR   0.011   0.001   TYR A 422 
 ARG   0.007   0.001   ARG A 155 

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A  166 PHE cc_start: 0.7681 (m-80) cc_final: 0.7476 (m-80)
REVERT: A  189 ARG cc_start: 0.8287 (mmt180) cc_final: 0.8040 (mmt180)
REVERT: A  204 MET cc_start: 0.8733 (mmt) cc_final: 0.8454 (mmt)
REVERT: A  230 MET cc_start: 0.7328 (ttm) cc_final: 0.7059 (ttm)
REVERT: A  286 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8315 (p)
REVERT: A  355 MET cc_start: 0.8238 (tmm) cc_final: 0.7718 (tmm)
REVERT: A  406 MET cc_start: 0.8090 (mmm) cc_final: 0.7861 (mtp)
  outliers start: 6
  outliers final: 5
  residues processed: 98
  average time/residue: 0.1075
  time to fit residues: 13.4086
Evaluate side-chains
  97 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  427 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 24 optimal weight:    0.4980
   chunk 22 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 3 optimal weight:    0.1980
   chunk 33 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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**
A 353 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.156846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.135754 restraints weight = 4511.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.139951 restraints weight = 2205.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.142771 restraints weight = 1341.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   2867  Z= 0.210
  Angle     :  0.718   9.198   3907  Z= 0.344
  Chirality :  0.043   0.145    477
  Planarity :  0.004   0.037    481
  Dihedral  :  6.097  52.750    401
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 30.95 %
    Favored  : 67.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.44), residues: 378
  helix:  1.09 (0.30), residues: 311
  sheet:  None (None), residues: 0
  loop : -1.54 (0.77), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 358 
 HIS   0.001   0.000   HIS A 414 
 PHE   0.037   0.002   PHE A 463 
 TYR   0.010   0.001   TYR A 422 
 ARG   0.006   0.001   ARG A 155 

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A  189 ARG cc_start: 0.8313 (mmt180) cc_final: 0.8062 (mmt180)
REVERT: A  204 MET cc_start: 0.8757 (mmt) cc_final: 0.8479 (mmt)
REVERT: A  230 MET cc_start: 0.7334 (ttm) cc_final: 0.7063 (ttm)
REVERT: A  286 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8305 (p)
REVERT: A  341 TYR cc_start: 0.8623 (t80) cc_final: 0.8281 (t80)
REVERT: A  355 MET cc_start: 0.8282 (tmm) cc_final: 0.7734 (tmm)
REVERT: A  402 MET cc_start: 0.8466 (tpp) cc_final: 0.7891 (mmm)
REVERT: A  406 MET cc_start: 0.8085 (mmm) cc_final: 0.7815 (mtp)
  outliers start: 5
  outliers final: 4
  residues processed: 98
  average time/residue: 0.1013
  time to fit residues: 12.7431
Evaluate side-chains
  96 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  209 SER
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  295 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 0 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 23 optimal weight:    0.3980
   chunk 8 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   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 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 353 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.156812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.135908 restraints weight = 4430.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.140046 restraints weight = 2184.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.142896 restraints weight = 1331.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.2912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2867  Z= 0.213
  Angle     :  0.722   9.211   3907  Z= 0.344
  Chirality :  0.043   0.144    477
  Planarity :  0.004   0.037    481
  Dihedral  :  6.104  52.865    401
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 30.27 %
    Favored  : 68.03 %
  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 (0.45), residues: 378
  helix:  1.10 (0.30), residues: 313
  sheet:  None (None), residues: 0
  loop : -1.71 (0.77), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 358 
 HIS   0.001   0.001   HIS A 414 
 PHE   0.033   0.002   PHE A 463 
 TYR   0.011   0.001   TYR A 422 
 ARG   0.006   0.001   ARG A 155 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1276.19 seconds
wall clock time: 22 minutes 58.10 seconds (1378.10 seconds total)