Starting phenix.real_space_refine
on Fri Aug 22 12:59:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wlm_37624/08_2025/8wlm_37624.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wlm_37624/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wlm_37624/08_2025/8wlm_37624.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wlm_37624/08_2025/8wlm_37624.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wlm_37624/08_2025/8wlm_37624.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wlm_37624/08_2025/8wlm_37624.map"
  }
  resolution = 3.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.097
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: {'ARG:plan': 3, 'TYR:plan': 3, 'PHE:plan': 2, '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: 0.97, per 1000 atoms: 0.35
  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: 0.27
  Conformation dependent library (CDL) restraints added in 123.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.10
  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: 0.41

  Time building geometry restraints manager: 0.38 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:             0.860
  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:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.010
  Find NCS groups from input model:        0.010
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.240
-------------------------------------------------------------------------------
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= 0.201
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  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
 ARG   0.004   0.001   ARG A 155 
 TYR   0.015   0.002   TYR A 422 
 PHE   0.022   0.002   PHE A 463 
 TRP   0.002   0.000   TRP A 358 
 HIS   0.001   0.000   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 2867)
  covalent geometry    : angle       0.79790 ( 3907)
  hydrogen bonds       : bond        0.08485 (  224)
  hydrogen bonds       : angle       5.21557 (  663)

*********************** 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  : 0.078 
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: 0.0510
  time to fit residues: 6.8262
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  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0060
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.5996

-------------------------------------------------------------------------------
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 = 0.3794 r_free = 0.3794 target = 0.151423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.131551 restraints weight = 4551.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.135333 restraints weight = 2390.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.138034 restraints weight = 1505.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.139807 restraints weight = 1061.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.141113 restraints weight = 816.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2867  Z= 0.148
  Angle     :  0.685   7.710   3907  Z= 0.336
  Chirality :  0.042   0.138    477
  Planarity :  0.005   0.037    481
  Dihedral  :  6.382  62.858    401
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 16.67 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.44), residues: 378
  helix:  1.06 (0.30), residues: 314
  sheet:  None (None), residues: 0
  loop : -2.09 (0.68), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 155 
 TYR   0.018   0.001   TYR A 422 
 PHE   0.017   0.002   PHE A 348 
 TRP   0.007   0.001   TRP A 318 
 HIS   0.001   0.001   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 2867)
  covalent geometry    : angle       0.68514 ( 3907)
  hydrogen bonds       : bond        0.04069 (  224)
  hydrogen bonds       : angle       4.60584 (  663)

*********************** 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  : 0.064 
Fit side-chains
REVERT: A  166 PHE cc_start: 0.7587 (m-80) cc_final: 0.7220 (m-80)
REVERT: A  204 MET cc_start: 0.8710 (mmt) cc_final: 0.8451 (mmt)
REVERT: A  230 MET cc_start: 0.7416 (ttm) cc_final: 0.7105 (ttm)
REVERT: A  353 HIS cc_start: 0.8554 (t-170) cc_final: 0.8183 (t-170)
  outliers start: 5
  outliers final: 5
  residues processed: 101
  average time/residue: 0.0381
  time to fit residues: 5.0894
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  : 0.155 
-------------------------------------------------------------------------------
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 37 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 19 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 12 optimal weight:    0.2980
   chunk 3 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3859 r_free = 0.3859 target = 0.156598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.136652 restraints weight = 4528.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.140714 restraints weight = 2315.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.143297 restraints weight = 1427.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.145292 restraints weight = 1012.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.146468 restraints weight = 771.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.1806

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= 0.147
  Angle     :  0.679   8.268   3907  Z= 0.331
  Chirality :  0.042   0.139    477
  Planarity :  0.004   0.036    481
  Dihedral  :  6.028  58.412    401
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.44), residues: 378
  helix:  1.15 (0.30), residues: 314
  sheet:  None (None), residues: 0
  loop : -1.93 (0.71), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 155 
 TYR   0.012   0.001   TYR A 422 
 PHE   0.019   0.001   PHE A 348 
 TRP   0.005   0.001   TRP A 358 
 HIS   0.001   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 2867)
  covalent geometry    : angle       0.67867 ( 3907)
  hydrogen bonds       : bond        0.03966 (  224)
  hydrogen bonds       : angle       4.52969 (  663)

*********************** 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
  103 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.065 
Fit side-chains
REVERT: A  166 PHE cc_start: 0.7451 (m-80) cc_final: 0.7124 (m-80)
REVERT: A  204 MET cc_start: 0.8718 (mmt) cc_final: 0.8406 (mmt)
REVERT: A  230 MET cc_start: 0.7401 (ttm) cc_final: 0.7071 (ttm)
REVERT: A  335 LEU cc_start: 0.8842 (tp) cc_final: 0.8607 (tp)
REVERT: A  353 HIS cc_start: 0.8556 (t-170) cc_final: 0.8273 (t70)
  outliers start: 8
  outliers final: 4
  residues processed: 99
  average time/residue: 0.0337
  time to fit residues: 4.4177
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  : 0.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 21 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 6 optimal weight:    0.4980
   chunk 37 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 19 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   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 ** 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 = 0.3849 r_free = 0.3849 target = 0.155987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.135970 restraints weight = 4463.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.140021 restraints weight = 2291.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.142568 restraints weight = 1419.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.144442 restraints weight = 1012.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.145529 restraints weight = 783.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.2063

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= 0.151
  Angle     :  0.681   8.395   3907  Z= 0.330
  Chirality :  0.043   0.140    477
  Planarity :  0.004   0.035    481
  Dihedral  :  5.900  55.882    401
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 24.15 %
    Favored  : 72.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.44), residues: 378
  helix:  1.20 (0.30), residues: 314
  sheet:  None (None), residues: 0
  loop : -1.87 (0.72), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 155 
 TYR   0.012   0.001   TYR A 422 
 PHE   0.020   0.001   PHE A 348 
 TRP   0.004   0.001   TRP A 358 
 HIS   0.001   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 2867)
  covalent geometry    : angle       0.68100 ( 3907)
  hydrogen bonds       : bond        0.03978 (  224)
  hydrogen bonds       : angle       4.48879 (  663)

*********************** 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
  104 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A  166 PHE cc_start: 0.7451 (m-80) cc_final: 0.7161 (m-80)
REVERT: A  204 MET cc_start: 0.8730 (mmt) cc_final: 0.8418 (mmt)
REVERT: A  230 MET cc_start: 0.7403 (ttm) cc_final: 0.7090 (ttm)
REVERT: A  286 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8321 (p)
REVERT: A  353 HIS cc_start: 0.8570 (t-170) cc_final: 0.8339 (t70)
  outliers start: 9
  outliers final: 3
  residues processed: 101
  average time/residue: 0.0422
  time to fit residues: 5.6132
Evaluate side-chains
  93 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 89
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 13 optimal weight:    0.0980
   chunk 8 optimal weight:    0.5980
   chunk 28 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 18 optimal weight:    0.3980
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3856 r_free = 0.3856 target = 0.156214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.136296 restraints weight = 4428.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.140283 restraints weight = 2246.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.142850 restraints weight = 1392.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.144731 restraints weight = 992.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.145876 restraints weight = 767.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   2867  Z= 0.144
  Angle     :  0.686   8.768   3907  Z= 0.329
  Chirality :  0.043   0.145    477
  Planarity :  0.004   0.035    481
  Dihedral  :  5.855  54.902    401
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 27.21 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.45), residues: 378
  helix:  1.23 (0.30), residues: 314
  sheet:  None (None), residues: 0
  loop : -1.52 (0.78), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 155 
 TYR   0.011   0.001   TYR A 422 
 PHE   0.021   0.001   PHE A 348 
 TRP   0.004   0.001   TRP A 358 
 HIS   0.001   0.000   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 2867)
  covalent geometry    : angle       0.68631 ( 3907)
  hydrogen bonds       : bond        0.03898 (  224)
  hydrogen bonds       : angle       4.45153 (  663)

*********************** 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
  102 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A  166 PHE cc_start: 0.7531 (m-80) cc_final: 0.7253 (m-80)
REVERT: A  204 MET cc_start: 0.8700 (mmt) cc_final: 0.8379 (mmt)
REVERT: A  230 MET cc_start: 0.7385 (ttm) cc_final: 0.7083 (ttm)
REVERT: A  286 THR cc_start: 0.8569 (m) cc_final: 0.8211 (p)
REVERT: A  355 MET cc_start: 0.8179 (tmm) cc_final: 0.7714 (tmm)
REVERT: A  402 MET cc_start: 0.8364 (tpp) cc_final: 0.7966 (mmm)
REVERT: A  453 MET cc_start: 0.8945 (mmm) cc_final: 0.8567 (mmm)
  outliers start: 7
  outliers final: 3
  residues processed: 98
  average time/residue: 0.0426
  time to fit residues: 5.5388
Evaluate side-chains
  94 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 91
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 11 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.3838 r_free = 0.3838 target = 0.154673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.134584 restraints weight = 4482.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.138406 restraints weight = 2260.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.141090 restraints weight = 1402.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.142773 restraints weight = 989.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.144037 restraints weight = 779.370|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.2493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2867  Z= 0.162
  Angle     :  0.719   9.758   3907  Z= 0.342
  Chirality :  0.043   0.143    477
  Planarity :  0.004   0.036    481
  Dihedral  :  5.879  54.353    401
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 28.57 %
    Favored  : 68.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.44), residues: 378
  helix:  1.32 (0.30), residues: 308
  sheet:  None (None), residues: 0
  loop : -2.02 (0.69), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 155 
 TYR   0.012   0.001   TYR A 422 
 PHE   0.022   0.002   PHE A 348 
 TRP   0.004   0.001   TRP A 358 
 HIS   0.002   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 2867)
  covalent geometry    : angle       0.71914 ( 3907)
  hydrogen bonds       : bond        0.04029 (  224)
  hydrogen bonds       : angle       4.43650 (  663)

*********************** 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
  104 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.061 
Fit side-chains
REVERT: A   22 ILE cc_start: 0.8831 (mp) cc_final: 0.8474 (mm)
REVERT: A  166 PHE cc_start: 0.7516 (m-80) cc_final: 0.7266 (m-80)
REVERT: A  189 ARG cc_start: 0.8339 (mmt180) cc_final: 0.8088 (mmt180)
REVERT: A  204 MET cc_start: 0.8721 (mmt) cc_final: 0.8420 (mmt)
REVERT: A  230 MET cc_start: 0.7402 (ttm) cc_final: 0.7105 (ttm)
REVERT: A  286 THR cc_start: 0.8624 (m) cc_final: 0.8274 (p)
REVERT: A  346 ASN cc_start: 0.8705 (m110) cc_final: 0.8397 (m110)
REVERT: A  453 MET cc_start: 0.9006 (mmm) cc_final: 0.8769 (mmm)
  outliers start: 8
  outliers final: 6
  residues processed: 99
  average time/residue: 0.0398
  time to fit residues: 5.1460
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  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
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 0 optimal weight:    8.9990
   chunk 14 optimal weight:    0.7980
   chunk 18 optimal weight:    6.9990
   chunk 13 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0770
   chunk 7 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.6138

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.155416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.134545 restraints weight = 4456.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.138652 restraints weight = 2176.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.141452 restraints weight = 1317.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.143290 restraints weight = 915.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.144545 restraints weight = 707.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.2607

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= 0.146
  Angle     :  0.705   9.036   3907  Z= 0.334
  Chirality :  0.042   0.144    477
  Planarity :  0.004   0.037    481
  Dihedral  :  5.784  48.570    401
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 29.59 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (0.45), residues: 378
  helix:  1.26 (0.30), residues: 314
  sheet:  None (None), residues: 0
  loop : -1.81 (0.76), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 155 
 TYR   0.012   0.001   TYR A 422 
 PHE   0.032   0.002   PHE A 463 
 TRP   0.004   0.001   TRP A 358 
 HIS   0.001   0.001   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 2867)
  covalent geometry    : angle       0.70457 ( 3907)
  hydrogen bonds       : bond        0.03908 (  224)
  hydrogen bonds       : angle       4.38208 (  663)

*********************** 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
  100 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.084 
Fit side-chains
REVERT: A  166 PHE cc_start: 0.7641 (m-80) cc_final: 0.7363 (m-80)
REVERT: A  189 ARG cc_start: 0.8324 (mmt180) cc_final: 0.8046 (mmt180)
REVERT: A  204 MET cc_start: 0.8718 (mmt) cc_final: 0.8452 (mmt)
REVERT: A  230 MET cc_start: 0.7439 (ttm) cc_final: 0.7134 (ttm)
REVERT: A  286 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8305 (p)
REVERT: A  406 MET cc_start: 0.8095 (mmm) cc_final: 0.7855 (mtp)
REVERT: A  453 MET cc_start: 0.8989 (mmm) cc_final: 0.8700 (mmm)
  outliers start: 8
  outliers final: 6
  residues processed: 95
  average time/residue: 0.0407
  time to fit residues: 4.9561
Evaluate side-chains
  98 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
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  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 2 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 17 optimal weight:    0.1980
   chunk 14 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   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 = 0.3828 r_free = 0.3828 target = 0.155216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.134007 restraints weight = 4511.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.138203 restraints weight = 2197.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.141018 restraints weight = 1328.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.142829 restraints weight = 923.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.144126 restraints weight = 717.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.2655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2867  Z= 0.148
  Angle     :  0.719   8.932   3907  Z= 0.342
  Chirality :  0.043   0.163    477
  Planarity :  0.004   0.037    481
  Dihedral  :  5.869  49.519    401
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 28.57 %
    Favored  : 68.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.45), residues: 378
  helix:  1.25 (0.30), residues: 314
  sheet:  None (None), residues: 0
  loop : -1.86 (0.76), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 155 
 TYR   0.011   0.001   TYR A 422 
 PHE   0.027   0.002   PHE A 463 
 TRP   0.004   0.001   TRP A 358 
 HIS   0.002   0.001   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 2867)
  covalent geometry    : angle       0.71892 ( 3907)
  hydrogen bonds       : bond        0.03876 (  224)
  hydrogen bonds       : angle       4.36627 (  663)

*********************** 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
  102 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.074 
Fit side-chains
REVERT: A  166 PHE cc_start: 0.7703 (m-80) cc_final: 0.7473 (m-80)
REVERT: A  189 ARG cc_start: 0.8316 (mmt180) cc_final: 0.7928 (mmt180)
REVERT: A  204 MET cc_start: 0.8721 (mmt) cc_final: 0.8497 (mmt)
REVERT: A  230 MET cc_start: 0.7402 (ttm) cc_final: 0.7118 (ttm)
REVERT: A  286 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8304 (p)
REVERT: A  355 MET cc_start: 0.8244 (tmm) cc_final: 0.7710 (tmm)
  outliers start: 8
  outliers final: 6
  residues processed: 98
  average time/residue: 0.0392
  time to fit residues: 4.9686
Evaluate side-chains
  101 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 94
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
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  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 1 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 18 optimal weight:    6.9990
   chunk 0 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0040
   chunk 19 optimal weight:    0.4980
   chunk 29 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.5192

-------------------------------------------------------------------------------
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 = 0.3835 r_free = 0.3835 target = 0.156026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.134768 restraints weight = 4581.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.138991 restraints weight = 2228.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.141804 restraints weight = 1345.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.143683 restraints weight = 937.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.144818 restraints weight = 723.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.2768

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= 0.140
  Angle     :  0.701   9.006   3907  Z= 0.331
  Chirality :  0.042   0.148    477
  Planarity :  0.004   0.037    481
  Dihedral  :  5.987  51.258    401
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 29.25 %
    Favored  : 68.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.45), residues: 378
  helix:  1.24 (0.30), residues: 314
  sheet:  None (None), residues: 0
  loop : -1.82 (0.77), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 155 
 TYR   0.009   0.001   TYR A 422 
 PHE   0.026   0.002   PHE A 463 
 TRP   0.003   0.001   TRP A 358 
 HIS   0.001   0.000   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 2867)
  covalent geometry    : angle       0.70093 ( 3907)
  hydrogen bonds       : bond        0.03793 (  224)
  hydrogen bonds       : angle       4.36535 (  663)

*********************** 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
  101 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 0.101 
Fit side-chains
REVERT: A  166 PHE cc_start: 0.7768 (m-80) cc_final: 0.7558 (m-80)
REVERT: A  189 ARG cc_start: 0.8270 (mmt180) cc_final: 0.7909 (mmt180)
REVERT: A  204 MET cc_start: 0.8758 (mmt) cc_final: 0.8462 (mmt)
REVERT: A  230 MET cc_start: 0.7375 (ttm) cc_final: 0.7102 (ttm)
REVERT: A  286 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8306 (p)
REVERT: A  341 TYR cc_start: 0.8545 (t80) cc_final: 0.8242 (t80)
REVERT: A  355 MET cc_start: 0.8245 (tmm) cc_final: 0.7735 (tmm)
  outliers start: 6
  outliers final: 4
  residues processed: 98
  average time/residue: 0.0398
  time to fit residues: 5.0694
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  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 28 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 36 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3825 r_free = 0.3825 target = 0.154698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.133750 restraints weight = 4559.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.137975 restraints weight = 2185.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.140678 restraints weight = 1315.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.142568 restraints weight = 921.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.143435 restraints weight = 711.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.2829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2867  Z= 0.151
  Angle     :  0.723   8.990   3907  Z= 0.342
  Chirality :  0.043   0.143    477
  Planarity :  0.004   0.037    481
  Dihedral  :  6.050  52.243    401
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.45), residues: 378
  helix:  1.15 (0.30), residues: 317
  sheet:  None (None), residues: 0
  loop : -1.72 (0.79), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 155 
 TYR   0.014   0.001   TYR A 422 
 PHE   0.031   0.002   PHE A 463 
 TRP   0.004   0.001   TRP A 358 
 HIS   0.002   0.001   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 2867)
  covalent geometry    : angle       0.72321 ( 3907)
  hydrogen bonds       : bond        0.03891 (  224)
  hydrogen bonds       : angle       4.36526 (  663)

********************** 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
  98 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A  204 MET cc_start: 0.8782 (mmt) cc_final: 0.8485 (mmt)
REVERT: A  230 MET cc_start: 0.7384 (ttm) cc_final: 0.7117 (ttm)
REVERT: A  286 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8362 (p)
REVERT: A  341 TYR cc_start: 0.8541 (t80) cc_final: 0.8065 (t80)
  outliers start: 6
  outliers final: 5
  residues processed: 95
  average time/residue: 0.0437
  time to fit residues: 5.3682
Evaluate side-chains
  98 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
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 27 optimal weight:    0.8980
   chunk 14 optimal weight:    0.4980
   chunk 36 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.3980
   chunk 17 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0770
   chunk 18 optimal weight:    0.0170
   chunk 15 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.3376

-------------------------------------------------------------------------------
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 = 0.3861 r_free = 0.3861 target = 0.158084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.137368 restraints weight = 4473.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.141691 restraints weight = 2151.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.144457 restraints weight = 1281.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.146295 restraints weight = 885.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.147562 restraints weight = 679.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
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      :  0.003   0.028   2867  Z= 0.137
  Angle     :  0.702   9.701   3907  Z= 0.330
  Chirality :  0.042   0.144    477
  Planarity :  0.004   0.038    481
  Dihedral  :  6.024  52.692    401
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 29.59 %
    Favored  : 68.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.45), residues: 378
  helix:  1.26 (0.30), residues: 312
  sheet:  None (None), residues: 0
  loop : -1.51 (0.79), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 155 
 TYR   0.011   0.001   TYR A 422 
 PHE   0.030   0.002   PHE A 463 
 TRP   0.003   0.000   TRP A 318 
 HIS   0.001   0.000   HIS A 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 2867)
  covalent geometry    : angle       0.70188 ( 3907)
  hydrogen bonds       : bond        0.03691 (  224)
  hydrogen bonds       : angle       4.33377 (  663)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 712.39 seconds
wall clock time: 12 minutes 48.25 seconds (768.25 seconds total)