Starting phenix.real_space_refine
on Tue Mar  3 13:14:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y4s_33606/03_2026/7y4s_33606.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y4s_33606/03_2026/7y4s_33606.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y4s_33606/03_2026/7y4s_33606.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y4s_33606/03_2026/7y4s_33606.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y4s_33606/03_2026/7y4s_33606.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y4s_33606/03_2026/7y4s_33606.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.097
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      12      5.16       5
     C    3126      2.51       5
     N     912      2.21       5
     O     890      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4940
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2470
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2470
          Classifications: {'peptide': 343}
          Incomplete info: {'truncation_to_alanine': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 319}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 264
          Unresolved non-hydrogen angles: 324
          Unresolved non-hydrogen dihedrals: 214
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 6, 'GLN:plan1': 9, 'GLU:plan': 13, 'ASN:plan1': 1, 'TYR:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 149
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.53, per 1000 atoms: 0.31
  Number of scatterers: 4940
  At special positions: 0
  Unit cell: (103.455, 176.605, 83.6, 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      12     16.00
     O     890      8.00
     N     912      7.00
     C    3126      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: 0.30
  Conformation dependent library (CDL) restraints added in 370.9 milliseconds
  

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1288

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 6 sheets defined
      40.4% alpha, 13.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 125 through 228
      Proline residue:  A 134  - end of helix
    Processing helix  chain 'A' and resid 235 through 254
      removed outlier: 4.212A  pdb=" N   CYS A 242 " --> pdb=" O   LEU A 238 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   LEU A 243 " --> pdb=" O   MET A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 285
      removed outlier: 3.749A  pdb=" N   PHE A 281 " --> pdb=" O   TRP A 277 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   ARG A 282 " --> pdb=" O   ARG A 278 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ALA A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 228
      Proline residue:  B 134  - end of helix
    Processing helix  chain 'B' and resid 235 through 254
      removed outlier: 4.212A  pdb=" N   CYS B 242 " --> pdb=" O   LEU B 238 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   LEU B 243 " --> pdb=" O   MET B 239 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 285
      removed outlier: 3.749A  pdb=" N   PHE B 281 " --> pdb=" O   TRP B 277 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   ARG B 282 " --> pdb=" O   ARG B 278 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ALA B 283 " --> pdb=" O   LYS B 279 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 302 through 304
      removed outlier: 3.556A  pdb=" N   VAL A 311 " --> pdb=" O   LEU A 467 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU A 467 " --> pdb=" O   VAL A 311 " (cutoff:3.500A)
      removed outlier: 6.016A  pdb=" N   LEU A 424 " --> pdb=" O   ALA A 440 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   ALA A 440 " --> pdb=" O   LEU A 424 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   PHE A 426 " --> pdb=" O   LEU A 438 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 333 through 335
    Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 386
    Processing sheet with id=AA4, first strand: chain 'B' and resid 302 through 304
      removed outlier: 3.556A  pdb=" N   VAL B 311 " --> pdb=" O   LEU B 467 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU B 467 " --> pdb=" O   VAL B 311 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   LEU B 424 " --> pdb=" O   ALA B 440 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   ALA B 440 " --> pdb=" O   LEU B 424 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   PHE B 426 " --> pdb=" O   LEU B 438 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 333 through 335
    Processing sheet with id=AA6, first strand: chain 'B' and resid 385 through 386

    299 hydrogen bonds defined for protein.
    873 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: 0.81

  Time building geometry restraints manager: 0.43 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1722
        1.34 -     1.46: 918
        1.46 -     1.58: 2394
        1.58 -     1.69: 0
        1.69 -     1.81: 18
  Bond restraints: 5052
  Sorted by residual:
  bond pdb=" CB  VAL A 375 "
       pdb=" CG1 VAL A 375 "
    ideal  model  delta    sigma   weight residual
    1.521  1.464  0.057 3.30e-02 9.18e+02 2.99e+00
  bond pdb=" CB  VAL B 375 "
       pdb=" CG1 VAL B 375 "
    ideal  model  delta    sigma   weight residual
    1.521  1.464  0.057 3.30e-02 9.18e+02 2.98e+00
  bond pdb=" CB  VAL A 375 "
       pdb=" CG2 VAL A 375 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.86e+00
  bond pdb=" CB  VAL B 375 "
       pdb=" CG2 VAL B 375 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.86e+00
  bond pdb=" CA  PRO B 448 "
       pdb=" C   PRO B 448 "
    ideal  model  delta    sigma   weight residual
    1.524  1.553 -0.029 2.00e-02 2.50e+03 2.03e+00
  ... (remaining 5047 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 6624
        1.62 -     3.24: 203
        3.24 -     4.87: 51
        4.87 -     6.49: 12
        6.49 -     8.11: 4
  Bond angle restraints: 6894
  Sorted by residual:
  angle pdb=" C   VAL B 375 "
        pdb=" CA  VAL B 375 "
        pdb=" CB  VAL B 375 "
      ideal   model   delta    sigma   weight residual
     109.33  112.78   -3.45 9.80e-01 1.04e+00 1.24e+01
  angle pdb=" C   ASP B 459 "
        pdb=" N   LYS B 460 "
        pdb=" CA  LYS B 460 "
      ideal   model   delta    sigma   weight residual
     121.54  127.67   -6.13 1.91e+00 2.74e-01 1.03e+01
  angle pdb=" C   ASP A 459 "
        pdb=" N   LYS A 460 "
        pdb=" CA  LYS A 460 "
      ideal   model   delta    sigma   weight residual
     121.54  127.63   -6.09 1.91e+00 2.74e-01 1.02e+01
  angle pdb=" CA  VAL B 375 "
        pdb=" C   VAL B 375 "
        pdb=" N   PRO B 376 "
      ideal   model   delta    sigma   weight residual
     116.57  119.49   -2.92 9.80e-01 1.04e+00 8.90e+00
  angle pdb=" CA  ARG A 404 "
        pdb=" CB  ARG A 404 "
        pdb=" CG  ARG A 404 "
      ideal   model   delta    sigma   weight residual
     114.10  119.40   -5.30 2.00e+00 2.50e-01 7.02e+00
  ... (remaining 6889 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.14: 2762
       15.14 -    30.28: 216
       30.28 -    45.41: 50
       45.41 -    60.55: 8
       60.55 -    75.69: 8
  Dihedral angle restraints: 3044
    sinusoidal: 1066
      harmonic: 1978
  Sorted by residual:
  dihedral pdb=" CA  SER A 430 "
           pdb=" C   SER A 430 "
           pdb=" N   ASP A 431 "
           pdb=" CA  ASP A 431 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.54   16.46     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CA  SER B 430 "
           pdb=" C   SER B 430 "
           pdb=" N   ASP B 431 "
           pdb=" CA  ASP B 431 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.54   16.46     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CB  MET A 285 "
           pdb=" CG  MET A 285 "
           pdb=" SD  MET A 285 "
           pdb=" CE  MET A 285 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.60  -59.60     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 3041 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 470
       0.031 -    0.061: 203
       0.061 -    0.092: 70
       0.092 -    0.122: 19
       0.122 -    0.153: 12
  Chirality restraints: 774
  Sorted by residual:
  chirality pdb=" CA  VAL B 395 "
            pdb=" N   VAL B 395 "
            pdb=" C   VAL B 395 "
            pdb=" CB  VAL B 395 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.85e-01
  chirality pdb=" CA  VAL A 395 "
            pdb=" N   VAL A 395 "
            pdb=" C   VAL A 395 "
            pdb=" CB  VAL A 395 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.84e-01
  chirality pdb=" CA  VAL B 304 "
            pdb=" N   VAL B 304 "
            pdb=" C   VAL B 304 "
            pdb=" CB  VAL B 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.36e-01
  ... (remaining 771 not shown)

  Planarity restraints: 928
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 399 "    0.042 5.00e-02 4.00e+02   6.45e-02 6.66e+00
        pdb=" N   PRO A 400 "   -0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO A 400 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 400 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 399 "   -0.042 5.00e-02 4.00e+02   6.43e-02 6.62e+00
        pdb=" N   PRO B 400 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO B 400 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 400 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 375 "   -0.036 5.00e-02 4.00e+02   5.42e-02 4.71e+00
        pdb=" N   PRO A 376 "    0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A 376 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 376 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 925 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.88: 1698
        2.88 -     3.38: 4794
        3.38 -     3.89: 7875
        3.89 -     4.39: 8095
        4.39 -     4.90: 14623
  Nonbonded interactions: 37085
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B 348 "
            pdb=" NH1 ARG B 412 "
     model   vdw
     2.373 3.120
  nonbonded pdb=" OE1 GLU A 348 "
            pdb=" NH1 ARG A 412 "
     model   vdw
     2.373 3.120
  nonbonded pdb=" O   THR A 292 "
            pdb=" N   HIS A 337 "
     model   vdw
     2.407 3.120
  nonbonded pdb=" O   THR B 292 "
            pdb=" N   HIS B 337 "
     model   vdw
     2.407 3.120
  nonbonded pdb=" OH  TYR A 346 "
            pdb=" OE2 GLU A 348 "
     model   vdw
     2.513 3.040
  ... (remaining 37080 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.480
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.950
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
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   0.057   5052  Z= 0.192
  Angle     :  0.740   8.109   6894  Z= 0.383
  Chirality :  0.042   0.153    774
  Planarity :  0.008   0.064    928
  Dihedral  : 12.744  75.690   1756
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  2.30 %
    Favored  : 97.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.31), residues: 678
  helix:  3.05 (0.26), residues: 276
  sheet: -0.87 (0.46), residues: 120
  loop : -0.26 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 404 
 TYR   0.006   0.002   TYR A 450 
 PHE   0.012   0.002   PHE A 426 
 TRP   0.007   0.002   TRP B 277 
 HIS   0.001   0.000   HIS B 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 5052)
  covalent geometry    : angle       0.74006 ( 6894)
  hydrogen bonds       : bond        0.10513 (  299)
  hydrogen bonds       : angle       4.95664 (  873)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 105
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A  389 LYS cc_start: 0.8458 (mtmt) cc_final: 0.8067 (mmtt)
REVERT: B  389 LYS cc_start: 0.8459 (mtmt) cc_final: 0.8068 (mmtt)
  outliers start: 2
  outliers final: 1
  residues processed: 107
  average time/residue: 0.1171
  time to fit residues: 14.7236
Evaluate side-chains
  72 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  396 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0370
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   overall best weight:    0.4658

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

Flipped N/Q/H residues before XYZ refinement:
A 338 GLN
** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 327 GLN
B 338 GLN
** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.181689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.143186 restraints weight = 5843.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.141340 restraints weight = 7459.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.144465 restraints weight = 6612.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.144202 restraints weight = 4411.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.144969 restraints weight = 4103.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5052  Z= 0.134
  Angle     :  0.570   5.711   6894  Z= 0.282
  Chirality :  0.039   0.132    774
  Planarity :  0.006   0.054    928
  Dihedral  :  4.611  58.682    741
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  :  9.22 %
    Favored  : 87.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.17 (0.33), residues: 678
  helix:  4.28 (0.29), residues: 246
  sheet: -0.90 (0.46), residues: 122
  loop :  0.10 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 207 
 TYR   0.005   0.001   TYR A 450 
 PHE   0.015   0.002   PHE B 452 
 TRP   0.013   0.001   TRP B 347 
 HIS   0.001   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 5052)
  covalent geometry    : angle       0.56964 ( 6894)
  hydrogen bonds       : bond        0.04549 (  299)
  hydrogen bonds       : angle       3.98162 (  873)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.193 
Fit side-chains
REVERT: A  387 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7803 (mp0)
REVERT: A  454 ASP cc_start: 0.6799 (t0) cc_final: 0.6114 (t0)
REVERT: B  387 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7749 (mp0)
REVERT: B  454 ASP cc_start: 0.6793 (t0) cc_final: 0.6103 (t0)
  outliers start: 15
  outliers final: 3
  residues processed: 97
  average time/residue: 0.1103
  time to fit residues: 12.6699
Evaluate side-chains
  69 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain B residue  431 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 44 optimal weight:   50.0000
   chunk 42 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 35 optimal weight:    9.9990
   chunk 58 optimal weight:    3.9990
   chunk 0 optimal weight:   50.0000
   chunk 20 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 327 GLN
A 338 GLN
** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 338 GLN
** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.168844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.131204 restraints weight = 5921.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.128875 restraints weight = 6329.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.130455 restraints weight = 7105.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.131612 restraints weight = 4915.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.131528 restraints weight = 4814.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.2646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.078   5052  Z= 0.375
  Angle     :  0.753   8.761   6894  Z= 0.368
  Chirality :  0.044   0.152    774
  Planarity :  0.007   0.051    928
  Dihedral  :  4.649  16.993    738
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 13.82 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.23 (0.34), residues: 678
  helix:  4.28 (0.30), residues: 246
  sheet: -1.58 (0.47), residues: 122
  loop :  0.54 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 198 
 TYR   0.009   0.002   TYR A 450 
 PHE   0.027   0.004   PHE A 452 
 TRP   0.024   0.003   TRP A 347 
 HIS   0.003   0.001   HIS B 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00921 ( 5052)
  covalent geometry    : angle       0.75327 ( 6894)
  hydrogen bonds       : bond        0.05051 (  299)
  hydrogen bonds       : angle       4.28146 (  873)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A  387 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7838 (mp0)
  outliers start: 16
  outliers final: 15
  residues processed: 72
  average time/residue: 0.0961
  time to fit residues: 8.5377
Evaluate side-chains
  71 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  353 ASP
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain B residue  158 LEU
Chi-restraints excluded: chain B residue  337 HIS
Chi-restraints excluded: chain B residue  353 ASP
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  396 GLU
Chi-restraints excluded: chain B residue  431 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 13 optimal weight:    6.9990
   chunk 50 optimal weight:    0.4980
   chunk 48 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 42 optimal weight:   10.0000
   chunk 56 optimal weight:    0.4980
   chunk 40 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 58 optimal weight:    6.9990
   chunk 16 optimal weight:    0.1980
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.174378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.136665 restraints weight = 5821.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.134244 restraints weight = 6636.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.136731 restraints weight = 6873.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.136690 restraints weight = 4864.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.137180 restraints weight = 4343.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5052  Z= 0.144
  Angle     :  0.597   6.598   6894  Z= 0.290
  Chirality :  0.039   0.129    774
  Planarity :  0.005   0.051    928
  Dihedral  :  4.169  16.386    738
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 14.06 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.26 (0.34), residues: 678
  helix:  4.46 (0.30), residues: 246
  sheet: -1.65 (0.44), residues: 138
  loop :  0.59 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 166 
 TYR   0.005   0.001   TYR B 450 
 PHE   0.014   0.002   PHE B 293 
 TRP   0.011   0.002   TRP A 347 
 HIS   0.001   0.000   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 5052)
  covalent geometry    : angle       0.59678 ( 6894)
  hydrogen bonds       : bond        0.04487 (  299)
  hydrogen bonds       : angle       3.89409 (  873)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A  387 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7814 (mp0)
REVERT: A  389 LYS cc_start: 0.8392 (mtmt) cc_final: 0.8115 (mmtt)
REVERT: B  387 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7892 (mp0)
  outliers start: 17
  outliers final: 11
  residues processed: 78
  average time/residue: 0.0855
  time to fit residues: 8.3755
Evaluate side-chains
  71 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  337 HIS
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  431 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 36 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 9 optimal weight:    8.9990
   chunk 49 optimal weight:    0.0980
   chunk 1 optimal weight:   30.0000
   chunk 67 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0470
   chunk 29 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.6680

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

Flipped N/Q/H residues before XYZ refinement:
** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 339 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.178762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.143789 restraints weight = 5774.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.140138 restraints weight = 6949.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.142160 restraints weight = 7560.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.142346 restraints weight = 5117.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.143536 restraints weight = 4520.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5052  Z= 0.154
  Angle     :  0.581   5.684   6894  Z= 0.283
  Chirality :  0.039   0.128    774
  Planarity :  0.005   0.049    928
  Dihedral  :  4.086  15.936    738
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 14.29 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.45 (0.34), residues: 678
  helix:  4.54 (0.29), residues: 246
  sheet: -1.54 (0.45), residues: 128
  loop :  0.68 (0.37), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 166 
 TYR   0.004   0.001   TYR A 450 
 PHE   0.022   0.002   PHE B 293 
 TRP   0.014   0.002   TRP A 347 
 HIS   0.001   0.000   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 5052)
  covalent geometry    : angle       0.58080 ( 6894)
  hydrogen bonds       : bond        0.04398 (  299)
  hydrogen bonds       : angle       3.83638 (  873)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.192 
Fit side-chains
REVERT: B  387 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7786 (mp0)
  outliers start: 16
  outliers final: 12
  residues processed: 78
  average time/residue: 0.0919
  time to fit residues: 8.9481
Evaluate side-chains
  70 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain B residue  337 HIS
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  431 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 43 optimal weight:   20.0000
   chunk 6 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0040
   chunk 19 optimal weight:    0.0170
   chunk 54 optimal weight:    0.8980
   chunk 25 optimal weight:    0.1980
   chunk 58 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   overall best weight:    0.4030

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

Flipped N/Q/H residues before XYZ refinement:
A 338 GLN
B 338 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.181284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.147042 restraints weight = 5859.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.142117 restraints weight = 6321.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.144194 restraints weight = 7870.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.144611 restraints weight = 5067.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.146171 restraints weight = 4379.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5052  Z= 0.123
  Angle     :  0.565   5.878   6894  Z= 0.277
  Chirality :  0.038   0.143    774
  Planarity :  0.005   0.049    928
  Dihedral  :  3.972  15.437    738
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 16.59 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.45 (0.34), residues: 678
  helix:  4.59 (0.29), residues: 246
  sheet: -1.51 (0.44), residues: 128
  loop :  0.61 (0.37), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 166 
 TYR   0.003   0.001   TYR A 450 
 PHE   0.023   0.002   PHE B 182 
 TRP   0.009   0.001   TRP A 347 
 HIS   0.001   0.000   HIS A 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 5052)
  covalent geometry    : angle       0.56537 ( 6894)
  hydrogen bonds       : bond        0.04294 (  299)
  hydrogen bonds       : angle       3.70963 (  873)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.186 
Fit side-chains
  outliers start: 17
  outliers final: 10
  residues processed: 76
  average time/residue: 0.0925
  time to fit residues: 8.6109
Evaluate side-chains
  67 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  431 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 46 optimal weight:   20.0000
   chunk 2 optimal weight:   20.0000
   chunk 45 optimal weight:    5.9990
   chunk 49 optimal weight:    0.0270
   chunk 39 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 42 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 50 optimal weight:    0.0870
   overall best weight:    0.5416

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
A 338 GLN
B 264 GLN
B 338 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.180497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.145772 restraints weight = 5750.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.142121 restraints weight = 7274.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.145097 restraints weight = 7165.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.144956 restraints weight = 4913.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.145366 restraints weight = 5004.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5052  Z= 0.137
  Angle     :  0.572   6.083   6894  Z= 0.280
  Chirality :  0.038   0.135    774
  Planarity :  0.005   0.048    928
  Dihedral  :  3.931  15.392    738
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 17.51 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.47 (0.34), residues: 678
  helix:  4.59 (0.29), residues: 246
  sheet: -1.57 (0.46), residues: 122
  loop :  0.63 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 166 
 TYR   0.003   0.001   TYR A 427 
 PHE   0.023   0.002   PHE B 182 
 TRP   0.012   0.001   TRP A 347 
 HIS   0.001   0.000   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 5052)
  covalent geometry    : angle       0.57190 ( 6894)
  hydrogen bonds       : bond        0.04263 (  299)
  hydrogen bonds       : angle       3.68535 (  873)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A  285 MET cc_start: 0.7818 (mtt) cc_final: 0.7590 (mtt)
  outliers start: 18
  outliers final: 9
  residues processed: 76
  average time/residue: 0.0960
  time to fit residues: 9.0693
Evaluate side-chains
  69 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  431 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 1 optimal weight:   30.0000
   chunk 16 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0170
   overall best weight:    0.7418

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
A 339 GLN
B 264 GLN
B 338 GLN
B 339 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.178858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.144109 restraints weight = 5842.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.140645 restraints weight = 6902.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.141595 restraints weight = 7786.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.142627 restraints weight = 5565.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.143223 restraints weight = 4806.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.2958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   5052  Z= 0.157
  Angle     :  0.584   6.459   6894  Z= 0.283
  Chirality :  0.039   0.143    774
  Planarity :  0.005   0.048    928
  Dihedral  :  3.939  15.613    738
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 18.66 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.47 (0.34), residues: 678
  helix:  4.59 (0.29), residues: 246
  sheet: -1.60 (0.46), residues: 122
  loop :  0.64 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 166 
 TYR   0.004   0.001   TYR B 427 
 PHE   0.016   0.002   PHE B 452 
 TRP   0.013   0.002   TRP A 347 
 HIS   0.001   0.000   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 5052)
  covalent geometry    : angle       0.58417 ( 6894)
  hydrogen bonds       : bond        0.04224 (  299)
  hydrogen bonds       : angle       3.71373 (  873)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A  285 MET cc_start: 0.7916 (mtt) cc_final: 0.7648 (mtt)
REVERT: B  285 MET cc_start: 0.7888 (mtt) cc_final: 0.7662 (mtt)
  outliers start: 13
  outliers final: 12
  residues processed: 73
  average time/residue: 0.0923
  time to fit residues: 8.3809
Evaluate side-chains
  73 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  337 HIS
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  431 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 31 optimal weight:    0.0570
   chunk 6 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 35 optimal weight:    8.9990
   chunk 46 optimal weight:   30.0000
   chunk 1 optimal weight:   30.0000
   chunk 40 optimal weight:    2.9990
   chunk 34 optimal weight:    8.9990
   chunk 48 optimal weight:    0.7980
   chunk 43 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.7298

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
A 338 GLN
** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 264 GLN
B 338 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.179499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.144949 restraints weight = 5741.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.141442 restraints weight = 7046.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.144440 restraints weight = 6594.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.143644 restraints weight = 4476.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.144360 restraints weight = 5032.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.3005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5052  Z= 0.158
  Angle     :  0.586   6.591   6894  Z= 0.285
  Chirality :  0.039   0.141    774
  Planarity :  0.005   0.049    928
  Dihedral  :  3.944  15.844    738
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 17.74 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.45 (0.34), residues: 678
  helix:  4.59 (0.29), residues: 246
  sheet: -1.61 (0.45), residues: 122
  loop :  0.60 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 166 
 TYR   0.004   0.001   TYR B 450 
 PHE   0.016   0.002   PHE B 452 
 TRP   0.014   0.002   TRP A 347 
 HIS   0.001   0.000   HIS B 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 5052)
  covalent geometry    : angle       0.58615 ( 6894)
  hydrogen bonds       : bond        0.04205 (  299)
  hydrogen bonds       : angle       3.68534 (  873)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.182 
Fit side-chains
REVERT: B  285 MET cc_start: 0.7922 (mtt) cc_final: 0.7647 (mtt)
  outliers start: 14
  outliers final: 13
  residues processed: 69
  average time/residue: 0.1044
  time to fit residues: 8.6968
Evaluate side-chains
  70 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  338 GLN
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  337 HIS
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  431 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 1 optimal weight:   20.0000
   chunk 43 optimal weight:    5.9990
   chunk 54 optimal weight:    0.6980
   chunk 47 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 34 optimal weight:   50.0000
   chunk 58 optimal weight:    0.0070
   chunk 46 optimal weight:    0.0970
   chunk 26 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 264 GLN
B 338 GLN
** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.179872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.144940 restraints weight = 5762.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.141558 restraints weight = 8596.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.144148 restraints weight = 8480.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.144658 restraints weight = 5377.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.144507 restraints weight = 5656.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5052  Z= 0.138
  Angle     :  0.579   6.763   6894  Z= 0.284
  Chirality :  0.038   0.141    774
  Planarity :  0.005   0.050    928
  Dihedral  :  3.914  15.850    738
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 17.51 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.44 (0.34), residues: 678
  helix:  4.60 (0.29), residues: 246
  sheet: -1.62 (0.45), residues: 122
  loop :  0.58 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 166 
 TYR   0.003   0.000   TYR B 427 
 PHE   0.014   0.002   PHE A 182 
 TRP   0.013   0.002   TRP A 347 
 HIS   0.002   0.000   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 5052)
  covalent geometry    : angle       0.57929 ( 6894)
  hydrogen bonds       : bond        0.04160 (  299)
  hydrogen bonds       : angle       3.66372 (  873)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.181 
Fit side-chains
REVERT: B  285 MET cc_start: 0.7888 (mtt) cc_final: 0.7647 (mtt)
  outliers start: 14
  outliers final: 10
  residues processed: 70
  average time/residue: 0.0989
  time to fit residues: 8.5097
Evaluate side-chains
  69 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  338 GLN
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  385 LEU
Chi-restraints excluded: chain B residue  431 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 14 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0670
   chunk 31 optimal weight:    0.8980
   chunk 34 optimal weight:   50.0000
   chunk 0 optimal weight:   50.0000
   chunk 38 optimal weight:    0.7980
   chunk 24 optimal weight:    0.2980
   chunk 32 optimal weight:    0.5980
   chunk 53 optimal weight:    0.0870
   chunk 9 optimal weight:    9.9990
   overall best weight:    0.3296

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
A 338 GLN
** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.180182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.145249 restraints weight = 5843.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.140116 restraints weight = 6378.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.143095 restraints weight = 6769.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.142968 restraints weight = 4650.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.143360 restraints weight = 4263.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.3016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.102   5052  Z= 0.191
  Angle     :  1.070  59.199   6894  Z= 0.626
  Chirality :  0.039   0.242    774
  Planarity :  0.005   0.050    928
  Dihedral  :  3.932  15.863    738
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 17.74 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.45 (0.34), residues: 678
  helix:  4.60 (0.29), residues: 246
  sheet: -1.62 (0.45), residues: 122
  loop :  0.60 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 166 
 TYR   0.003   0.000   TYR B 427 
 PHE   0.014   0.002   PHE A 182 
 TRP   0.012   0.001   TRP A 347 
 HIS   0.004   0.001   HIS B 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 5052)
  covalent geometry    : angle       1.07015 ( 6894)
  hydrogen bonds       : bond        0.04151 (  299)
  hydrogen bonds       : angle       3.66414 (  873)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1059.45 seconds
wall clock time: 18 minutes 49.88 seconds (1129.88 seconds total)