Starting phenix.real_space_refine
on Wed Feb 12 04:21:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xja_33223/02_2025/7xja_33223.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xja_33223/02_2025/7xja_33223.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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xja_33223/02_2025/7xja_33223.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xja_33223/02_2025/7xja_33223.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xja_33223/02_2025/7xja_33223.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xja_33223/02_2025/7xja_33223.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      44      5.16       5
     C    4808      2.51       5
     N    1184      2.21       5
     O    1240      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7276
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 472, 3638
          Classifications: {'peptide': 472}
          Link IDs: {'PTRANS': 22, 'TRANS': 449}
    Chain: "B"
      Number of atoms: 3638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 472, 3638
          Classifications: {'peptide': 472}
          Link IDs: {'PTRANS': 22, 'TRANS': 449}
  Time building chain proxies: 4.88, per 1000 atoms: 0.67
  Number of scatterers: 7276
  At special positions: 0
  Unit cell: (80.413, 113.573, 79.584, 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      44     16.00
     O    1240      8.00
     N    1184      7.00
     C    4808      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: 1.83
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1744

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 3 sheets defined
      81.5% alpha, 1.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 89 through 126
    Processing helix  chain 'A' and resid 129 through 156
      Proline residue:  A 141  - end of helix
    Processing helix  chain 'A' and resid 157 through 160
    Processing helix  chain 'A' and resid 163 through 172
    Processing helix  chain 'A' and resid 176 through 180
    Processing helix  chain 'A' and resid 181 through 198
    Processing helix  chain 'A' and resid 204 through 225
    Processing helix  chain 'A' and resid 226 through 231
      removed outlier: 6.910A  pdb=" N   ILE A 229 " --> pdb=" O   PHE A 226 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   TYR A 230 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 253
      removed outlier: 3.609A  pdb=" N   PHE A 252 " --> pdb=" O   VAL A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 267
      removed outlier: 3.614A  pdb=" N   SER A 267 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 296
    Processing helix  chain 'A' and resid 317 through 319
      No H-bonds generated for 'chain 'A' and resid 317 through 319'
    Processing helix  chain 'A' and resid 320 through 352
      removed outlier: 3.514A  pdb=" N   GLN A 352 " --> pdb=" O   VAL A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 362
    Processing helix  chain 'A' and resid 364 through 378
      removed outlier: 3.556A  pdb=" N   ALA A 368 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 386
      removed outlier: 3.726A  pdb=" N   GLN A 385 " --> pdb=" O   GLY A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 401
    Processing helix  chain 'A' and resid 419 through 425
    Processing helix  chain 'A' and resid 430 through 450
      removed outlier: 4.142A  pdb=" N   TRP A 444 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 481
    Processing helix  chain 'A' and resid 495 through 513
      removed outlier: 3.872A  pdb=" N   TYR A 499 " --> pdb=" O   VAL A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 526
      removed outlier: 4.425A  pdb=" N   VAL A 519 " --> pdb=" O   VAL A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 549
    Processing helix  chain 'A' and resid 551 through 560
    Processing helix  chain 'B' and resid 90 through 126
      removed outlier: 3.514A  pdb=" N   LEU B 126 " --> pdb=" O   MET B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 156
      Proline residue:  B 141  - end of helix
    Processing helix  chain 'B' and resid 157 through 160
    Processing helix  chain 'B' and resid 163 through 173
    Processing helix  chain 'B' and resid 176 through 180
    Processing helix  chain 'B' and resid 181 through 198
    Processing helix  chain 'B' and resid 204 through 225
      removed outlier: 3.854A  pdb=" N   LEU B 225 " --> pdb=" O   LYS B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 231
      removed outlier: 7.085A  pdb=" N   ILE B 229 " --> pdb=" O   PHE B 226 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   TYR B 230 " --> pdb=" O   GLY B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 253
      removed outlier: 3.647A  pdb=" N   PHE B 252 " --> pdb=" O   VAL B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 267
      removed outlier: 3.716A  pdb=" N   VAL B 259 " --> pdb=" O   PRO B 255 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   SER B 267 " --> pdb=" O   ILE B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 296
    Processing helix  chain 'B' and resid 317 through 319
      No H-bonds generated for 'chain 'B' and resid 317 through 319'
    Processing helix  chain 'B' and resid 320 through 352
    Processing helix  chain 'B' and resid 352 through 363
    Processing helix  chain 'B' and resid 364 through 378
      removed outlier: 3.574A  pdb=" N   ALA B 368 " --> pdb=" O   LEU B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 386
      removed outlier: 3.674A  pdb=" N   GLN B 385 " --> pdb=" O   GLY B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 401
    Processing helix  chain 'B' and resid 405 through 409
    Processing helix  chain 'B' and resid 419 through 425
    Processing helix  chain 'B' and resid 430 through 450
      removed outlier: 4.073A  pdb=" N   TRP B 444 " --> pdb=" O   LEU B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 481
    Processing helix  chain 'B' and resid 495 through 513
      removed outlier: 3.866A  pdb=" N   TYR B 499 " --> pdb=" O   VAL B 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 516 through 526
    Processing helix  chain 'B' and resid 530 through 549
    Processing helix  chain 'B' and resid 551 through 560
    Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 271
    Processing sheet with id=AA2, first strand: chain 'A' and resid 485 through 487
    Processing sheet with id=AA3, first strand: chain 'B' and resid 485 through 487

    569 hydrogen bonds defined for protein.
    1635 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: 2.26

  Time building geometry restraints manager: 2.10 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2238
        1.35 -     1.46: 1850
        1.46 -     1.58: 3298
        1.58 -     1.70: 0
        1.70 -     1.82: 74
  Bond restraints: 7460
  Sorted by residual:
  bond pdb=" CA  VAL A 175 "
       pdb=" CB  VAL A 175 "
    ideal  model  delta    sigma   weight residual
    1.530  1.541 -0.011 1.11e-02 8.12e+03 9.56e-01
  bond pdb=" N   PRO B 453 "
       pdb=" CA  PRO B 453 "
    ideal  model  delta    sigma   weight residual
    1.469  1.481 -0.012 1.28e-02 6.10e+03 9.45e-01
  bond pdb=" N   PRO A 453 "
       pdb=" CA  PRO A 453 "
    ideal  model  delta    sigma   weight residual
    1.469  1.481 -0.012 1.28e-02 6.10e+03 9.26e-01
  bond pdb=" CA  VAL B 175 "
       pdb=" CB  VAL B 175 "
    ideal  model  delta    sigma   weight residual
    1.530  1.540 -0.011 1.11e-02 8.12e+03 8.99e-01
  bond pdb=" CB  PRO A 381 "
       pdb=" CG  PRO A 381 "
    ideal  model  delta    sigma   weight residual
    1.492  1.447  0.045 5.00e-02 4.00e+02 8.13e-01
  ... (remaining 7455 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 9958
        1.74 -     3.49: 167
        3.49 -     5.23: 24
        5.23 -     6.97: 7
        6.97 -     8.72: 4
  Bond angle restraints: 10160
  Sorted by residual:
  angle pdb=" CB  MET B 167 "
        pdb=" CG  MET B 167 "
        pdb=" SD  MET B 167 "
      ideal   model   delta    sigma   weight residual
     112.70  103.98    8.72 3.00e+00 1.11e-01 8.44e+00
  angle pdb=" CB  MET A 167 "
        pdb=" CG  MET A 167 "
        pdb=" SD  MET A 167 "
      ideal   model   delta    sigma   weight residual
     112.70  104.08    8.62 3.00e+00 1.11e-01 8.26e+00
  angle pdb=" C   TYR B 230 "
        pdb=" N   GLU B 231 "
        pdb=" CA  GLU B 231 "
      ideal   model   delta    sigma   weight residual
     121.94  116.23    5.71 2.00e+00 2.50e-01 8.16e+00
  angle pdb=" CB  MET A 460 "
        pdb=" CG  MET A 460 "
        pdb=" SD  MET A 460 "
      ideal   model   delta    sigma   weight residual
     112.70  120.99   -8.29 3.00e+00 1.11e-01 7.63e+00
  angle pdb=" CB  MET B 360 "
        pdb=" CG  MET B 360 "
        pdb=" SD  MET B 360 "
      ideal   model   delta    sigma   weight residual
     112.70  120.21   -7.51 3.00e+00 1.11e-01 6.26e+00
  ... (remaining 10155 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.10: 3975
       16.10 -    32.21: 260
       32.21 -    48.31: 70
       48.31 -    64.41: 17
       64.41 -    80.52: 20
  Dihedral angle restraints: 4342
    sinusoidal: 1636
      harmonic: 2706
  Sorted by residual:
  dihedral pdb=" CG  ARG A 558 "
           pdb=" CD  ARG A 558 "
           pdb=" NE  ARG A 558 "
           pdb=" CZ  ARG A 558 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -138.50  -41.50     2      1.50e+01 4.44e-03 9.37e+00
  dihedral pdb=" CG  ARG B 558 "
           pdb=" CD  ARG B 558 "
           pdb=" NE  ARG B 558 "
           pdb=" CZ  ARG B 558 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -138.57  -41.43     2      1.50e+01 4.44e-03 9.34e+00
  dihedral pdb=" CG  ARG A 350 "
           pdb=" CD  ARG A 350 "
           pdb=" NE  ARG A 350 "
           pdb=" CZ  ARG A 350 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -138.90  -41.10     2      1.50e+01 4.44e-03 9.22e+00
  ... (remaining 4339 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 734
       0.029 -    0.057: 286
       0.057 -    0.086: 125
       0.086 -    0.114: 44
       0.114 -    0.143: 11
  Chirality restraints: 1200
  Sorted by residual:
  chirality pdb=" CA  GLU B 231 "
            pdb=" N   GLU B 231 "
            pdb=" C   GLU B 231 "
            pdb=" CB  GLU B 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.10e-01
  chirality pdb=" CA  PHE B 284 "
            pdb=" N   PHE B 284 "
            pdb=" C   PHE B 284 "
            pdb=" CB  PHE B 284 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.52e-01
  chirality pdb=" CA  VAL B 454 "
            pdb=" N   VAL B 454 "
            pdb=" C   VAL B 454 "
            pdb=" CB  VAL B 454 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.19e-01
  ... (remaining 1197 not shown)

  Planarity restraints: 1256
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 444 "   -0.019 2.00e-02 2.50e+03   1.45e-02 5.28e+00
        pdb=" CG  TRP A 444 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 444 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 444 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 444 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 444 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 444 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 444 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 444 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 444 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 444 "    0.012 2.00e-02 2.50e+03   1.25e-02 3.89e+00
        pdb=" CG  TRP B 444 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 444 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 444 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 444 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 444 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 444 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 444 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 444 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 444 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 379 "   -0.026 5.00e-02 4.00e+02   4.00e-02 2.56e+00
        pdb=" N   PRO B 380 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 380 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 380 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1253 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 271
        2.73 -     3.27: 7852
        3.27 -     3.81: 12578
        3.81 -     4.36: 13994
        4.36 -     4.90: 24526
  Nonbonded interactions: 59221
  Sorted by model distance:
  nonbonded pdb=" O   GLU B 166 "
            pdb=" OG1 THR B 169 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" OE2 GLU A 320 "
            pdb=" OH  TYR A 499 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" OE2 GLU B 320 "
            pdb=" OH  TYR B 499 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   GLU A 166 "
            pdb=" OG1 THR A 169 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   ASP A 402 "
            pdb=" NH1 ARG A 471 "
     model   vdw
     2.284 3.120
  ... (remaining 59216 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: 0.04
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:             0.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.440
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.020
  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:             0.010
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
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      :  0.003   0.045   7460  Z= 0.170
  Angle     :  0.596   8.715  10160  Z= 0.332
  Chirality :  0.039   0.143   1200
  Planarity :  0.004   0.040   1256
  Dihedral  : 13.731  80.517   2598
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.28), residues: 940
  helix:  1.78 (0.20), residues: 692
  sheet:  None (None), residues: 0
  loop : -0.40 (0.41), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 444 
 HIS   0.012   0.002   HIS B 210 
 PHE   0.021   0.001   PHE B 147 
 TYR   0.016   0.001   TYR A 140 
 ARG   0.011   0.001   ARG B 277 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 279
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 LEU cc_start: 0.7116 (tt) cc_final: 0.6626 (pt)
REVERT: A  170 ILE cc_start: 0.9021 (mm) cc_final: 0.8773 (mm)
REVERT: A  288 ILE cc_start: 0.7953 (mm) cc_final: 0.7742 (mt)
REVERT: A  309 ARG cc_start: 0.6199 (ttp-170) cc_final: 0.5062 (mmt-90)
REVERT: A  374 ILE cc_start: 0.7585 (tt) cc_final: 0.7118 (mt)
REVERT: A  433 LEU cc_start: 0.7917 (tp) cc_final: 0.7463 (mt)
REVERT: A  515 VAL cc_start: 0.8225 (t) cc_final: 0.7969 (t)
REVERT: B  153 GLN cc_start: 0.7612 (tp40) cc_final: 0.7344 (tm-30)
REVERT: B  309 ARG cc_start: 0.5313 (mtm180) cc_final: 0.4758 (mmt-90)
REVERT: B  320 GLU cc_start: 0.6376 (mt-10) cc_final: 0.5887 (mt-10)
REVERT: B  433 LEU cc_start: 0.8048 (tp) cc_final: 0.7664 (mt)
REVERT: B  477 MET cc_start: 0.7560 (ttm) cc_final: 0.7334 (ttt)
REVERT: B  540 LEU cc_start: 0.8499 (mt) cc_final: 0.8255 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 279
  average time/residue: 0.1977
  time to fit residues: 72.5971
Evaluate side-chains
  179 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    0.0270
   chunk 71 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 44 optimal weight:    0.3980
   chunk 54 optimal weight:    2.9990
   chunk 85 optimal weight:    0.4980
   overall best weight:    0.7040

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 425 ASN
A 542 ASN
A 546 GLN
B 542 ASN
B 546 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.188672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.159177 restraints weight = 9696.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.162730 restraints weight = 6354.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.165165 restraints weight = 4855.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7460  Z= 0.213
  Angle     :  0.582   8.146  10160  Z= 0.301
  Chirality :  0.042   0.192   1200
  Planarity :  0.005   0.040   1256
  Dihedral  :  3.563  14.796   1002
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 10.18 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.43 (0.28), residues: 940
  helix:  2.22 (0.19), residues: 700
  sheet:  None (None), residues: 0
  loop : -0.19 (0.46), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 444 
 HIS   0.005   0.002   HIS A 513 
 PHE   0.019   0.002   PHE A 185 
 TYR   0.013   0.002   TYR B 340 
 ARG   0.004   0.001   ARG B 277 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 191
  time to evaluate  : 0.769 
Fit side-chains
REVERT: A  131 LEU cc_start: 0.7584 (tt) cc_final: 0.7114 (pt)
REVERT: A  309 ARG cc_start: 0.6552 (ttp-170) cc_final: 0.5349 (mmt-90)
REVERT: A  408 ARG cc_start: 0.4714 (mmp-170) cc_final: 0.4120 (tpp-160)
REVERT: B  108 MET cc_start: 0.7620 (mtt) cc_final: 0.7304 (mtp)
REVERT: B  222 PHE cc_start: 0.6957 (t80) cc_final: 0.5062 (m-80)
REVERT: B  309 ARG cc_start: 0.5510 (mtm180) cc_final: 0.4921 (mmt-90)
REVERT: B  408 ARG cc_start: 0.3901 (mmm160) cc_final: 0.3460 (tpp-160)
REVERT: B  433 LEU cc_start: 0.8071 (tp) cc_final: 0.7826 (mt)
REVERT: B  483 ASP cc_start: 0.6503 (t70) cc_final: 0.6252 (t0)
  outliers start: 21
  outliers final: 14
  residues processed: 203
  average time/residue: 0.1728
  time to fit residues: 48.0171
Evaluate side-chains
  177 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 163
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  542 ASN
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  516 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0070
   chunk 65 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 82 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 33 optimal weight:    0.4980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.8000

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

Flipped N/Q/H residues before XYZ refinement:
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 542 ASN
B 425 ASN
B 542 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.177712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.148488 restraints weight = 9879.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.151635 restraints weight = 6678.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.153698 restraints weight = 5233.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.3830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7460  Z= 0.209
  Angle     :  0.573   7.901  10160  Z= 0.298
  Chirality :  0.042   0.159   1200
  Planarity :  0.005   0.039   1256
  Dihedral  :  3.472  13.863   1002
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 12.66 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.54 (0.28), residues: 940
  helix:  2.35 (0.19), residues: 704
  sheet:  None (None), residues: 0
  loop : -0.38 (0.45), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 444 
 HIS   0.005   0.002   HIS A 513 
 PHE   0.026   0.002   PHE B 289 
 TYR   0.017   0.002   TYR A 134 
 ARG   0.005   0.000   ARG B 277 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 176
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.7639 (mtp) cc_final: 0.7388 (mtp)
REVERT: A  222 PHE cc_start: 0.7178 (t80) cc_final: 0.5045 (m-10)
REVERT: A  309 ARG cc_start: 0.6655 (ttp-170) cc_final: 0.5330 (mmt-90)
REVERT: A  408 ARG cc_start: 0.4946 (mmp-170) cc_final: 0.4425 (tpp-160)
REVERT: B  108 MET cc_start: 0.7755 (mtt) cc_final: 0.7470 (mtp)
REVERT: B  222 PHE cc_start: 0.6709 (t80) cc_final: 0.5042 (m-80)
REVERT: B  309 ARG cc_start: 0.5778 (mtm180) cc_final: 0.5034 (mmt-90)
REVERT: B  408 ARG cc_start: 0.4103 (mmm160) cc_final: 0.3628 (tpp-160)
REVERT: B  483 ASP cc_start: 0.6632 (t70) cc_final: 0.6322 (t0)
  outliers start: 17
  outliers final: 12
  residues processed: 187
  average time/residue: 0.1751
  time to fit residues: 44.7058
Evaluate side-chains
  176 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 164
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  516 SER
Chi-restraints excluded: chain B residue  555 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0770
   chunk 44 optimal weight:    0.0370
   chunk 69 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 3 optimal weight:    4.9990
   chunk 52 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.4216

-------------------------------------------------------------------------------
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 = 0.3941 r_free = 0.3941 target = 0.177229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.146083 restraints weight = 9915.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.149670 restraints weight = 6397.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.152007 restraints weight = 4903.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.4310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7460  Z= 0.173
  Angle     :  0.548   9.826  10160  Z= 0.280
  Chirality :  0.041   0.149   1200
  Planarity :  0.004   0.038   1256
  Dihedral  :  3.376  13.132   1002
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 14.75 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.54 (0.28), residues: 940
  helix:  2.40 (0.19), residues: 702
  sheet:  None (None), residues: 0
  loop : -0.56 (0.44), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 444 
 HIS   0.006   0.002   HIS A 210 
 PHE   0.023   0.001   PHE A 314 
 TYR   0.024   0.002   TYR B 134 
 ARG   0.004   0.000   ARG A 350 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 168
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.7656 (mtp) cc_final: 0.7434 (mtp)
REVERT: A  167 MET cc_start: 0.7715 (mmm) cc_final: 0.7512 (mmm)
REVERT: A  309 ARG cc_start: 0.6584 (ttp-170) cc_final: 0.5216 (mmt-90)
REVERT: A  408 ARG cc_start: 0.5179 (mmp-170) cc_final: 0.4607 (tpp-160)
REVERT: A  439 ILE cc_start: 0.7824 (mm) cc_final: 0.7547 (mt)
REVERT: B  108 MET cc_start: 0.7764 (mtt) cc_final: 0.7510 (mtp)
REVERT: B  222 PHE cc_start: 0.6564 (t80) cc_final: 0.4947 (m-80)
REVERT: B  264 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7013 (mm-30)
REVERT: B  309 ARG cc_start: 0.5746 (mtm180) cc_final: 0.5017 (mmt-90)
REVERT: B  408 ARG cc_start: 0.4007 (mmm160) cc_final: 0.3436 (tpp-160)
REVERT: B  483 ASP cc_start: 0.6624 (t70) cc_final: 0.5939 (m-30)
  outliers start: 14
  outliers final: 10
  residues processed: 179
  average time/residue: 0.1872
  time to fit residues: 45.6814
Evaluate side-chains
  167 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 157
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  555 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 84 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 73 optimal weight:    4.9990
   overall best weight:    1.3188

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

Flipped N/Q/H residues before XYZ refinement:
** A 403 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 = 0.3788 r_free = 0.3788 target = 0.163762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.132801 restraints weight = 10097.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.135835 restraints weight = 6790.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.137837 restraints weight = 5374.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.5392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   7460  Z= 0.284
  Angle     :  0.628   7.405  10160  Z= 0.333
  Chirality :  0.045   0.162   1200
  Planarity :  0.005   0.046   1256
  Dihedral  :  3.576  12.177   1002
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 14.36 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.27), residues: 940
  helix:  2.20 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.82 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  91 
 HIS   0.005   0.002   HIS A 513 
 PHE   0.024   0.002   PHE B 208 
 TYR   0.018   0.002   TYR A 134 
 ARG   0.008   0.001   ARG A 273 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 161
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 ARG cc_start: 0.6725 (ttp-170) cc_final: 0.5115 (mmt-90)
REVERT: A  361 ARG cc_start: 0.7043 (mmt180) cc_final: 0.6629 (mtp180)
REVERT: A  408 ARG cc_start: 0.5473 (mmp-170) cc_final: 0.4783 (tpp-160)
REVERT: A  523 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7608 (mt-10)
REVERT: B  108 MET cc_start: 0.7897 (mtt) cc_final: 0.7689 (mtp)
REVERT: B  222 PHE cc_start: 0.6731 (t80) cc_final: 0.4943 (m-80)
REVERT: B  264 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7204 (mm-30)
REVERT: B  309 ARG cc_start: 0.5642 (mtm180) cc_final: 0.4657 (mmt-90)
REVERT: B  408 ARG cc_start: 0.4264 (mmm160) cc_final: 0.3709 (tpp-160)
REVERT: B  483 ASP cc_start: 0.6811 (t70) cc_final: 0.6215 (m-30)
REVERT: B  557 ILE cc_start: 0.8220 (tp) cc_final: 0.7980 (tp)
  outliers start: 26
  outliers final: 20
  residues processed: 181
  average time/residue: 0.1846
  time to fit residues: 45.4284
Evaluate side-chains
  173 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 153
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  516 SER
Chi-restraints excluded: chain B residue  555 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 89 optimal weight:    0.4980
   chunk 91 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 86 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 76 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 527 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.164868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.134727 restraints weight = 10000.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.137868 restraints weight = 6647.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.139916 restraints weight = 5208.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.5648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7460  Z= 0.214
  Angle     :  0.570  10.360  10160  Z= 0.294
  Chirality :  0.042   0.187   1200
  Planarity :  0.004   0.043   1256
  Dihedral  :  3.428  11.398   1002
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 17.89 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.44 (0.28), residues: 940
  helix:  2.47 (0.19), residues: 692
  sheet:  None (None), residues: 0
  loop : -0.95 (0.41), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 444 
 HIS   0.004   0.002   HIS A 513 
 PHE   0.027   0.002   PHE A 147 
 TYR   0.024   0.002   TYR B 134 
 ARG   0.003   0.000   ARG B 277 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 168
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 MET cc_start: 0.7798 (mmm) cc_final: 0.7488 (mmm)
REVERT: A  309 ARG cc_start: 0.6559 (ttp-170) cc_final: 0.5121 (mmt-90)
REVERT: A  385 GLN cc_start: 0.8194 (pp30) cc_final: 0.7973 (pt0)
REVERT: A  408 ARG cc_start: 0.5509 (mmp-170) cc_final: 0.4784 (tpp-160)
REVERT: A  425 ASN cc_start: 0.7732 (t0) cc_final: 0.7427 (m-40)
REVERT: B  108 MET cc_start: 0.7976 (mtt) cc_final: 0.7755 (mtp)
REVERT: B  222 PHE cc_start: 0.6804 (t80) cc_final: 0.5168 (m-10)
REVERT: B  264 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7156 (mm-30)
REVERT: B  309 ARG cc_start: 0.5707 (mtm180) cc_final: 0.4644 (mmt-90)
REVERT: B  320 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6112 (mt-10)
REVERT: B  348 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8256 (m)
REVERT: B  408 ARG cc_start: 0.4204 (mmm160) cc_final: 0.3696 (tpp-160)
REVERT: B  483 ASP cc_start: 0.6764 (t70) cc_final: 0.6209 (m-30)
REVERT: B  557 ILE cc_start: 0.8185 (tp) cc_final: 0.7896 (tp)
  outliers start: 17
  outliers final: 12
  residues processed: 180
  average time/residue: 0.1926
  time to fit residues: 46.2979
Evaluate side-chains
  170 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 157
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  369 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 87 optimal weight:    0.1980
   chunk 13 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9980
   chunk 56 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3849 r_free = 0.3849 target = 0.169561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.139932 restraints weight = 9860.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.143349 restraints weight = 6371.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.145609 restraints weight = 4893.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.5894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7460  Z= 0.205
  Angle     :  0.572   6.824  10160  Z= 0.295
  Chirality :  0.041   0.143   1200
  Planarity :  0.004   0.041   1256
  Dihedral  :  3.416  11.384   1002
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 17.36 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.47 (0.28), residues: 940
  helix:  2.49 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.97 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 444 
 HIS   0.004   0.002   HIS A 513 
 PHE   0.021   0.002   PHE A 279 
 TYR   0.017   0.001   TYR A 275 
 ARG   0.004   0.000   ARG A 273 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 161
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 MET cc_start: 0.7741 (mmm) cc_final: 0.7468 (mmm)
REVERT: A  309 ARG cc_start: 0.6556 (ttp-170) cc_final: 0.5137 (mmt-90)
REVERT: A  320 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6037 (mt-10)
REVERT: A  348 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8047 (m)
REVERT: A  385 GLN cc_start: 0.8233 (pp30) cc_final: 0.8004 (pt0)
REVERT: A  408 ARG cc_start: 0.5587 (mmp-170) cc_final: 0.4887 (tpp-160)
REVERT: A  425 ASN cc_start: 0.7733 (t0) cc_final: 0.7445 (m-40)
REVERT: B  222 PHE cc_start: 0.6403 (t80) cc_final: 0.5148 (m-10)
REVERT: B  309 ARG cc_start: 0.5712 (mtm180) cc_final: 0.4662 (mmt-90)
REVERT: B  348 VAL cc_start: 0.8673 (t) cc_final: 0.8251 (m)
REVERT: B  408 ARG cc_start: 0.4206 (mmm160) cc_final: 0.3700 (tpp-160)
REVERT: B  483 ASP cc_start: 0.6645 (t70) cc_final: 0.6180 (m-30)
REVERT: B  557 ILE cc_start: 0.8127 (tp) cc_final: 0.7861 (tp)
  outliers start: 22
  outliers final: 17
  residues processed: 178
  average time/residue: 0.1902
  time to fit residues: 45.5378
Evaluate side-chains
  176 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  516 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 23 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0060
   chunk 81 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0370
   chunk 28 optimal weight:    0.0970
   chunk 33 optimal weight:    5.9990
   overall best weight:    0.3472

-------------------------------------------------------------------------------
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 = 0.3822 r_free = 0.3822 target = 0.166847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.136742 restraints weight = 10117.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.139901 restraints weight = 6713.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.141997 restraints weight = 5236.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.5976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7460  Z= 0.171
  Angle     :  0.562   7.220  10160  Z= 0.288
  Chirality :  0.041   0.198   1200
  Planarity :  0.004   0.040   1256
  Dihedral  :  3.340  13.128   1002
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 18.02 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.57 (0.28), residues: 940
  helix:  2.56 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -0.93 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 444 
 HIS   0.004   0.001   HIS A 513 
 PHE   0.021   0.001   PHE A 279 
 TYR   0.024   0.001   TYR B 134 
 ARG   0.004   0.000   ARG A 273 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 171
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 ARG cc_start: 0.6394 (ttp-170) cc_final: 0.5055 (mmt-90)
REVERT: A  348 VAL cc_start: 0.8466 (OUTLIER) cc_final: 0.8083 (m)
REVERT: A  385 GLN cc_start: 0.8212 (pp30) cc_final: 0.8011 (pt0)
REVERT: A  408 ARG cc_start: 0.5549 (mmp-170) cc_final: 0.4679 (tpp-160)
REVERT: A  425 ASN cc_start: 0.7726 (t0) cc_final: 0.7443 (m-40)
REVERT: B  222 PHE cc_start: 0.6737 (t80) cc_final: 0.5034 (m-80)
REVERT: B  309 ARG cc_start: 0.5813 (mtm180) cc_final: 0.4677 (mmt-90)
REVERT: B  348 VAL cc_start: 0.8661 (t) cc_final: 0.8279 (m)
REVERT: B  408 ARG cc_start: 0.4301 (mmm160) cc_final: 0.3736 (tpp-160)
REVERT: B  475 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8282 (mm-30)
REVERT: B  483 ASP cc_start: 0.6582 (t70) cc_final: 0.6114 (m-30)
REVERT: B  557 ILE cc_start: 0.8117 (tp) cc_final: 0.7853 (tp)
  outliers start: 21
  outliers final: 19
  residues processed: 185
  average time/residue: 0.1998
  time to fit residues: 49.2016
Evaluate side-chains
  183 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 163
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  252 PHE
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  507 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 82 optimal weight:    0.0670
   chunk 53 optimal weight:    0.0370
   chunk 55 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   chunk 88 optimal weight:    0.7980
   chunk 85 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0000
   chunk 23 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.3200

-------------------------------------------------------------------------------
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 = 0.3829 r_free = 0.3829 target = 0.167120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.137548 restraints weight = 10108.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.140699 restraints weight = 6646.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.142796 restraints weight = 5171.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.6119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7460  Z= 0.181
  Angle     :  0.602  10.516  10160  Z= 0.302
  Chirality :  0.042   0.295   1200
  Planarity :  0.004   0.040   1256
  Dihedral  :  3.313  12.578   1002
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 18.41 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.61 (0.28), residues: 940
  helix:  2.62 (0.19), residues: 692
  sheet:  None (None), residues: 0
  loop : -0.96 (0.42), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 444 
 HIS   0.004   0.002   HIS A 513 
 PHE   0.024   0.001   PHE A 279 
 TYR   0.013   0.001   TYR A 275 
 ARG   0.004   0.000   ARG A 350 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 165
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 ARG cc_start: 0.6502 (ttp-170) cc_final: 0.5147 (mmt-90)
REVERT: A  348 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8079 (m)
REVERT: A  361 ARG cc_start: 0.7222 (mmt180) cc_final: 0.6532 (mtp180)
REVERT: A  408 ARG cc_start: 0.5578 (mmp-170) cc_final: 0.4724 (tpp-160)
REVERT: A  425 ASN cc_start: 0.7719 (t0) cc_final: 0.7454 (m-40)
REVERT: B  222 PHE cc_start: 0.6786 (t80) cc_final: 0.5141 (m-10)
REVERT: B  309 ARG cc_start: 0.5818 (mtm180) cc_final: 0.4706 (mmt-90)
REVERT: B  348 VAL cc_start: 0.8647 (t) cc_final: 0.8250 (m)
REVERT: B  363 ARG cc_start: 0.4645 (ptp90) cc_final: 0.4215 (ptp-170)
REVERT: B  408 ARG cc_start: 0.4286 (mmm160) cc_final: 0.3925 (tpm170)
REVERT: B  483 ASP cc_start: 0.6427 (t70) cc_final: 0.5932 (m-30)
REVERT: B  557 ILE cc_start: 0.8107 (tp) cc_final: 0.7855 (tp)
  outliers start: 20
  outliers final: 17
  residues processed: 178
  average time/residue: 0.2178
  time to fit residues: 50.6791
Evaluate side-chains
  181 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 163
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  252 PHE
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  516 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0270
   chunk 26 optimal weight:    4.9990
   chunk 67 optimal weight:    0.0270
   chunk 63 optimal weight:    6.9990
   chunk 71 optimal weight:    4.9990
   chunk 87 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.9500

-------------------------------------------------------------------------------
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 = 0.3771 r_free = 0.3771 target = 0.161864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.131960 restraints weight = 10323.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.135060 restraints weight = 6827.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.137055 restraints weight = 5333.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.6421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7460  Z= 0.240
  Angle     :  0.645  12.409  10160  Z= 0.328
  Chirality :  0.045   0.362   1200
  Planarity :  0.005   0.040   1256
  Dihedral  :  3.436  12.064   1002
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 18.54 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.42 (0.28), residues: 940
  helix:  2.47 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -1.05 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 295 
 HIS   0.004   0.002   HIS A 513 
 PHE   0.020   0.002   PHE B 280 
 TYR   0.032   0.002   TYR B 134 
 ARG   0.008   0.001   ARG A 343 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 158
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 ARG cc_start: 0.6512 (ttp-170) cc_final: 0.5064 (mmt-90)
REVERT: A  361 ARG cc_start: 0.7315 (mmt180) cc_final: 0.6087 (mtp-110)
REVERT: A  408 ARG cc_start: 0.5589 (mmp-170) cc_final: 0.4639 (tpp-160)
REVERT: A  425 ASN cc_start: 0.7745 (t0) cc_final: 0.7448 (m-40)
REVERT: B  108 MET cc_start: 0.7727 (mtp) cc_final: 0.7410 (mtp)
REVERT: B  124 ARG cc_start: 0.5149 (ttm170) cc_final: 0.4353 (tmm160)
REVERT: B  222 PHE cc_start: 0.6877 (t80) cc_final: 0.5119 (m-10)
REVERT: B  262 SER cc_start: 0.8740 (t) cc_final: 0.8500 (m)
REVERT: B  309 ARG cc_start: 0.5809 (mtm180) cc_final: 0.4583 (mmt-90)
REVERT: B  348 VAL cc_start: 0.8646 (t) cc_final: 0.8266 (m)
REVERT: B  363 ARG cc_start: 0.4826 (ptp90) cc_final: 0.4309 (ptp-170)
REVERT: B  408 ARG cc_start: 0.4426 (mmm160) cc_final: 0.4019 (tpm170)
REVERT: B  483 ASP cc_start: 0.6478 (t70) cc_final: 0.6203 (m-30)
REVERT: B  557 ILE cc_start: 0.8190 (tp) cc_final: 0.7965 (tp)
  outliers start: 16
  outliers final: 14
  residues processed: 171
  average time/residue: 0.2112
  time to fit residues: 47.6551
Evaluate side-chains
  164 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 150
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  252 PHE
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  431 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 49 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 40 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 92 optimal weight:    0.8980
   chunk 75 optimal weight:    0.0060
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.6796

-------------------------------------------------------------------------------
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 = 0.3790 r_free = 0.3790 target = 0.163198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.133237 restraints weight = 10081.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.136288 restraints weight = 6744.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.138211 restraints weight = 5313.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.6516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7460  Z= 0.210
  Angle     :  0.636  13.051  10160  Z= 0.319
  Chirality :  0.044   0.396   1200
  Planarity :  0.004   0.039   1256
  Dihedral  :  3.388  12.366   1002
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 18.54 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.28), residues: 940
  helix:  2.48 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -1.16 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 444 
 HIS   0.005   0.002   HIS B 210 
 PHE   0.024   0.002   PHE A 279 
 TYR   0.011   0.001   TYR A 275 
 ARG   0.006   0.000   ARG A 343 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2514.44 seconds
wall clock time: 45 minutes 45.05 seconds (2745.05 seconds total)