Starting phenix.real_space_refine
on Sat Apr 26 18:38:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ybe_39117/04_2025/8ybe_39117.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ybe_39117/04_2025/8ybe_39117.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ybe_39117/04_2025/8ybe_39117.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ybe_39117/04_2025/8ybe_39117.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ybe_39117/04_2025/8ybe_39117.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ybe_39117/04_2025/8ybe_39117.cif"
  }
  resolution = 2.3
  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=   0.018
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       6      5.16       5
     C    1873      2.51       5
     N     473      2.21       5
     O     758      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 3110
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2890
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 370, 2879
          Classifications: {'peptide': 370}
          Link IDs: {'PTRANS': 21, 'TRANS': 348}
      Conformer: "B"
        Number of residues, atoms: 370, 2879
          Classifications: {'peptide': 370}
          Link IDs: {'PTRANS': 21, 'TRANS': 348}
          bond proxies already assigned to first conformer: 2936
    Chain: "B"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'GLC': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 197
          Classifications: {'water': 197}
          Link IDs: {None: 196}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG A 393 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 393 " occ=0.50
  Time building chain proxies: 4.17, per 1000 atoms: 1.34
  Number of scatterers: 3110
  At special positions: 0
  Unit cell: (50.0692, 62.7628, 77.572, 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       6     16.00
     O     758      8.00
     N     473      7.00
     C    1873      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
  Links applied
    ALPHA1-4
      " GLC B   1 " - " GLC B   2 "
  Time building additional restraints: 0.76
  Conformation dependent library (CDL) restraints added in 613.6 milliseconds
  

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  684

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 4 sheets defined
      54.9% alpha, 11.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 42 through 58
    Processing helix  chain 'A' and resid 68 through 80
      Proline residue:  A  74  - end of helix
    Processing helix  chain 'A' and resid 90 through 100
      removed outlier: 3.716A  pdb=" N   GLY A  94 " --> pdb=" O   HIS A  90 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   GLY A  95 " --> pdb=" O   ASP A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 115
    Processing helix  chain 'A' and resid 116 through 123
    Processing helix  chain 'A' and resid 157 through 168
    Processing helix  chain 'A' and resid 179 through 190
      removed outlier: 3.768A  pdb=" N   THR A 183 " --> pdb=" O   GLU A 179 " (cutoff:3.500A)
      Proline residue:  A 185  - end of helix
      removed outlier: 4.339A  pdb=" N   ASP A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 227
    Processing helix  chain 'A' and resid 235 through 245
    Processing helix  chain 'A' and resid 254 through 256
      No H-bonds generated for 'chain 'A' and resid 254 through 256'
    Processing helix  chain 'A' and resid 257 through 265
    Processing helix  chain 'A' and resid 298 through 309
    Processing helix  chain 'A' and resid 312 through 323
    Processing helix  chain 'A' and resid 330 through 338
      removed outlier: 3.795A  pdb=" N   GLU A 336 " --> pdb=" O   SER A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 353
    Processing helix  chain 'A' and resid 360 through 379
      removed outlier: 4.457A  pdb=" N   ALA A 364 " --> pdb=" O   PRO A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 396
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 64
      removed outlier: 6.350A  pdb=" N   LEU A  33 " --> pdb=" O   THR A  62 " (cutoff:3.500A)
      removed outlier: 7.328A  pdb=" N   GLU A  64 " --> pdb=" O   LEU A  33 " (cutoff:3.500A)
      removed outlier: 5.914A  pdb=" N   ILE A  35 " --> pdb=" O   GLU A  64 " (cutoff:3.500A)
      removed outlier: 7.508A  pdb=" N   ILE A  85 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   VAL A  34 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   PHE A  87 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   TRP A  36 " --> pdb=" O   PHE A  87 " (cutoff:3.500A)
      removed outlier: 8.578A  pdb=" N   ALA A  89 " --> pdb=" O   TRP A  36 " (cutoff:3.500A)
      removed outlier: 5.990A  pdb=" N   ALA A 290 " --> pdb=" O   PRO A 133 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 125
    Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173
      removed outlier: 8.222A  pdb=" N   SER A 171 " --> pdb=" O   ALA A 249 " (cutoff:3.500A)
      removed outlier: 7.455A  pdb=" N   THR A 251 " --> pdb=" O   SER A 171 " (cutoff:3.500A)
      removed outlier: 8.173A  pdb=" N   LEU A 173 " --> pdb=" O   THR A 251 " (cutoff:3.500A)
      removed outlier: 10.897A  pdb=" N   ASN A 253 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   ALA A 249 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 196 through 198
      removed outlier: 3.668A  pdb=" N   LYS A 196 " --> pdb=" O   ASP A 203 " (cutoff:3.500A)

    149 hydrogen bonds defined for protein.
    433 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: 0.87

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 544
        1.32 -     1.44: 729
        1.44 -     1.56: 1698
        1.56 -     1.68: 0
        1.68 -     1.81: 12
  Bond restraints: 2983
  Sorted by residual:
  bond pdb=" C   ALA A 172 "
       pdb=" O   ALA A 172 "
    ideal  model  delta    sigma   weight residual
    1.236  1.199  0.037 1.15e-02 7.56e+03 1.05e+01
  bond pdb=" CA  ARG A 380 "
       pdb=" C   ARG A 380 "
    ideal  model  delta    sigma   weight residual
    1.524  1.484  0.039 1.29e-02 6.01e+03 9.19e+00
  bond pdb=" CA  LYS A 201 "
       pdb=" C   LYS A 201 "
    ideal  model  delta    sigma   weight residual
    1.519  1.486  0.034 1.14e-02 7.69e+03 8.68e+00
  bond pdb=" C   ALA A 327 "
       pdb=" O   ALA A 327 "
    ideal  model  delta    sigma   weight residual
    1.234  1.202  0.032 1.22e-02 6.72e+03 6.97e+00
  bond pdb=" CA  LYS A  32 "
       pdb=" C   LYS A  32 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 1.24e-02 6.50e+03 6.66e+00
  ... (remaining 2978 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 3842
        1.80 -     3.60: 166
        3.60 -     5.40: 33
        5.40 -     7.20: 6
        7.20 -     9.00: 3
  Bond angle restraints: 4050
  Sorted by residual:
  angle pdb=" N   PRO A 357 "
        pdb=" CA  PRO A 357 "
        pdb=" C   PRO A 357 "
      ideal   model   delta    sigma   weight residual
     111.68  102.68    9.00 1.67e+00 3.59e-01 2.90e+01
  angle pdb=" N   SER A 296 "
        pdb=" CA  SER A 296 "
        pdb=" C   SER A 296 "
      ideal   model   delta    sigma   weight residual
     109.48  116.86   -7.38 1.44e+00 4.82e-01 2.63e+01
  angle pdb=" N   PRO A 297 "
        pdb=" CA  PRO A 297 "
        pdb=" C   PRO A 297 "
      ideal   model   delta    sigma   weight residual
     114.35  108.38    5.97 1.25e+00 6.40e-01 2.28e+01
  angle pdb=" C   MET A 356 "
        pdb=" N   PRO A 357 "
        pdb=" CA  PRO A 357 "
      ideal   model   delta    sigma   weight residual
     120.14  115.17    4.97 1.06e+00 8.90e-01 2.20e+01
  angle pdb=" O   ASP A  91 "
        pdb=" C   ASP A  91 "
        pdb=" N   ARG A  92 "
      ideal   model   delta    sigma   weight residual
     122.20  127.09   -4.89 1.14e+00 7.69e-01 1.84e+01
  ... (remaining 4045 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.04: 1614
       17.04 -    34.09: 132
       34.09 -    51.13: 48
       51.13 -    68.17: 16
       68.17 -    85.21: 4
  Dihedral angle restraints: 1814
    sinusoidal: 744
      harmonic: 1070
  Sorted by residual:
  dihedral pdb=" CA  ASP A  56 "
           pdb=" C   ASP A  56 "
           pdb=" N   THR A  57 "
           pdb=" CA  THR A  57 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.28  -15.72     0      5.00e+00 4.00e-02 9.89e+00
  dihedral pdb=" CB  GLU A 137 "
           pdb=" CG  GLU A 137 "
           pdb=" CD  GLU A 137 "
           pdb=" OE1 GLU A 137 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.21  -85.21     1      3.00e+01 1.11e-03 9.78e+00
  dihedral pdb=" N   GLN A 381 "
           pdb=" CA  GLN A 381 "
           pdb=" CB  GLN A 381 "
           pdb=" CG  GLN A 381 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.35  -58.65     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 1811 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 374
       0.068 -    0.136: 65
       0.136 -    0.204: 6
       0.204 -    0.273: 0
       0.273 -    0.341: 1
  Chirality restraints: 446
  Sorted by residual:
  chirality pdb=" C1  GLC B   2 "
            pdb=" O4  GLC B   1 "
            pdb=" C2  GLC B   2 "
            pdb=" O5  GLC B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.44   -0.04 2.00e-02 2.50e+03 4.34e+00
  chirality pdb=" C1  GLC B   1 "
            pdb=" C2  GLC B   1 "
            pdb=" O1  GLC B   1 "
            pdb=" O5  GLC B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.04   -2.38    0.34 2.00e-01 2.50e+01 2.90e+00
  chirality pdb=" CA  MET A 347 "
            pdb=" N   MET A 347 "
            pdb=" C   MET A 347 "
            pdb=" CB  MET A 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.80e-01
  ... (remaining 443 not shown)

  Planarity restraints: 521
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A  92 "   -0.022 2.00e-02 2.50e+03   4.43e-02 1.97e+01
        pdb=" C   ARG A  92 "    0.077 2.00e-02 2.50e+03
        pdb=" O   ARG A  92 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   PHE A  93 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 392 "   -0.014 2.00e-02 2.50e+03   2.83e-02 8.02e+00
        pdb=" C   THR A 392 "    0.049 2.00e-02 2.50e+03
        pdb=" O   THR A 392 "   -0.018 2.00e-02 2.50e+03
        pdb=" N  AARG A 393 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 392 "   -0.014 2.00e-02 2.50e+03   2.76e-02 7.64e+00
        pdb=" C   THR A 392 "    0.048 2.00e-02 2.50e+03
        pdb=" O   THR A 392 "   -0.018 2.00e-02 2.50e+03
        pdb=" N  BARG A 393 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 518 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 772
        2.77 -     3.30: 3381
        3.30 -     3.83: 6978
        3.83 -     4.37: 8256
        4.37 -     4.90: 12524
  Nonbonded interactions: 31911
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 193 "
            pdb=" OD1 ASP A 206 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   VAL A  76 "
            pdb=" OG1 THR A  79 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   HOH A 454 "
            pdb=" O   HOH A 592 "
     model   vdw
     2.327 3.040
  nonbonded pdb=" OD2 ASP A 262 "
            pdb=" O   HOH A 401 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" O   THR A 248 "
            pdb=" O   HOH A 402 "
     model   vdw
     2.330 3.040
  ... (remaining 31906 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.530
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.640
  Find NCS groups from input model:        0.040
  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:             0.000
  Load rotamer database and sin/cos tables:12.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
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      :  0.006   0.042   2984  Z= 0.389
  Angle     :  0.890   9.000   4053  Z= 0.530
  Chirality :  0.053   0.341    446
  Planarity :  0.008   0.061    521
  Dihedral  : 15.835  85.214   1130
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 18.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 13.38 %
    Favored  : 84.28 %
  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:  1.36 (0.41), residues: 371
  helix:  0.91 (0.33), residues: 192
  sheet:  0.98 (0.79), residues: 29
  loop :  1.15 (0.54), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A  88 
 HIS   0.004   0.001   HIS A 229 
 PHE   0.013   0.002   PHE A 220 
 TYR   0.022   0.002   TYR A 181 
 ARG   0.003   0.001   ARG A 370 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00673 (    1)
  link_ALPHA1-4        : angle       2.23068 (    3)
  hydrogen bonds       : bond        0.15308 (  149)
  hydrogen bonds       : angle       6.09893 (  433)
  covalent geometry    : bond        0.00611 ( 2983)
  covalent geometry    : angle       0.88797 ( 4050)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.416 
Fit side-chains
REVERT: A   29 GLU cc_start: 0.6751 (tt0) cc_final: 0.5984 (mm-30)
REVERT: A   98 GLN cc_start: 0.7692 (tp40) cc_final: 0.7436 (tm-30)
REVERT: A  128 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7932 (mtpm)
REVERT: A  197 TYR cc_start: 0.7370 (t80) cc_final: 0.6600 (t80)
REVERT: A  284 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.6140 (m-10)
REVERT: A  354 GLU cc_start: 0.7668 (mm-30) cc_final: 0.6670 (pm20)
  outliers start: 6
  outliers final: 1
  residues processed: 55
  average time/residue: 1.4152
  time to fit residues: 79.9413
Evaluate side-chains
  37 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 35
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  284 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 15 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 17 optimal weight:    0.2980
   chunk 21 optimal weight:    0.0570
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.4298

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

Flipped N/Q/H residues before XYZ refinement:
A  38 ASN
A 279 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.145462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.129598 restraints weight = 11288.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 1.84
r_work: 0.3288 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3145
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3145 r_free = 0.3145    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3145 r_free = 0.3145    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3145
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.1237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2984  Z= 0.177
  Angle     :  0.634   6.990   4053  Z= 0.336
  Chirality :  0.043   0.147    446
  Planarity :  0.005   0.054    521
  Dihedral  :  6.881  63.999    439
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 15.72 %
    Favored  : 81.94 %
  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:  1.47 (0.42), residues: 371
  helix:  0.93 (0.35), residues: 192
  sheet:  0.71 (0.96), residues: 24
  loop :  1.38 (0.53), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 184 
 HIS   0.002   0.001   HIS A  65 
 PHE   0.012   0.002   PHE A 175 
 TYR   0.024   0.002   TYR A 181 
 ARG   0.002   0.000   ARG A 124 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00620 (    1)
  link_ALPHA1-4        : angle       1.74979 (    3)
  hydrogen bonds       : bond        0.05746 (  149)
  hydrogen bonds       : angle       5.55038 (  433)
  covalent geometry    : bond        0.00374 ( 2983)
  covalent geometry    : angle       0.63245 ( 4050)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.376 
Fit side-chains
REVERT: A   98 GLN cc_start: 0.7922 (tp40) cc_final: 0.7612 (tm-30)
REVERT: A  128 LYS cc_start: 0.8109 (mtpt) cc_final: 0.7900 (mtpm)
REVERT: A  179 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8168 (mm-30)
  outliers start: 6
  outliers final: 1
  residues processed: 45
  average time/residue: 1.2793
  time to fit residues: 59.3507
Evaluate side-chains
  35 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 34
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 14 optimal weight:    0.0980
   chunk 33 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.145049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.129218 restraints weight = 10338.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 1.80
r_work: 0.3292 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3137
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3137
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.1522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2984  Z= 0.174
  Angle     :  0.604   6.974   4053  Z= 0.317
  Chirality :  0.043   0.120    446
  Planarity :  0.005   0.051    521
  Dihedral  :  5.203  52.766    436
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 15.72 %
    Favored  : 83.28 %
  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:  1.46 (0.43), residues: 371
  helix:  0.88 (0.35), residues: 192
  sheet:  0.31 (0.98), residues: 24
  loop :  1.52 (0.55), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 184 
 HIS   0.003   0.002   HIS A  90 
 PHE   0.012   0.002   PHE A 243 
 TYR   0.019   0.001   TYR A 181 
 ARG   0.001   0.000   ARG A 342 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00387 (    1)
  link_ALPHA1-4        : angle       1.53572 (    3)
  hydrogen bonds       : bond        0.05451 (  149)
  hydrogen bonds       : angle       5.52016 (  433)
  covalent geometry    : bond        0.00374 ( 2983)
  covalent geometry    : angle       0.60308 ( 4050)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 44
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A   98 GLN cc_start: 0.7916 (tp40) cc_final: 0.7603 (tm-30)
REVERT: A  179 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8140 (mm-30)
REVERT: A  203 ASP cc_start: 0.7889 (t0) cc_final: 0.7507 (t0)
REVERT: A  317 GLU cc_start: 0.8027 (tt0) cc_final: 0.7821 (tt0)
REVERT: A  321 LYS cc_start: 0.8073 (mptp) cc_final: 0.7490 (tttm)
  outliers start: 2
  outliers final: 1
  residues processed: 46
  average time/residue: 1.3510
  time to fit residues: 63.9168
Evaluate side-chains
  38 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 37
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0070
   chunk 8 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0980
   chunk 11 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.4198

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.147014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.133925 restraints weight = 5888.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 1.29
r_work: 0.3378 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3263 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3246
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3246 r_free = 0.3246    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3246 r_free = 0.3246    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3246
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2984  Z= 0.155
  Angle     :  0.582   6.642   4053  Z= 0.301
  Chirality :  0.042   0.120    446
  Planarity :  0.004   0.048    521
  Dihedral  :  5.109  53.093    436
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 16.72 %
    Favored  : 81.94 %
  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:  1.38 (0.44), residues: 371
  helix:  0.80 (0.35), residues: 195
  sheet:  0.06 (0.96), residues: 24
  loop :  1.56 (0.58), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 184 
 HIS   0.003   0.002   HIS A  90 
 PHE   0.012   0.002   PHE A 243 
 TYR   0.017   0.001   TYR A 181 
 ARG   0.001   0.000   ARG A 342 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00336 (    1)
  link_ALPHA1-4        : angle       1.51796 (    3)
  hydrogen bonds       : bond        0.05043 (  149)
  hydrogen bonds       : angle       5.45081 (  433)
  covalent geometry    : bond        0.00337 ( 2983)
  covalent geometry    : angle       0.58028 ( 4050)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.737 
Fit side-chains
REVERT: A   92 ARG cc_start: 0.8145 (mmt180) cc_final: 0.7630 (mmm160)
REVERT: A   98 GLN cc_start: 0.7862 (tp40) cc_final: 0.7608 (tm-30)
REVERT: A  179 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8078 (mm-30)
REVERT: A  317 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7687 (tt0)
REVERT: A  321 LYS cc_start: 0.7920 (mptp) cc_final: 0.7388 (tttm)
  outliers start: 3
  outliers final: 1
  residues processed: 41
  average time/residue: 1.4704
  time to fit residues: 61.9359
Evaluate side-chains
  40 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 PHE
Chi-restraints excluded: chain A residue  317 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.144630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.129524 restraints weight = 8499.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.62
r_work: 0.3312 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3188 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3164
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3164
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2984  Z= 0.180
  Angle     :  0.602   7.020   4053  Z= 0.310
  Chirality :  0.042   0.119    446
  Planarity :  0.005   0.048    521
  Dihedral  :  5.144  52.847    436
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 15.72 %
    Favored  : 82.94 %
  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:  1.47 (0.44), residues: 371
  helix:  0.92 (0.35), residues: 192
  sheet: -0.13 (0.98), residues: 24
  loop :  1.57 (0.57), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 184 
 HIS   0.004   0.002   HIS A  90 
 PHE   0.013   0.002   PHE A 243 
 TYR   0.016   0.001   TYR A 181 
 ARG   0.001   0.000   ARG A 342 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00447 (    1)
  link_ALPHA1-4        : angle       1.59949 (    3)
  hydrogen bonds       : bond        0.05279 (  149)
  hydrogen bonds       : angle       5.53864 (  433)
  covalent geometry    : bond        0.00392 ( 2983)
  covalent geometry    : angle       0.60038 ( 4050)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.5352 (OUTLIER) cc_final: 0.4710 (mtmt)
REVERT: A   92 ARG cc_start: 0.8086 (mmt180) cc_final: 0.7690 (mmm160)
REVERT: A   98 GLN cc_start: 0.7909 (tp40) cc_final: 0.7610 (tm-30)
REVERT: A  179 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8120 (mm-30)
REVERT: A  317 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7735 (tt0)
REVERT: A  321 LYS cc_start: 0.7969 (mptp) cc_final: 0.7398 (tttm)
  outliers start: 3
  outliers final: 1
  residues processed: 43
  average time/residue: 1.4639
  time to fit residues: 64.5891
Evaluate side-chains
  41 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LYS
Chi-restraints excluded: chain A residue  284 PHE
Chi-restraints excluded: chain A residue  317 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 1 optimal weight:    0.4980
   chunk 9 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.144276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.128634 restraints weight = 9432.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 1.72
r_work: 0.3292 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3137
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3137
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   2984  Z= 0.184
  Angle     :  0.609   6.785   4053  Z= 0.314
  Chirality :  0.043   0.119    446
  Planarity :  0.005   0.048    521
  Dihedral  :  5.171  52.842    436
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 15.72 %
    Favored  : 82.94 %
  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:  1.35 (0.45), residues: 371
  helix:  0.80 (0.35), residues: 195
  sheet: -0.25 (1.00), residues: 24
  loop :  1.57 (0.58), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 184 
 HIS   0.005   0.002   HIS A  90 
 PHE   0.013   0.002   PHE A 243 
 TYR   0.015   0.001   TYR A 181 
 ARG   0.001   0.000   ARG A 342 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00422 (    1)
  link_ALPHA1-4        : angle       1.62815 (    3)
  hydrogen bonds       : bond        0.05317 (  149)
  hydrogen bonds       : angle       5.57175 (  433)
  covalent geometry    : bond        0.00404 ( 2983)
  covalent geometry    : angle       0.60736 ( 4050)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A   27 LYS cc_start: 0.5411 (OUTLIER) cc_final: 0.4822 (mtmt)
REVERT: A   92 ARG cc_start: 0.8168 (mmt180) cc_final: 0.7768 (mmm160)
REVERT: A   98 GLN cc_start: 0.7918 (tp40) cc_final: 0.7621 (tm-30)
REVERT: A  179 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8165 (mm-30)
REVERT: A  237 SER cc_start: 0.8378 (m) cc_final: 0.8137 (t)
REVERT: A  304 GLU cc_start: 0.8385 (tp30) cc_final: 0.8169 (tp30)
REVERT: A  317 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7781 (tt0)
REVERT: A  321 LYS cc_start: 0.8006 (mptp) cc_final: 0.7430 (tttm)
  outliers start: 3
  outliers final: 1
  residues processed: 41
  average time/residue: 1.4459
  time to fit residues: 60.9484
Evaluate side-chains
  40 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LYS
Chi-restraints excluded: chain A residue  284 PHE
Chi-restraints excluded: chain A residue  317 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 12 optimal weight:    0.0060
   chunk 21 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0970
   chunk 25 optimal weight:    0.0970
   chunk 27 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 28 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.2792

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.150022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.137003 restraints weight = 5666.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 1.27
r_work: 0.3418 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3303 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3285
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3285
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2984  Z= 0.134
  Angle     :  0.555   6.105   4053  Z= 0.284
  Chirality :  0.041   0.119    446
  Planarity :  0.004   0.045    521
  Dihedral  :  4.993  53.773    436
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 15.72 %
    Favored  : 82.94 %
  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:  1.43 (0.45), residues: 371
  helix:  0.90 (0.36), residues: 195
  sheet: -0.25 (1.02), residues: 24
  loop :  1.54 (0.58), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 184 
 HIS   0.003   0.002   HIS A  90 
 PHE   0.010   0.002   PHE A 175 
 TYR   0.016   0.001   TYR A 181 
 ARG   0.001   0.000   ARG A 342 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00247 (    1)
  link_ALPHA1-4        : angle       1.44250 (    3)
  hydrogen bonds       : bond        0.04587 (  149)
  hydrogen bonds       : angle       5.36224 (  433)
  covalent geometry    : bond        0.00289 ( 2983)
  covalent geometry    : angle       0.55370 ( 4050)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A   92 ARG cc_start: 0.7968 (mmt180) cc_final: 0.7622 (mmm160)
REVERT: A  179 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7984 (mm-30)
REVERT: A  304 GLU cc_start: 0.8280 (tp30) cc_final: 0.8002 (tp30)
REVERT: A  314 GLU cc_start: 0.7107 (mp0) cc_final: 0.6870 (mp0)
REVERT: A  317 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7622 (tt0)
REVERT: A  321 LYS cc_start: 0.7876 (mptp) cc_final: 0.7351 (tttm)
  outliers start: 3
  outliers final: 1
  residues processed: 43
  average time/residue: 1.4445
  time to fit residues: 63.8209
Evaluate side-chains
  39 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 PHE
Chi-restraints excluded: chain A residue  317 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.145002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.128850 restraints weight = 9676.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.77
r_work: 0.3289 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3131
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3131 r_free = 0.3131    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3131 r_free = 0.3131    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3131
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2984  Z= 0.193
  Angle     :  0.621   6.990   4053  Z= 0.318
  Chirality :  0.043   0.121    446
  Planarity :  0.004   0.047    521
  Dihedral  :  5.161  52.853    436
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 17.06 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.45), residues: 371
  helix:  0.84 (0.36), residues: 195
  sheet: -0.39 (1.01), residues: 24
  loop :  1.61 (0.59), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 184 
 HIS   0.005   0.002   HIS A  90 
 PHE   0.014   0.002   PHE A 243 
 TYR   0.013   0.002   TYR A 181 
 ARG   0.001   0.000   ARG A 342 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00433 (    1)
  link_ALPHA1-4        : angle       1.64298 (    3)
  hydrogen bonds       : bond        0.05312 (  149)
  hydrogen bonds       : angle       5.57738 (  433)
  covalent geometry    : bond        0.00425 ( 2983)
  covalent geometry    : angle       0.61917 ( 4050)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A   92 ARG cc_start: 0.8155 (mmt180) cc_final: 0.7750 (mmm160)
REVERT: A  179 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8170 (mm-30)
REVERT: A  203 ASP cc_start: 0.7663 (t0) cc_final: 0.7301 (t0)
REVERT: A  304 GLU cc_start: 0.8415 (tp30) cc_final: 0.8167 (tp30)
REVERT: A  317 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7781 (tt0)
REVERT: A  321 LYS cc_start: 0.7989 (mptp) cc_final: 0.7424 (tttm)
  outliers start: 4
  outliers final: 1
  residues processed: 40
  average time/residue: 1.3797
  time to fit residues: 56.7935
Evaluate side-chains
  38 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 PHE
Chi-restraints excluded: chain A residue  317 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 29 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0870
   chunk 9 optimal weight:    0.0870
   chunk 6 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.4136

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.148214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.133406 restraints weight = 7591.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.54
r_work: 0.3356 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3213
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3212
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2984  Z= 0.153
  Angle     :  0.585   6.552   4053  Z= 0.299
  Chirality :  0.041   0.120    446
  Planarity :  0.004   0.045    521
  Dihedral  :  5.075  53.453    436
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 17.06 %
    Favored  : 81.61 %
  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:  1.42 (0.45), residues: 371
  helix:  0.89 (0.36), residues: 195
  sheet: -0.38 (1.02), residues: 24
  loop :  1.58 (0.58), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  88 
 HIS   0.003   0.002   HIS A  90 
 PHE   0.011   0.002   PHE A 243 
 TYR   0.016   0.001   TYR A 181 
 ARG   0.001   0.000   ARG A 342 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00316 (    1)
  link_ALPHA1-4        : angle       1.53294 (    3)
  hydrogen bonds       : bond        0.04822 (  149)
  hydrogen bonds       : angle       5.43729 (  433)
  covalent geometry    : bond        0.00335 ( 2983)
  covalent geometry    : angle       0.58371 ( 4050)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.356 
Fit side-chains
REVERT: A   92 ARG cc_start: 0.8124 (mmt180) cc_final: 0.7715 (mmm160)
REVERT: A  179 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8084 (mm-30)
REVERT: A  304 GLU cc_start: 0.8354 (tp30) cc_final: 0.8064 (tp30)
REVERT: A  314 GLU cc_start: 0.7185 (mp0) cc_final: 0.6904 (mp0)
REVERT: A  317 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7727 (tt0)
REVERT: A  321 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7395 (tttm)
  outliers start: 3
  outliers final: 1
  residues processed: 41
  average time/residue: 1.4102
  time to fit residues: 59.4443
Evaluate side-chains
  41 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 PHE
Chi-restraints excluded: chain A residue  317 GLU
Chi-restraints excluded: chain A residue  321 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0060
   chunk 34 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 15 optimal weight:    0.1980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.146821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.131707 restraints weight = 7877.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 1.58
r_work: 0.3332 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3190
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3190
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2984  Z= 0.169
  Angle     :  0.606   6.762   4053  Z= 0.309
  Chirality :  0.042   0.119    446
  Planarity :  0.004   0.046    521
  Dihedral  :  5.113  53.369    436
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 17.73 %
    Favored  : 80.94 %
  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:  1.40 (0.45), residues: 371
  helix:  0.86 (0.36), residues: 195
  sheet: -0.38 (1.01), residues: 24
  loop :  1.60 (0.58), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  88 
 HIS   0.004   0.002   HIS A  90 
 PHE   0.012   0.002   PHE A 243 
 TYR   0.014   0.001   TYR A 181 
 ARG   0.001   0.000   ARG A 342 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00424 (    1)
  link_ALPHA1-4        : angle       1.56795 (    3)
  hydrogen bonds       : bond        0.05003 (  149)
  hydrogen bonds       : angle       5.49953 (  433)
  covalent geometry    : bond        0.00373 ( 2983)
  covalent geometry    : angle       0.60449 ( 4050)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 37
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A   92 ARG cc_start: 0.8155 (mmt180) cc_final: 0.7750 (mmm160)
REVERT: A  179 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8111 (mm-30)
REVERT: A  304 GLU cc_start: 0.8388 (tp30) cc_final: 0.8136 (tp30)
REVERT: A  314 GLU cc_start: 0.7215 (mp0) cc_final: 0.6928 (mp0)
REVERT: A  317 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7754 (tt0)
REVERT: A  321 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7381 (tttm)
  outliers start: 3
  outliers final: 1
  residues processed: 38
  average time/residue: 1.4243
  time to fit residues: 55.6069
Evaluate side-chains
  39 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 PHE
Chi-restraints excluded: chain A residue  317 GLU
Chi-restraints excluded: chain A residue  321 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0040
   overall best weight:    0.8794

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.142794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.130515 restraints weight = 4636.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 1.11
r_work: 0.3346 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3211
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3211
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   2984  Z= 0.217
  Angle     :  0.662   7.446   4053  Z= 0.340
  Chirality :  0.044   0.120    446
  Planarity :  0.005   0.047    521
  Dihedral  :  5.305  52.177    436
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 17.06 %
    Favored  : 80.94 %
  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:  1.27 (0.45), residues: 371
  helix:  0.73 (0.36), residues: 195
  sheet: -0.56 (1.00), residues: 24
  loop :  1.59 (0.58), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  88 
 HIS   0.006   0.002   HIS A  90 
 PHE   0.015   0.003   PHE A 243 
 TYR   0.013   0.002   TYR A 181 
 ARG   0.002   0.001   ARG A  92 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00618 (    1)
  link_ALPHA1-4        : angle       1.80135 (    3)
  hydrogen bonds       : bond        0.05617 (  149)
  hydrogen bonds       : angle       5.68109 (  433)
  covalent geometry    : bond        0.00482 ( 2983)
  covalent geometry    : angle       0.66062 ( 4050)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3153.72 seconds
wall clock time: 54 minutes 34.00 seconds (3274.00 seconds total)