Starting phenix.real_space_refine
on Fri Aug 22 12:58:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cgg_16642/08_2025/8cgg_16642.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cgg_16642/08_2025/8cgg_16642.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cgg_16642/08_2025/8cgg_16642.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cgg_16642/08_2025/8cgg_16642.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cgg_16642/08_2025/8cgg_16642.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cgg_16642/08_2025/8cgg_16642.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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      40      5.16       5
     C    1590      2.51       5
     N     530      2.21       5
     O     550      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2710
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "U"
      Number of atoms: 542
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 542
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 2, 'TRANS': 77}
  Restraints were copied for chains:
    A, B, C, D
  Time building chain proxies: 0.46, per 1000 atoms: 0.17
  Number of scatterers: 2710
  At special positions: 0
  Unit cell: (67.08, 67.94, 44.72, 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      40     16.00
     O     550      8.00
     N     530      7.00
     C    1590      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.12
  Conformation dependent library (CDL) restraints added in 74.5 milliseconds
  
  Enol-peptide restraints added in 0.0 nanoseconds
  

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  590

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 7 sheets defined
      0.0% alpha, 40.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 297 through 303
      removed outlier: 9.112A  pdb=" N   GLY A 298 " --> pdb=" O   LEU B 299 " (cutoff:3.500A)
      removed outlier: 10.594A  pdb=" N   ASN B 301 " --> pdb=" O   GLY A 298 " (cutoff:3.500A)
      removed outlier: 5.982A  pdb=" N   GLY A 300 " --> pdb=" O   ASN B 301 " (cutoff:3.500A)
      removed outlier: 8.617A  pdb=" N   GLN B 303 " --> pdb=" O   GLY A 300 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   ASN A 302 " --> pdb=" O   GLN B 303 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   GLY B 298 " --> pdb=" O   ALA U 297 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   LEU U 299 " --> pdb=" O   GLY B 298 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   GLY B 300 " --> pdb=" O   LEU U 299 " (cutoff:3.500A)
      removed outlier: 7.037A  pdb=" N   ASN U 301 " --> pdb=" O   GLY B 300 " (cutoff:3.500A)
      removed outlier: 9.112A  pdb=" N   GLY U 298 " --> pdb=" O   LEU C 299 " (cutoff:3.500A)
      removed outlier: 10.595A  pdb=" N   ASN C 301 " --> pdb=" O   GLY U 298 " (cutoff:3.500A)
      removed outlier: 5.982A  pdb=" N   GLY U 300 " --> pdb=" O   ASN C 301 " (cutoff:3.500A)
      removed outlier: 8.617A  pdb=" N   GLN C 303 " --> pdb=" O   GLY U 300 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   ASN U 302 " --> pdb=" O   GLN C 303 " (cutoff:3.500A)
      removed outlier: 9.111A  pdb=" N   GLY C 298 " --> pdb=" O   LEU D 299 " (cutoff:3.500A)
      removed outlier: 10.595A  pdb=" N   ASN D 301 " --> pdb=" O   GLY C 298 " (cutoff:3.500A)
      removed outlier: 5.982A  pdb=" N   GLY C 300 " --> pdb=" O   ASN D 301 " (cutoff:3.500A)
      removed outlier: 8.616A  pdb=" N   GLN D 303 " --> pdb=" O   GLY C 300 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   ASN C 302 " --> pdb=" O   GLN D 303 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 306 through 308
      removed outlier: 6.692A  pdb=" N   ASN U 306 " --> pdb=" O   MET B 307 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 311 through 318
      removed outlier: 6.687A  pdb=" N   MET A 311 " --> pdb=" O   ASN B 312 " (cutoff:3.500A)
      removed outlier: 8.454A  pdb=" N   GLY B 314 " --> pdb=" O   MET A 311 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   PHE A 313 " --> pdb=" O   GLY B 314 " (cutoff:3.500A)
      removed outlier: 8.270A  pdb=" N   PHE B 316 " --> pdb=" O   PHE A 313 " (cutoff:3.500A)
      removed outlier: 8.823A  pdb=" N   ALA A 315 " --> pdb=" O   PHE B 316 " (cutoff:3.500A)
      removed outlier: 8.169A  pdb=" N   ILE B 318 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
      removed outlier: 9.237A  pdb=" N   SER A 317 " --> pdb=" O   ILE B 318 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   SER B 317 " --> pdb=" O   PHE U 316 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   ILE U 318 " --> pdb=" O   SER B 317 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   MET U 311 " --> pdb=" O   ASN C 312 " (cutoff:3.500A)
      removed outlier: 8.453A  pdb=" N   GLY C 314 " --> pdb=" O   MET U 311 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   PHE U 313 " --> pdb=" O   GLY C 314 " (cutoff:3.500A)
      removed outlier: 8.270A  pdb=" N   PHE C 316 " --> pdb=" O   PHE U 313 " (cutoff:3.500A)
      removed outlier: 8.824A  pdb=" N   ALA U 315 " --> pdb=" O   PHE C 316 " (cutoff:3.500A)
      removed outlier: 8.169A  pdb=" N   ILE C 318 " --> pdb=" O   ALA U 315 " (cutoff:3.500A)
      removed outlier: 9.238A  pdb=" N   SER U 317 " --> pdb=" O   ILE C 318 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   MET C 311 " --> pdb=" O   ASN D 312 " (cutoff:3.500A)
      removed outlier: 8.453A  pdb=" N   GLY D 314 " --> pdb=" O   MET C 311 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   PHE C 313 " --> pdb=" O   GLY D 314 " (cutoff:3.500A)
      removed outlier: 8.269A  pdb=" N   PHE D 316 " --> pdb=" O   PHE C 313 " (cutoff:3.500A)
      removed outlier: 8.823A  pdb=" N   ALA C 315 " --> pdb=" O   PHE D 316 " (cutoff:3.500A)
      removed outlier: 8.168A  pdb=" N   ILE D 318 " --> pdb=" O   ALA C 315 " (cutoff:3.500A)
      removed outlier: 9.238A  pdb=" N   SER C 317 " --> pdb=" O   ILE D 318 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 331
      removed outlier: 6.725A  pdb=" N   ALA A 321 " --> pdb=" O   MET B 322 " (cutoff:3.500A)
      removed outlier: 8.451A  pdb=" N   ALA B 324 " --> pdb=" O   ALA A 321 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   MET A 323 " --> pdb=" O   ALA B 324 " (cutoff:3.500A)
      removed outlier: 8.461A  pdb=" N   ALA B 326 " --> pdb=" O   MET A 323 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   ALA A 325 " --> pdb=" O   ALA B 326 " (cutoff:3.500A)
      removed outlier: 8.178A  pdb=" N   ALA B 328 " --> pdb=" O   ALA A 325 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   GLN A 327 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 8.510A  pdb=" N   LEU B 330 " --> pdb=" O   GLN A 327 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   ALA A 329 " --> pdb=" O   LEU B 330 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   ALA U 321 " --> pdb=" O   MET C 322 " (cutoff:3.500A)
      removed outlier: 8.451A  pdb=" N   ALA C 324 " --> pdb=" O   ALA U 321 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   MET U 323 " --> pdb=" O   ALA C 324 " (cutoff:3.500A)
      removed outlier: 8.461A  pdb=" N   ALA C 326 " --> pdb=" O   MET U 323 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   ALA U 325 " --> pdb=" O   ALA C 326 " (cutoff:3.500A)
      removed outlier: 8.179A  pdb=" N   ALA C 328 " --> pdb=" O   ALA U 325 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   GLN U 327 " --> pdb=" O   ALA C 328 " (cutoff:3.500A)
      removed outlier: 8.510A  pdb=" N   LEU C 330 " --> pdb=" O   GLN U 327 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   ALA U 329 " --> pdb=" O   LEU C 330 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ALA C 321 " --> pdb=" O   MET D 322 " (cutoff:3.500A)
      removed outlier: 8.451A  pdb=" N   ALA D 324 " --> pdb=" O   ALA C 321 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   MET C 323 " --> pdb=" O   ALA D 324 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   ALA D 326 " --> pdb=" O   MET C 323 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   ALA C 325 " --> pdb=" O   ALA D 326 " (cutoff:3.500A)
      removed outlier: 8.178A  pdb=" N   ALA D 328 " --> pdb=" O   ALA C 325 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   GLN C 327 " --> pdb=" O   ALA D 328 " (cutoff:3.500A)
      removed outlier: 8.510A  pdb=" N   LEU D 330 " --> pdb=" O   GLN C 327 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   ALA C 329 " --> pdb=" O   LEU D 330 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 334 through 336
      removed outlier: 6.471A  pdb=" N   GLY A 335 " --> pdb=" O   MET B 336 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   GLY U 335 " --> pdb=" O   MET C 336 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   GLY C 335 " --> pdb=" O   MET D 336 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 344 through 347
      removed outlier: 6.619A  pdb=" N   GLN A 344 " --> pdb=" O   ASN B 345 " (cutoff:3.500A)
      removed outlier: 8.346A  pdb=" N   SER B 347 " --> pdb=" O   GLN A 344 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   GLN A 346 " --> pdb=" O   SER B 347 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   GLN U 344 " --> pdb=" O   ASN C 345 " (cutoff:3.500A)
      removed outlier: 8.346A  pdb=" N   SER C 347 " --> pdb=" O   GLN U 344 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   GLN U 346 " --> pdb=" O   SER C 347 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   GLN C 344 " --> pdb=" O   ASN D 345 " (cutoff:3.500A)
      removed outlier: 8.345A  pdb=" N   SER D 347 " --> pdb=" O   GLN C 344 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   GLN C 346 " --> pdb=" O   SER D 347 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 355
      removed outlier: 6.771A  pdb=" N   GLN A 354 " --> pdb=" O   ASN B 355 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   GLN U 354 " --> pdb=" O   ASN C 355 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   GLN C 354 " --> pdb=" O   ASN D 355 " (cutoff:3.500A)

    30 hydrogen bonds defined for protein.
    90 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: 0.35

  Time building geometry restraints manager: 0.16 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 936
        1.34 -     1.47: 704
        1.47 -     1.60: 1025
        1.60 -     1.73: 0
        1.73 -     1.86: 80
  Bond restraints: 2745
  Sorted by residual:
  bond pdb=" C   GLN D 360 "
       pdb=" O   GLN D 360 "
    ideal  model  delta    sigma   weight residual
    1.231  1.301 -0.070 2.00e-02 2.50e+03 1.22e+01
  bond pdb=" C   GLN C 360 "
       pdb=" O   GLN C 360 "
    ideal  model  delta    sigma   weight residual
    1.231  1.301 -0.070 2.00e-02 2.50e+03 1.22e+01
  bond pdb=" C   GLN U 360 "
       pdb=" O   GLN U 360 "
    ideal  model  delta    sigma   weight residual
    1.231  1.301 -0.070 2.00e-02 2.50e+03 1.21e+01
  bond pdb=" C   GLN A 360 "
       pdb=" O   GLN A 360 "
    ideal  model  delta    sigma   weight residual
    1.231  1.300 -0.069 2.00e-02 2.50e+03 1.21e+01
  bond pdb=" C   GLN B 360 "
       pdb=" O   GLN B 360 "
    ideal  model  delta    sigma   weight residual
    1.231  1.300 -0.069 2.00e-02 2.50e+03 1.20e+01
  ... (remaining 2740 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 2527
        1.55 -     3.09: 898
        3.09 -     4.64: 155
        4.64 -     6.19: 60
        6.19 -     7.73: 10
  Bond angle restraints: 3650
  Sorted by residual:
  angle pdb=" N   GLY D 298 "
        pdb=" CA  GLY D 298 "
        pdb=" C   GLY D 298 "
      ideal   model   delta    sigma   weight residual
     110.45  116.59   -6.14 1.30e+00 5.92e-01 2.23e+01
  angle pdb=" N   GLY U 298 "
        pdb=" CA  GLY U 298 "
        pdb=" C   GLY U 298 "
      ideal   model   delta    sigma   weight residual
     110.45  116.58   -6.13 1.30e+00 5.92e-01 2.22e+01
  angle pdb=" N   GLY A 298 "
        pdb=" CA  GLY A 298 "
        pdb=" C   GLY A 298 "
      ideal   model   delta    sigma   weight residual
     110.45  116.58   -6.13 1.30e+00 5.92e-01 2.22e+01
  angle pdb=" N   GLY B 298 "
        pdb=" CA  GLY B 298 "
        pdb=" C   GLY B 298 "
      ideal   model   delta    sigma   weight residual
     110.45  116.57   -6.12 1.30e+00 5.92e-01 2.22e+01
  angle pdb=" N   GLY C 298 "
        pdb=" CA  GLY C 298 "
        pdb=" C   GLY C 298 "
      ideal   model   delta    sigma   weight residual
     110.45  116.56   -6.11 1.30e+00 5.92e-01 2.21e+01
  ... (remaining 3645 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.04 -    15.37: 1351
       15.37 -    30.71: 144
       30.71 -    46.04: 35
       46.04 -    61.37: 20
       61.37 -    76.70: 10
  Dihedral angle restraints: 1560
    sinusoidal: 575
      harmonic: 985
  Sorted by residual:
  dihedral pdb=" CA  GLN C 327 "
           pdb=" C   GLN C 327 "
           pdb=" N   ALA C 328 "
           pdb=" CA  ALA C 328 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.31  -22.69     0      5.00e+00 4.00e-02 2.06e+01
  dihedral pdb=" CA  GLN B 327 "
           pdb=" C   GLN B 327 "
           pdb=" N   ALA B 328 "
           pdb=" CA  ALA B 328 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.32  -22.68     0      5.00e+00 4.00e-02 2.06e+01
  dihedral pdb=" CA  GLN A 327 "
           pdb=" C   GLN A 327 "
           pdb=" N   ALA A 328 "
           pdb=" CA  ALA A 328 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.35  -22.65     0      5.00e+00 4.00e-02 2.05e+01
  ... (remaining 1557 not shown)

  Histogram of chiral volume deviations from ideal:
       0.003 -    0.042: 110
       0.042 -    0.080: 102
       0.080 -    0.119: 58
       0.119 -    0.157: 30
       0.157 -    0.196: 15
  Chirality restraints: 315
  Sorted by residual:
  chirality pdb=" CA  LEU B 299 "
            pdb=" N   LEU B 299 "
            pdb=" C   LEU B 299 "
            pdb=" CB  LEU B 299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.61e-01
  chirality pdb=" CA  LEU D 299 "
            pdb=" N   LEU D 299 "
            pdb=" C   LEU D 299 "
            pdb=" CB  LEU D 299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.56e-01
  chirality pdb=" CA  LEU C 299 "
            pdb=" N   LEU C 299 "
            pdb=" C   LEU C 299 "
            pdb=" CB  LEU C 299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.55e-01
  ... (remaining 312 not shown)

  Planarity restraints: 545
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 334 "   -0.038 2.00e-02 2.50e+03   2.54e-02 1.61e+01
        pdb=" CG  TRP C 334 "    0.066 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 334 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 334 "    0.007 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 334 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 334 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 334 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 334 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 334 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 334 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 334 "   -0.038 2.00e-02 2.50e+03   2.53e-02 1.60e+01
        pdb=" CG  TRP A 334 "    0.066 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 334 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 334 "    0.007 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 334 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 334 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 334 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 334 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 334 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 334 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP U 334 "   -0.038 2.00e-02 2.50e+03   2.53e-02 1.60e+01
        pdb=" CG  TRP U 334 "    0.066 2.00e-02 2.50e+03
        pdb=" CD1 TRP U 334 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TRP U 334 "    0.007 2.00e-02 2.50e+03
        pdb=" NE1 TRP U 334 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE2 TRP U 334 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE3 TRP U 334 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP U 334 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ3 TRP U 334 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP U 334 "    0.009 2.00e-02 2.50e+03
  ... (remaining 542 not shown)

  Histogram of nonbonded interaction distances:
        2.64 -     3.09: 1721
        3.09 -     3.54: 2400
        3.54 -     3.99: 4064
        3.99 -     4.45: 4901
        4.45 -     4.90: 7677
  Nonbonded interactions: 20763
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 315 "
            pdb=" OG  SER B 317 "
     model   vdw
     2.637 3.040
  nonbonded pdb=" O   ALA C 315 "
            pdb=" OG  SER C 317 "
     model   vdw
     2.637 3.040
  nonbonded pdb=" O   ALA U 315 "
            pdb=" OG  SER U 317 "
     model   vdw
     2.638 3.040
  nonbonded pdb=" O   ALA D 315 "
            pdb=" OG  SER D 317 "
     model   vdw
     2.638 3.040
  nonbonded pdb=" O   ALA A 315 "
            pdb=" OG  SER A 317 "
     model   vdw
     2.638 3.040
  ... (remaining 20758 not shown)

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

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 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:             1.070
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     3.280
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:6.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9119
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      :  0.011   0.070   2745  Z= 0.721
  Angle     :  1.669   7.732   3650  Z= 1.087
  Chirality :  0.081   0.196    315
  Planarity :  0.007   0.025    545
  Dihedral  : 16.619  76.701    970
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.54 %
    Favored  : 88.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.62 (0.16), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.28 (0.12), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 293 
 PHE   0.009   0.003   PHE B 313 
 TRP   0.066   0.017   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.01110 ( 2745)
  covalent geometry    : angle       1.66864 ( 3650)
  hydrogen bonds       : bond        0.29984 (   30)
  hydrogen bonds       : angle       6.34445 (   90)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.118 
Fit side-chains
REVERT: U  359 MET cc_start: 0.9206 (ttm) cc_final: 0.8973 (ttm)
REVERT: U  360 GLN cc_start: 0.8028 (mt0) cc_final: 0.7256 (tm-30)
REVERT: A  337 MET cc_start: 0.8073 (mtm) cc_final: 0.7860 (mtt)
REVERT: A  360 GLN cc_start: 0.8219 (mt0) cc_final: 0.7481 (tm-30)
REVERT: B  322 MET cc_start: 0.9289 (mtt) cc_final: 0.9064 (mtt)
REVERT: B  360 GLN cc_start: 0.7926 (mt0) cc_final: 0.7288 (tm-30)
REVERT: C  293 ARG cc_start: 0.7001 (mtp85) cc_final: 0.5748 (mmp-170)
REVERT: C  336 MET cc_start: 0.8879 (ttm) cc_final: 0.8612 (ttp)
REVERT: C  359 MET cc_start: 0.9181 (ttm) cc_final: 0.8717 (ttm)
REVERT: C  360 GLN cc_start: 0.7942 (mt0) cc_final: 0.7313 (tm-30)
REVERT: D  336 MET cc_start: 0.8655 (ttm) cc_final: 0.8390 (ttp)
REVERT: D  360 GLN cc_start: 0.8028 (mt0) cc_final: 0.7431 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.4702
  time to fit residues: 33.6525
Evaluate side-chains
  67 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    7.9990
   chunk 25 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
B 345 ASN
C 345 ASN
D 345 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.104450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.079944 restraints weight = 2903.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 2.34
r_work: 0.3069 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8961
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2745  Z= 0.185
  Angle     :  0.832   6.394   3650  Z= 0.439
  Chirality :  0.040   0.116    315
  Planarity :  0.002   0.012    545
  Dihedral  :  5.920  18.746    400
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 0.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  9.20 %
    Favored  : 89.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.35 (0.15), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.07 (0.12), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 293 
 PHE   0.011   0.002   PHE B 283 
 TRP   0.023   0.005   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 2745)
  covalent geometry    : angle       0.83233 ( 3650)
  hydrogen bonds       : bond        0.04349 (   30)
  hydrogen bonds       : angle       5.21077 (   90)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.105 
Fit side-chains
REVERT: U  360 GLN cc_start: 0.7703 (mt0) cc_final: 0.7008 (tm-30)
REVERT: A  337 MET cc_start: 0.8080 (mtm) cc_final: 0.7800 (mtt)
REVERT: A  360 GLN cc_start: 0.7889 (mt0) cc_final: 0.7228 (tm-30)
REVERT: B  360 GLN cc_start: 0.7636 (mt0) cc_final: 0.7106 (tm-30)
REVERT: C  359 MET cc_start: 0.9146 (ttm) cc_final: 0.8871 (ttm)
REVERT: C  360 GLN cc_start: 0.7627 (mt0) cc_final: 0.7109 (tm-30)
REVERT: D  336 MET cc_start: 0.8562 (ttm) cc_final: 0.8266 (ttp)
REVERT: D  360 GLN cc_start: 0.7689 (mt0) cc_final: 0.7311 (tm-30)
  outliers start: 3
  outliers final: 2
  residues processed: 64
  average time/residue: 0.5137
  time to fit residues: 33.6459
Evaluate side-chains
  57 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  292 SER
Chi-restraints excluded: chain D residue  292 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 2 optimal weight:    8.9990
   chunk 1 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 17 optimal weight:    7.9990
   chunk 4 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    2.1386

-------------------------------------------------------------------------------
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 = 0.3544 r_free = 0.3544 target = 0.105948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.081129 restraints weight = 2914.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 2.37
r_work: 0.3094 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2984 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8938
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2745  Z= 0.125
  Angle     :  0.690   5.202   3650  Z= 0.362
  Chirality :  0.038   0.114    315
  Planarity :  0.002   0.014    545
  Dihedral  :  5.154  17.314    400
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 0.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  9.60 %
    Favored  : 89.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.16 (0.15), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.93 (0.12), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 293 
 PHE   0.014   0.002   PHE C 283 
 TRP   0.016   0.003   TRP C 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 2745)
  covalent geometry    : angle       0.69039 ( 3650)
  hydrogen bonds       : bond        0.03180 (   30)
  hydrogen bonds       : angle       4.99540 (   90)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.104 
Fit side-chains
REVERT: U  360 GLN cc_start: 0.7708 (mt0) cc_final: 0.7081 (tm-30)
REVERT: A  337 MET cc_start: 0.8036 (mtm) cc_final: 0.7806 (mtt)
REVERT: A  360 GLN cc_start: 0.7864 (mt0) cc_final: 0.7216 (tm-30)
REVERT: B  360 GLN cc_start: 0.7594 (mt0) cc_final: 0.7105 (tm-30)
REVERT: C  359 MET cc_start: 0.9205 (ttm) cc_final: 0.8878 (ttm)
REVERT: C  360 GLN cc_start: 0.7591 (mt0) cc_final: 0.7172 (tm-30)
REVERT: D  336 MET cc_start: 0.8489 (ttm) cc_final: 0.8187 (ttp)
REVERT: D  360 GLN cc_start: 0.7715 (mt0) cc_final: 0.7354 (tm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 58
  average time/residue: 0.6251
  time to fit residues: 37.0018
Evaluate side-chains
  57 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  292 SER
Chi-restraints excluded: chain D residue  292 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 13 optimal weight:    5.9990
   chunk 2 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   chunk 16 optimal weight:    9.9990
   chunk 32 optimal weight:   10.0000
   chunk 14 optimal weight:    0.0770
   chunk 37 optimal weight:    7.9990
   chunk 4 optimal weight:    4.9990
   overall best weight:    2.7744

-------------------------------------------------------------------------------
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 = 0.3533 r_free = 0.3533 target = 0.105183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.080303 restraints weight = 2858.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 2.35
r_work: 0.3081 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8950
moved from start:          0.2027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2745  Z= 0.144
  Angle     :  0.713   4.813   3650  Z= 0.379
  Chirality :  0.038   0.114    315
  Planarity :  0.002   0.016    545
  Dihedral  :  5.143  17.700    400
  Min Nonbonded Distance : 2.646

Molprobity Statistics.
  All-atom Clashscore : 0.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 11.60 %
    Favored  : 87.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.05 (0.16), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.84 (0.12), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 293 
 PHE   0.013   0.002   PHE B 283 
 TRP   0.016   0.003   TRP D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 2745)
  covalent geometry    : angle       0.71345 ( 3650)
  hydrogen bonds       : bond        0.03501 (   30)
  hydrogen bonds       : angle       4.87226 (   90)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.116 
Fit side-chains
REVERT: U  360 GLN cc_start: 0.7792 (mt0) cc_final: 0.7132 (tm-30)
REVERT: A  337 MET cc_start: 0.8085 (mtm) cc_final: 0.7835 (mtt)
REVERT: A  360 GLN cc_start: 0.7886 (mt0) cc_final: 0.7255 (tm-30)
REVERT: B  360 GLN cc_start: 0.7637 (mt0) cc_final: 0.7131 (tm-30)
REVERT: C  359 MET cc_start: 0.9178 (ttm) cc_final: 0.8867 (ttm)
REVERT: C  360 GLN cc_start: 0.7714 (mt0) cc_final: 0.7086 (tm-30)
REVERT: D  336 MET cc_start: 0.8326 (ttm) cc_final: 0.8047 (ttp)
REVERT: D  360 GLN cc_start: 0.7732 (mt0) cc_final: 0.7446 (tm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 57
  average time/residue: 0.6094
  time to fit residues: 35.4179
Evaluate side-chains
  57 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  292 SER
Chi-restraints excluded: chain D residue  292 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 19 optimal weight:   10.0000
   chunk 12 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 3 optimal weight:   10.0000
   chunk 24 optimal weight:    6.9990
   chunk 16 optimal weight:   20.0000
   chunk 18 optimal weight:   10.0000
   chunk 17 optimal weight:   20.0000
   chunk 5 optimal weight:    9.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    4.7988

-------------------------------------------------------------------------------
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 = 0.3497 r_free = 0.3497 target = 0.103354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.078244 restraints weight = 2881.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 2.36
r_work: 0.3036 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8983
moved from start:          0.1986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2745  Z= 0.215
  Angle     :  0.822   5.650   3650  Z= 0.443
  Chirality :  0.040   0.114    315
  Planarity :  0.003   0.017    545
  Dihedral  :  5.509  19.644    400
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 0.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 10.80 %
    Favored  : 88.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.03 (0.16), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.83 (0.12), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 293 
 PHE   0.018   0.003   PHE C 283 
 TRP   0.021   0.004   TRP D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 2745)
  covalent geometry    : angle       0.82178 ( 3650)
  hydrogen bonds       : bond        0.04682 (   30)
  hydrogen bonds       : angle       4.94096 (   90)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.087 
Fit side-chains
REVERT: U  360 GLN cc_start: 0.7723 (mt0) cc_final: 0.7240 (tm-30)
REVERT: A  337 MET cc_start: 0.8051 (mtm) cc_final: 0.7712 (mtt)
REVERT: A  360 GLN cc_start: 0.7945 (mt0) cc_final: 0.7320 (tm-30)
REVERT: B  360 GLN cc_start: 0.7709 (mt0) cc_final: 0.7232 (tm-30)
REVERT: C  359 MET cc_start: 0.9215 (ttm) cc_final: 0.8896 (ttm)
REVERT: C  360 GLN cc_start: 0.7806 (mt0) cc_final: 0.7189 (tm-30)
REVERT: D  360 GLN cc_start: 0.7799 (mt0) cc_final: 0.7549 (tm-30)
  outliers start: 3
  outliers final: 1
  residues processed: 57
  average time/residue: 0.6131
  time to fit residues: 35.6272
Evaluate side-chains
  56 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  292 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 9 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 38 optimal weight:    9.9990
   chunk 0 optimal weight:   30.0000
   chunk 22 optimal weight:    9.9990
   chunk 11 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 21 optimal weight:    9.9990
   chunk 17 optimal weight:    7.9990
   overall best weight:    5.9990

-------------------------------------------------------------------------------
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 = 0.3500 r_free = 0.3500 target = 0.102759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.077705 restraints weight = 2904.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 2.36
r_work: 0.3033 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8998
moved from start:          0.1883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   2745  Z= 0.259
  Angle     :  0.893   6.219   3650  Z= 0.484
  Chirality :  0.042   0.115    315
  Planarity :  0.003   0.018    545
  Dihedral  :  5.727  19.765    400
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 0.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.60 %
    Favored  : 88.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.02 (0.16), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.82 (0.12), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 293 
 PHE   0.018   0.003   PHE B 283 
 TRP   0.023   0.005   TRP D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 ( 2745)
  covalent geometry    : angle       0.89252 ( 3650)
  hydrogen bonds       : bond        0.05320 (   30)
  hydrogen bonds       : angle       5.05441 (   90)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.123 
Fit side-chains
REVERT: U  360 GLN cc_start: 0.7791 (mt0) cc_final: 0.7364 (tm-30)
REVERT: A  337 MET cc_start: 0.8092 (mtm) cc_final: 0.7769 (mtt)
REVERT: A  360 GLN cc_start: 0.8095 (mt0) cc_final: 0.7445 (tm-30)
REVERT: B  360 GLN cc_start: 0.7809 (mt0) cc_final: 0.7245 (tm-30)
REVERT: C  360 GLN cc_start: 0.7830 (mt0) cc_final: 0.7237 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.5976
  time to fit residues: 34.1120
Evaluate side-chains
  56 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 5 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 10 optimal weight:    0.6980
   chunk 29 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 19 optimal weight:    9.9990
   chunk 22 optimal weight:    2.9990
   chunk 9 optimal weight:    9.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    4.1388

-------------------------------------------------------------------------------
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 = 0.3521 r_free = 0.3521 target = 0.103746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.078702 restraints weight = 2926.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 2.37
r_work: 0.3055 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8974
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2745  Z= 0.192
  Angle     :  0.806   6.566   3650  Z= 0.430
  Chirality :  0.040   0.115    315
  Planarity :  0.003   0.018    545
  Dihedral  :  5.446  19.016    400
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 0.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 13.20 %
    Favored  : 86.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.97 (0.16), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.78 (0.12), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 293 
 PHE   0.017   0.002   PHE C 283 
 TRP   0.019   0.004   TRP D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 2745)
  covalent geometry    : angle       0.80597 ( 3650)
  hydrogen bonds       : bond        0.04275 (   30)
  hydrogen bonds       : angle       4.95863 (   90)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.070 
Fit side-chains
REVERT: U  360 GLN cc_start: 0.7751 (mt0) cc_final: 0.7360 (tm-30)
REVERT: A  337 MET cc_start: 0.8070 (mtm) cc_final: 0.7748 (mtt)
REVERT: A  360 GLN cc_start: 0.8075 (mt0) cc_final: 0.7467 (tm-30)
REVERT: B  360 GLN cc_start: 0.7811 (mt0) cc_final: 0.7280 (tm-30)
REVERT: C  359 MET cc_start: 0.9087 (ttm) cc_final: 0.8775 (ttm)
REVERT: C  360 GLN cc_start: 0.7721 (mt0) cc_final: 0.7221 (tm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 56
  average time/residue: 0.5862
  time to fit residues: 33.4605
Evaluate side-chains
  57 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  292 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    9.9990
   chunk 36 optimal weight:    3.9990
   chunk 26 optimal weight:   20.0000
   chunk 17 optimal weight:   20.0000
   chunk 10 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 3 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
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 = 0.3514 r_free = 0.3514 target = 0.103426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.078312 restraints weight = 2966.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3169 rms_B_bonded: 2.38
r_work: 0.3046 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8981
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2745  Z= 0.210
  Angle     :  0.835   6.444   3650  Z= 0.447
  Chirality :  0.040   0.115    315
  Planarity :  0.003   0.018    545
  Dihedral  :  5.506  19.391    400
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 0.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 13.20 %
    Favored  : 86.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.97 (0.17), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.78 (0.13), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 293 
 PHE   0.019   0.002   PHE B 283 
 TRP   0.020   0.004   TRP D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 2745)
  covalent geometry    : angle       0.83480 ( 3650)
  hydrogen bonds       : bond        0.04543 (   30)
  hydrogen bonds       : angle       4.99365 (   90)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.100 
Fit side-chains
REVERT: U  360 GLN cc_start: 0.7827 (mt0) cc_final: 0.7405 (tm-30)
REVERT: A  337 MET cc_start: 0.8047 (mtm) cc_final: 0.7716 (mtt)
REVERT: A  360 GLN cc_start: 0.8059 (mt0) cc_final: 0.7509 (tm-30)
REVERT: B  360 GLN cc_start: 0.7828 (mt0) cc_final: 0.7319 (tm-30)
REVERT: C  360 GLN cc_start: 0.7747 (mt0) cc_final: 0.7255 (tm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 57
  average time/residue: 0.6087
  time to fit residues: 35.3865
Evaluate side-chains
  57 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  292 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 13 optimal weight:    8.9990
   chunk 9 optimal weight:    9.9990
   chunk 27 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9980
   chunk 21 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    2.5386

-------------------------------------------------------------------------------
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 = 0.3545 r_free = 0.3545 target = 0.105154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.080089 restraints weight = 2966.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 2.40
r_work: 0.3080 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8948
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2745  Z= 0.137
  Angle     :  0.710   5.863   3650  Z= 0.375
  Chirality :  0.038   0.115    315
  Planarity :  0.002   0.017    545
  Dihedral  :  5.052  17.230    400
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 0.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.60 %
    Favored  : 86.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.90 (0.17), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.72 (0.13), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 293 
 PHE   0.018   0.002   PHE C 283 
 TRP   0.015   0.003   TRP A 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 2745)
  covalent geometry    : angle       0.70998 ( 3650)
  hydrogen bonds       : bond        0.03272 (   30)
  hydrogen bonds       : angle       4.81925 (   90)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.078 
Fit side-chains
REVERT: U  360 GLN cc_start: 0.7847 (mt0) cc_final: 0.7366 (tm-30)
REVERT: A  337 MET cc_start: 0.8056 (mtm) cc_final: 0.7741 (mtt)
REVERT: A  360 GLN cc_start: 0.8095 (mt0) cc_final: 0.7536 (tm-30)
REVERT: B  360 GLN cc_start: 0.7841 (mt0) cc_final: 0.7372 (tm-30)
REVERT: C  360 GLN cc_start: 0.7794 (mt0) cc_final: 0.7293 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.6153
  time to fit residues: 34.4771
Evaluate side-chains
  55 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 8 optimal weight:   20.0000
   chunk 19 optimal weight:   20.0000
   chunk 34 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 3 optimal weight:    5.9990
   chunk 4 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 30 optimal weight:    8.9990
   overall best weight:    5.5990

-------------------------------------------------------------------------------
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 = 0.3516 r_free = 0.3516 target = 0.103089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.077959 restraints weight = 2962.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 2.37
r_work: 0.3046 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8992
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   2745  Z= 0.245
  Angle     :  0.877   6.144   3650  Z= 0.474
  Chirality :  0.041   0.116    315
  Planarity :  0.003   0.019    545
  Dihedral  :  5.586  19.884    400
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 0.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.20 %
    Favored  : 86.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.97 (0.17), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.78 (0.13), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 293 
 PHE   0.019   0.003   PHE B 283 
 TRP   0.021   0.005   TRP D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 ( 2745)
  covalent geometry    : angle       0.87703 ( 3650)
  hydrogen bonds       : bond        0.05092 (   30)
  hydrogen bonds       : angle       5.03110 (   90)

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.114 
Fit side-chains
REVERT: U  360 GLN cc_start: 0.7737 (mt0) cc_final: 0.7354 (tm-30)
REVERT: A  337 MET cc_start: 0.8072 (mtm) cc_final: 0.7742 (mtt)
REVERT: A  360 GLN cc_start: 0.8069 (mt0) cc_final: 0.7546 (tm-30)
REVERT: B  360 GLN cc_start: 0.7863 (mt0) cc_final: 0.7389 (tm-30)
REVERT: C  360 GLN cc_start: 0.7763 (mt0) cc_final: 0.7274 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.6205
  time to fit residues: 35.4367
Evaluate side-chains
  56 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 2 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 26 optimal weight:    8.9990
   chunk 17 optimal weight:   20.0000
   chunk 37 optimal weight:    6.9990
   chunk 13 optimal weight:    8.9990
   chunk 23 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    5.1988

-------------------------------------------------------------------------------
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 = 0.3507 r_free = 0.3507 target = 0.103081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.077999 restraints weight = 2926.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 2.36
r_work: 0.3040 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8985
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   2745  Z= 0.231
  Angle     :  0.858   6.061   3650  Z= 0.462
  Chirality :  0.041   0.116    315
  Planarity :  0.003   0.017    545
  Dihedral  :  5.524  19.633    400
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 0.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.60 %
    Favored  : 86.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.97 (0.17), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.78 (0.13), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B 293 
 PHE   0.021   0.003   PHE U 283 
 TRP   0.021   0.004   TRP D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 2745)
  covalent geometry    : angle       0.85840 ( 3650)
  hydrogen bonds       : bond        0.04879 (   30)
  hydrogen bonds       : angle       5.02596 (   90)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1079.32 seconds
wall clock time: 19 minutes 3.94 seconds (1143.94 seconds total)