Starting phenix.real_space_refine
on Wed Mar  5 16:26:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cgg_16642/03_2025/8cgg_16642.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cgg_16642/03_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_16642/03_2025/8cgg_16642.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cgg_16642/03_2025/8cgg_16642.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cgg_16642/03_2025/8cgg_16642.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cgg_16642/03_2025/8cgg_16642.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 2710
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      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:
    C, B, U, D
  Time building chain proxies: 1.36, per 1000 atoms: 0.50
  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: 0.58
  Conformation dependent library (CDL) restraints added in 343.0 milliseconds
  

  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: 0.39
  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: 0.59

  Time building geometry restraints manager: 0.70 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'U'
  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:             0.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.170
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.180
-------------------------------------------------------------------------------
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 (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: -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
 TRP   0.066   0.017   TRP C 334 
 PHE   0.009   0.003   PHE B 313 
 ARG   0.001   0.000   ARG D 293 

*********************** 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  : 0.314 
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: 1.2764
  time to fit residues: 91.3730
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  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    0.0970
   chunk 30 optimal weight:    5.9990
   chunk 16 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.9580

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.109156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.085520 restraints weight = 2914.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 2.33
r_work: 0.3184 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3079 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8865
moved from start:          0.2157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2745  Z= 0.135
  Angle     :  0.651   5.472   3650  Z= 0.333
  Chirality :  0.037   0.117    315
  Planarity :  0.002   0.007    545
  Dihedral  :  5.101  16.819    400
  Min Nonbonded Distance : 2.652

Molprobity Statistics.
  All-atom Clashscore : 0.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  8.80 %
    Favored  : 90.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -5.15 (0.15), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.92 (0.12), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP B 334 
 PHE   0.013   0.001   PHE B 283 
 ARG   0.000   0.000   ARG D 293 

*********************** 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
  69 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 67
  time to evaluate  : 0.260 
Fit side-chains
REVERT: U  360 GLN cc_start: 0.7727 (mt0) cc_final: 0.7006 (tm-30)
REVERT: A  336 MET cc_start: 0.8456 (ttp) cc_final: 0.8218 (ttm)
REVERT: A  337 MET cc_start: 0.7988 (mtm) cc_final: 0.7713 (mtt)
REVERT: A  360 GLN cc_start: 0.7868 (mt0) cc_final: 0.7219 (tm-30)
REVERT: B  360 GLN cc_start: 0.7575 (mt0) cc_final: 0.7061 (tm-30)
REVERT: C  359 MET cc_start: 0.9156 (ttm) cc_final: 0.8860 (ttm)
REVERT: C  360 GLN cc_start: 0.7672 (mt0) cc_final: 0.7222 (tm-30)
REVERT: D  360 GLN cc_start: 0.7586 (mt0) cc_final: 0.7155 (tm-30)
  outliers start: 2
  outliers final: 0
  residues processed: 69
  average time/residue: 1.1915
  time to fit residues: 84.1449
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  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 25 optimal weight:   30.0000
   chunk 26 optimal weight:    6.9990
   chunk 6 optimal weight:    0.7980
   chunk 17 optimal weight:   10.0000
   chunk 38 optimal weight:    9.9990
   chunk 28 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 23 optimal weight:   20.0000
   chunk 24 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   overall best weight:    4.9588

-------------------------------------------------------------------------------
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 = 0.3496 r_free = 0.3496 target = 0.103252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.078266 restraints weight = 2860.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 2.36
r_work: 0.3040 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2932 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8988
moved from start:          0.1925

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= 0.304
  Angle     :  0.871   6.198   3650  Z= 0.466
  Chirality :  0.041   0.115    315
  Planarity :  0.003   0.013    545
  Dihedral  :  5.673  19.665    400
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 0.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  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 (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: -5.21 (0.15), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.96 (0.12), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.005   TRP D 334 
 PHE   0.016   0.002   PHE U 283 
 ARG   0.001   0.000   ARG B 293 

*********************** 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: 3
    poor density    : 55
  time to evaluate  : 0.263 
Fit side-chains
REVERT: U  360 GLN cc_start: 0.7648 (mt0) cc_final: 0.7154 (tm-30)
REVERT: A  336 MET cc_start: 0.8480 (ttp) cc_final: 0.8257 (ttm)
REVERT: A  337 MET cc_start: 0.8059 (mtm) cc_final: 0.7764 (mtt)
REVERT: A  360 GLN cc_start: 0.7885 (mt0) cc_final: 0.7214 (tm-30)
REVERT: B  360 GLN cc_start: 0.7598 (mt0) cc_final: 0.7136 (tm-30)
REVERT: C  360 GLN cc_start: 0.7660 (mt0) cc_final: 0.7130 (tm-30)
REVERT: D  360 GLN cc_start: 0.7642 (mt0) cc_final: 0.7265 (tm-30)
  outliers start: 3
  outliers final: 1
  residues processed: 57
  average time/residue: 1.4593
  time to fit residues: 84.8789
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  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  355 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 16 optimal weight:    0.0770
   chunk 9 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 33 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 1 optimal weight:   20.0000
   overall best weight:    3.6146

-------------------------------------------------------------------------------
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 = 0.104256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.079055 restraints weight = 2924.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 2.39
r_work: 0.3057 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2950 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8963
moved from start:          0.2094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2745  Z= 0.235
  Angle     :  0.775   5.392   3650  Z= 0.411
  Chirality :  0.039   0.115    315
  Planarity :  0.002   0.015    545
  Dihedral  :  5.365  18.735    400
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 0.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 12.00 %
    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 (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: -5.06 (0.16), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.85 (0.12), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.004   TRP D 334 
 PHE   0.016   0.002   PHE U 283 
 ARG   0.000   0.000   ARG U 293 

*********************** 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
  58 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.280 
Fit side-chains
REVERT: U  360 GLN cc_start: 0.7690 (mt0) cc_final: 0.7154 (tm-30)
REVERT: A  337 MET cc_start: 0.8001 (mtm) cc_final: 0.7675 (mtt)
REVERT: A  360 GLN cc_start: 0.7932 (mt0) cc_final: 0.7282 (tm-30)
REVERT: B  360 GLN cc_start: 0.7615 (mt0) cc_final: 0.7137 (tm-30)
REVERT: C  360 GLN cc_start: 0.7708 (mt0) cc_final: 0.7129 (tm-30)
REVERT: D  360 GLN cc_start: 0.7674 (mt0) cc_final: 0.7421 (tm-30)
  outliers start: 3
  outliers final: 2
  residues processed: 58
  average time/residue: 1.4244
  time to fit residues: 84.3569
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  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  292 SER
Chi-restraints excluded: chain D residue  355 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   chunk 19 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 23 optimal weight:    9.9990
   chunk 0 optimal weight:   30.0000
   chunk 37 optimal weight:    0.9990
   chunk 27 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 20 optimal weight:    7.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
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 = 0.3502 r_free = 0.3502 target = 0.103474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.078067 restraints weight = 2898.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 2.38
r_work: 0.3039 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2931 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8990
moved from start:          0.2052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   2745  Z= 0.305
  Angle     :  0.849   5.897   3650  Z= 0.456
  Chirality :  0.041   0.114    315
  Planarity :  0.003   0.019    545
  Dihedral  :  5.588  19.738    400
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 0.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.40 %
    Favored  : 86.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -5.04 (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
 TRP   0.022   0.005   TRP D 334 
 PHE   0.019   0.003   PHE C 283 
 ARG   0.001   0.000   ARG B 293 

*********************** 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
  59 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.219 
Fit side-chains
REVERT: U  360 GLN cc_start: 0.7704 (mt0) cc_final: 0.7242 (tm-30)
REVERT: A  337 MET cc_start: 0.8080 (mtm) cc_final: 0.7747 (mtt)
REVERT: A  360 GLN cc_start: 0.7979 (mt0) cc_final: 0.7364 (tm-30)
REVERT: B  360 GLN cc_start: 0.7703 (mt0) cc_final: 0.7180 (tm-30)
REVERT: C  360 GLN cc_start: 0.7752 (mt0) cc_final: 0.7189 (tm-30)
REVERT: D  360 GLN cc_start: 0.7785 (mt0) cc_final: 0.7565 (tm-30)
  outliers start: 4
  outliers final: 1
  residues processed: 58
  average time/residue: 1.4422
  time to fit residues: 85.3084
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  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  355 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 31 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 29 optimal weight:    8.9990
   chunk 25 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 1 optimal weight:   20.0000
   chunk 39 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   overall best weight:    2.7588

-------------------------------------------------------------------------------
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 = 0.3536 r_free = 0.3536 target = 0.105372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.079926 restraints weight = 2972.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 2.43
r_work: 0.3075 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8954
moved from start:          0.2236

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= 0.193
  Angle     :  0.714   4.735   3650  Z= 0.378
  Chirality :  0.038   0.115    315
  Planarity :  0.002   0.016    545
  Dihedral  :  5.137  17.934    400
  Min Nonbonded Distance : 2.646

Molprobity Statistics.
  All-atom Clashscore : 0.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 13.20 %
    Favored  : 85.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.93 (0.16), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.75 (0.13), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP A 334 
 PHE   0.018   0.002   PHE U 283 
 ARG   0.000   0.000   ARG A 293 

*********************** 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
  58 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.296 
Fit side-chains
REVERT: U  360 GLN cc_start: 0.7773 (mt0) cc_final: 0.7174 (tm-30)
REVERT: A  337 MET cc_start: 0.8046 (mtm) cc_final: 0.7714 (mtt)
REVERT: A  360 GLN cc_start: 0.8043 (mt0) cc_final: 0.7414 (tm-30)
REVERT: B  360 GLN cc_start: 0.7691 (mt0) cc_final: 0.7188 (tm-30)
REVERT: C  360 GLN cc_start: 0.7786 (mt0) cc_final: 0.7192 (tm-30)
  outliers start: 3
  outliers final: 2
  residues processed: 58
  average time/residue: 1.3475
  time to fit residues: 79.7972
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  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  355 ASN
Chi-restraints excluded: chain C residue  292 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 24 optimal weight:    7.9990
   chunk 10 optimal weight:   10.0000
   chunk 36 optimal weight:    0.0670
   chunk 8 optimal weight:   20.0000
   chunk 9 optimal weight:    9.9990
   chunk 30 optimal weight:    2.9990
   chunk 17 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 31 optimal weight:    8.9990
   chunk 13 optimal weight:    8.9990
   overall best weight:    4.4126

-------------------------------------------------------------------------------
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 = 0.3518 r_free = 0.3518 target = 0.103986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.078475 restraints weight = 3027.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 2.44
r_work: 0.3051 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8984
moved from start:          0.2195

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= 0.278
  Angle     :  0.818   5.388   3650  Z= 0.438
  Chirality :  0.040   0.115    315
  Planarity :  0.003   0.017    545
  Dihedral  :  5.432  19.269    400
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 0.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 13.60 %
    Favored  : 85.20 %
  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: -4.96 (0.16), 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
 TRP   0.019   0.004   TRP D 334 
 PHE   0.019   0.003   PHE C 283 
 ARG   0.001   0.000   ARG B 293 

*********************** 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
  58 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.280 
Fit side-chains
REVERT: U  360 GLN cc_start: 0.7800 (mt0) cc_final: 0.7388 (tm-30)
REVERT: A  337 MET cc_start: 0.8064 (mtm) cc_final: 0.7722 (mtt)
REVERT: A  360 GLN cc_start: 0.8082 (mt0) cc_final: 0.7473 (tm-30)
REVERT: B  360 GLN cc_start: 0.7729 (mt0) cc_final: 0.7266 (tm-30)
REVERT: C  360 GLN cc_start: 0.7743 (mt0) cc_final: 0.7221 (tm-30)
  outliers start: 3
  outliers final: 1
  residues processed: 58
  average time/residue: 1.4179
  time to fit residues: 84.0142
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  : 0.295 
-------------------------------------------------------------------------------
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 33 optimal weight:   20.0000
   chunk 31 optimal weight:    9.9990
   chunk 17 optimal weight:   20.0000
   chunk 39 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 22 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9990
   chunk 1 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   overall best weight:    3.1988

-------------------------------------------------------------------------------
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 = 0.3535 r_free = 0.3535 target = 0.104731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.079546 restraints weight = 2923.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 2.40
r_work: 0.3074 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8959
moved from start:          0.2293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2745  Z= 0.219
  Angle     :  0.745   4.711   3650  Z= 0.396
  Chirality :  0.038   0.115    315
  Planarity :  0.002   0.017    545
  Dihedral  :  5.176  18.189    400
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 0.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 15.20 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.93 (0.17), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.75 (0.13), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP A 334 
 PHE   0.018   0.002   PHE U 283 
 ARG   0.000   0.000   ARG C 293 

*********************** 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
  56 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.292 
Fit side-chains
REVERT: U  360 GLN cc_start: 0.7775 (mt0) cc_final: 0.7298 (tm-30)
REVERT: A  337 MET cc_start: 0.8056 (mtm) cc_final: 0.7736 (mtt)
REVERT: A  360 GLN cc_start: 0.8096 (mt0) cc_final: 0.7494 (tm-30)
REVERT: B  360 GLN cc_start: 0.7755 (mt0) cc_final: 0.7300 (tm-30)
REVERT: C  360 GLN cc_start: 0.7747 (mt0) cc_final: 0.7214 (tm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 56
  average time/residue: 1.4264
  time to fit residues: 81.5380
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  : 0.293 
-------------------------------------------------------------------------------
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 15 optimal weight:    8.9990
   chunk 11 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 6 optimal weight:   10.0000
   chunk 32 optimal weight:   20.0000
   chunk 21 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0000
   chunk 7 optimal weight:    9.9990
   overall best weight:    2.9992

-------------------------------------------------------------------------------
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 = 0.3538 r_free = 0.3538 target = 0.104876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.079694 restraints weight = 2937.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 2.40
r_work: 0.3076 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8954
moved from start:          0.2322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2745  Z= 0.211
  Angle     :  0.735   4.690   3650  Z= 0.390
  Chirality :  0.038   0.115    315
  Planarity :  0.002   0.016    545
  Dihedral  :  5.139  18.066    400
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 0.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 15.20 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.90 (0.17), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.73 (0.13), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP A 334 
 PHE   0.019   0.002   PHE C 283 
 ARG   0.001   0.000   ARG B 293 

*********************** 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
  57 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.259 
Fit side-chains
REVERT: U  360 GLN cc_start: 0.7820 (mt0) cc_final: 0.7336 (tm-30)
REVERT: A  337 MET cc_start: 0.8057 (mtm) cc_final: 0.7734 (mtt)
REVERT: A  360 GLN cc_start: 0.8073 (mt0) cc_final: 0.7506 (tm-30)
REVERT: B  360 GLN cc_start: 0.7789 (mt0) cc_final: 0.7361 (tm-30)
REVERT: C  360 GLN cc_start: 0.7743 (mt0) cc_final: 0.7220 (tm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 57
  average time/residue: 1.4331
  time to fit residues: 83.3399
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  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  355 ASN
Chi-restraints excluded: chain C residue  292 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 14 optimal weight:    7.9990
   chunk 17 optimal weight:   20.0000
   chunk 35 optimal weight:    8.9990
   chunk 30 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 21 optimal weight:   10.0000
   chunk 20 optimal weight:    7.9990
   chunk 9 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
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 = 0.3519 r_free = 0.3519 target = 0.103363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.078144 restraints weight = 2944.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 2.38
r_work: 0.3051 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2940 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8988
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   2745  Z= 0.329
  Angle     :  0.869   5.826   3650  Z= 0.469
  Chirality :  0.041   0.116    315
  Planarity :  0.003   0.016    545
  Dihedral  :  5.562  19.763    400
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 0.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 15.60 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -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
 TRP   0.021   0.004   TRP D 334 
 PHE   0.019   0.003   PHE U 283 
 ARG   0.000   0.000   ARG B 293 

********************** 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
  57 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.395 
Fit side-chains
REVERT: U  360 GLN cc_start: 0.7721 (mt0) cc_final: 0.7355 (tm-30)
REVERT: A  337 MET cc_start: 0.8061 (mtm) cc_final: 0.7707 (mtt)
REVERT: A  360 GLN cc_start: 0.8080 (mt0) cc_final: 0.7541 (tm-30)
REVERT: B  360 GLN cc_start: 0.7824 (mt0) cc_final: 0.7337 (tm-30)
REVERT: C  360 GLN cc_start: 0.7785 (mt0) cc_final: 0.7239 (tm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 57
  average time/residue: 1.4353
  time to fit residues: 83.5816
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  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  292 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 2 optimal weight:    9.9990
   chunk 20 optimal weight:    0.8980
   chunk 39 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 26 optimal weight:    4.9990
   chunk 21 optimal weight:    0.6980
   chunk 10 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 1 optimal weight:   20.0000
   chunk 23 optimal weight:    8.9990
   overall best weight:    3.1186

-------------------------------------------------------------------------------
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 = 0.3535 r_free = 0.3535 target = 0.104786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.079615 restraints weight = 2891.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 2.38
r_work: 0.3075 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8959
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2745  Z= 0.220
  Angle     :  0.748   5.257   3650  Z= 0.397
  Chirality :  0.039   0.115    315
  Planarity :  0.002   0.016    545
  Dihedral  :  5.198  18.132    400
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 0.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 14.40 %
    Favored  : 85.20 %
  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: -4.92 (0.17), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.74 (0.13), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.004   TRP A 334 
 PHE   0.020   0.002   PHE U 283 
 ARG   0.001   0.000   ARG B 293 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2557.46 seconds
wall clock time: 44 minutes 9.20 seconds (2649.20 seconds total)