Starting phenix.real_space_refine
on Thu Jul  2 06:54:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uqk_42472/07_2026/8uqk_42472.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uqk_42472/07_2026/8uqk_42472.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uqk_42472/07_2026/8uqk_42472.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uqk_42472/07_2026/8uqk_42472.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uqk_42472/07_2026/8uqk_42472.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uqk_42472/07_2026/8uqk_42472.cif"
  }
  resolution = 4.61
  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=   0.009
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      18      5.16       5
     C    4630      2.51       5
     N    1332      2.21       5
     O    1338      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7318
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 3659
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 481, 3659
          Classifications: {'peptide': 481}
          Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 445}
    Chain: "A"
      Number of atoms: 3659
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 481, 3659
          Classifications: {'peptide': 481}
          Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 445}
  Time building chain proxies: 1.92, per 1000 atoms: 0.26
  Number of scatterers: 7318
  At special positions: 0
  Unit cell: (78.07, 114.995, 121.325, 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      18     16.00
     O    1338      8.00
     N    1332      7.00
     C    4630      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: 0.57
  Conformation dependent library (CDL) restraints added in 404.3 milliseconds
  

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1776

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 6 sheets defined
      42.5% alpha, 13.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'B' and resid 17 through 21
    Processing helix  chain 'B' and resid 44 through 52
      removed outlier: 3.717A  pdb=" N   GLN B  48 " --> pdb=" O   SER B  44 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ALA B  49 " --> pdb=" O   ALA B  45 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   LEU B  50 " --> pdb=" O   ASN B  46 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU B  51 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 59
    Processing helix  chain 'B' and resid 62 through 67
      removed outlier: 3.658A  pdb=" N   VAL B  66 " --> pdb=" O   THR B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 73
    Processing helix  chain 'B' and resid 74 through 82
      removed outlier: 4.813A  pdb=" N   ALA B  80 " --> pdb=" O   GLU B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 130
      removed outlier: 4.016A  pdb=" N   ARG B 126 " --> pdb=" O   LEU B 122 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   SER B 130 " --> pdb=" O   ARG B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 154
    Processing helix  chain 'B' and resid 194 through 204
    Processing helix  chain 'B' and resid 242 through 253
    Processing helix  chain 'B' and resid 283 through 319
      removed outlier: 3.560A  pdb=" N   CYS B 290 " --> pdb=" O   ARG B 286 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   GLU B 291 " --> pdb=" O   ARG B 287 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   VAL B 292 " --> pdb=" O   ARG B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 327
    Processing helix  chain 'B' and resid 332 through 340
    Processing helix  chain 'B' and resid 340 through 349
      removed outlier: 3.549A  pdb=" N   VAL B 344 " --> pdb=" O   ASP B 340 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLU B 346 " --> pdb=" O   ALA B 342 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   THR B 348 " --> pdb=" O   VAL B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 381
      removed outlier: 4.111A  pdb=" N   ALA B 381 " --> pdb=" O   ALA B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 398
    Processing helix  chain 'B' and resid 399 through 402
    Processing helix  chain 'B' and resid 460 through 468
    Processing helix  chain 'B' and resid 475 through 481
      removed outlier: 3.513A  pdb=" N   LEU B 479 " --> pdb=" O   LYS B 475 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA B 481 " --> pdb=" O   ALA B 477 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 481 through 487
      removed outlier: 3.508A  pdb=" N   PHE B 485 " --> pdb=" O   ALA B 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 17 through 21
    Processing helix  chain 'A' and resid 44 through 52
      removed outlier: 3.712A  pdb=" N   GLN A  48 " --> pdb=" O   SER A  44 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   ALA A  49 " --> pdb=" O   ALA A  45 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   LEU A  50 " --> pdb=" O   ASN A  46 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LEU A  51 " --> pdb=" O   THR A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 59
    Processing helix  chain 'A' and resid 62 through 67
    Processing helix  chain 'A' and resid 68 through 73
      removed outlier: 3.509A  pdb=" N   TRP A  72 " --> pdb=" O   PRO A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 82
      removed outlier: 4.475A  pdb=" N   ALA A  80 " --> pdb=" O   GLU A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 130
      removed outlier: 3.578A  pdb=" N   SER A 130 " --> pdb=" O   ARG A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 154
      removed outlier: 3.828A  pdb=" N   LEU A 142 " --> pdb=" O   THR A 138 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ALA A 151 " --> pdb=" O   ASN A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 193
      removed outlier: 3.506A  pdb=" N   ASP A 192 " --> pdb=" O   PRO A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 204
    Processing helix  chain 'A' and resid 242 through 253
    Processing helix  chain 'A' and resid 283 through 319
      removed outlier: 3.540A  pdb=" N   ARG A 288 " --> pdb=" O   TYR A 284 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ALA A 289 " --> pdb=" O   GLU A 285 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLU A 291 " --> pdb=" O   ARG A 287 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   VAL A 292 " --> pdb=" O   ARG A 288 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU A 293 " --> pdb=" O   ALA A 289 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   THR A 294 " --> pdb=" O   CYS A 290 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   GLN A 295 " --> pdb=" O   GLU A 291 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU A 296 " --> pdb=" O   VAL A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 327
      removed outlier: 3.897A  pdb=" N   SER A 326 " --> pdb=" O   PRO A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 340
      removed outlier: 3.831A  pdb=" N   ASP A 340 " --> pdb=" O   ALA A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 349
      removed outlier: 3.633A  pdb=" N   VAL A 344 " --> pdb=" O   ASP A 340 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   GLU A 346 " --> pdb=" O   ALA A 342 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LEU A 347 " --> pdb=" O   ARG A 343 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   THR A 348 " --> pdb=" O   VAL A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 380
    Processing helix  chain 'A' and resid 393 through 398
    Processing helix  chain 'A' and resid 399 through 405
    Processing helix  chain 'A' and resid 460 through 468
    Processing helix  chain 'A' and resid 475 through 481
      removed outlier: 3.840A  pdb=" N   LEU A 479 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 487
      removed outlier: 3.770A  pdb=" N   PHE A 485 " --> pdb=" O   ALA A 481 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 33
      removed outlier: 3.563A  pdb=" N   THR B 104 " --> pdb=" O   PHE B  33 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 187 through 188
      removed outlier: 3.813A  pdb=" N   LEU B 172 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   VAL B 160 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 5.288A  pdb=" N   GLU B 174 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   VAL B 158 " --> pdb=" O   GLU B 174 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   LEU B 271 " --> pdb=" O   TYR B 161 " (cutoff:3.500A)
      removed outlier: 5.174A  pdb=" N   LEU B 268 " --> pdb=" O   LYS B 264 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   LYS B 264 " --> pdb=" O   LEU B 268 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 388 through 390
      removed outlier: 3.736A  pdb=" N   PHE B 389 " --> pdb=" O   ALA B 413 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 29 through 33
      removed outlier: 3.974A  pdb=" N   VAL A  29 " --> pdb=" O   LEU A 108 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   LEU A 108 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   PHE A  33 " --> pdb=" O   THR A 104 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR A 104 " --> pdb=" O   PHE A  33 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 188
      removed outlier: 3.809A  pdb=" N   LEU A 172 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   VAL A 160 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
      removed outlier: 5.363A  pdb=" N   GLU A 174 " --> pdb=" O   VAL A 158 " (cutoff:3.500A)
      removed outlier: 7.457A  pdb=" N   VAL A 158 " --> pdb=" O   GLU A 174 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   LEU A 262 " --> pdb=" O   TRP A 269 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   LEU A 271 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   LEU A 260 " --> pdb=" O   LEU A 271 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   ALA A 273 " --> pdb=" O   PHE A 258 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   PHE A 258 " --> pdb=" O   ALA A 273 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   HIS A 275 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ALA A 256 " --> pdb=" O   HIS A 275 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ARG A 207 " --> pdb=" O   SER A 259 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 355
      removed outlier: 3.510A  pdb=" N   GLY A 352 " --> pdb=" O   PHE A 427 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ALA A 354 " --> pdb=" O   LEU A 425 " (cutoff:3.500A)

    283 hydrogen bonds defined for protein.
    783 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: 1.14

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2519
        1.34 -     1.46: 1454
        1.46 -     1.58: 3479
        1.58 -     1.69: 0
        1.69 -     1.81: 30
  Bond restraints: 7482
  Sorted by residual:
  bond pdb=" N   PRO A  54 "
       pdb=" CA  PRO A  54 "
    ideal  model  delta    sigma   weight residual
    1.457  1.475 -0.018 1.31e-02 5.83e+03 1.79e+00
  bond pdb=" N   VAL A 254 "
       pdb=" CA  VAL A 254 "
    ideal  model  delta    sigma   weight residual
    1.459  1.472 -0.013 1.19e-02 7.06e+03 1.22e+00
  bond pdb=" CA  ASP A 116 "
       pdb=" CB  ASP A 116 "
    ideal  model  delta    sigma   weight residual
    1.527  1.545 -0.018 1.70e-02 3.46e+03 1.14e+00
  bond pdb=" N   VAL B 254 "
       pdb=" CA  VAL B 254 "
    ideal  model  delta    sigma   weight residual
    1.460  1.474 -0.014 1.42e-02 4.96e+03 9.76e-01
  bond pdb=" C   VAL B 224 "
       pdb=" O   VAL B 224 "
    ideal  model  delta    sigma   weight residual
    1.232  1.241 -0.008 8.90e-03 1.26e+04 8.61e-01
  ... (remaining 7477 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.45: 9975
        2.45 -     4.89: 197
        4.89 -     7.34: 21
        7.34 -     9.78: 1
        9.78 -    12.23: 2
  Bond angle restraints: 10196
  Sorted by residual:
  angle pdb=" N   GLY B 358 "
        pdb=" CA  GLY B 358 "
        pdb=" C   GLY B 358 "
      ideal   model   delta    sigma   weight residual
     114.25  109.51    4.74 1.30e+00 5.92e-01 1.33e+01
  angle pdb=" C   PRO A 115 "
        pdb=" N   ASP A 116 "
        pdb=" CA  ASP A 116 "
      ideal   model   delta    sigma   weight residual
     122.46  127.59   -5.13 1.41e+00 5.03e-01 1.33e+01
  angle pdb=" CA  LEU A 122 "
        pdb=" CB  LEU A 122 "
        pdb=" CG  LEU A 122 "
      ideal   model   delta    sigma   weight residual
     116.30  128.53  -12.23 3.50e+00 8.16e-02 1.22e+01
  angle pdb=" N   GLU A 123 "
        pdb=" CA  GLU A 123 "
        pdb=" C   GLU A 123 "
      ideal   model   delta    sigma   weight residual
     112.23  107.92    4.31 1.26e+00 6.30e-01 1.17e+01
  angle pdb=" N   ALA A  83 "
        pdb=" CA  ALA A  83 "
        pdb=" C   ALA A  83 "
      ideal   model   delta    sigma   weight residual
     108.46  113.37   -4.91 1.51e+00 4.39e-01 1.06e+01
  ... (remaining 10191 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.62: 4115
       17.62 -    35.24: 364
       35.24 -    52.86: 44
       52.86 -    70.48: 11
       70.48 -    88.10: 8
  Dihedral angle restraints: 4542
    sinusoidal: 1792
      harmonic: 2750
  Sorted by residual:
  dihedral pdb=" CA  SER A 388 "
           pdb=" C   SER A 388 "
           pdb=" N   PHE A 389 "
           pdb=" CA  PHE A 389 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.13   22.87     0      5.00e+00 4.00e-02 2.09e+01
  dihedral pdb=" CA  ASP A 156 "
           pdb=" C   ASP A 156 "
           pdb=" N   ARG A 157 "
           pdb=" CA  ARG A 157 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.17  -20.83     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  ALA A  83 "
           pdb=" C   ALA A  83 "
           pdb=" N   LEU A  84 "
           pdb=" CA  LEU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.32   20.68     0      5.00e+00 4.00e-02 1.71e+01
  ... (remaining 4539 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 842
       0.038 -    0.076: 220
       0.076 -    0.113: 77
       0.113 -    0.151: 16
       0.151 -    0.189: 3
  Chirality restraints: 1158
  Sorted by residual:
  chirality pdb=" CG  LEU B 206 "
            pdb=" CB  LEU B 206 "
            pdb=" CD1 LEU B 206 "
            pdb=" CD2 LEU B 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 8.92e-01
  chirality pdb=" CA  ASP A 116 "
            pdb=" N   ASP A 116 "
            pdb=" C   ASP A 116 "
            pdb=" CB  ASP A 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.38e-01
  chirality pdb=" CA  ARG B 457 "
            pdb=" N   ARG B 457 "
            pdb=" C   ARG B 457 "
            pdb=" CB  ARG B 457 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.78e-01
  ... (remaining 1155 not shown)

  Planarity restraints: 1342
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 229 "   -0.041 5.00e-02 4.00e+02   6.25e-02 6.26e+00
        pdb=" N   PRO A 230 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A 230 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 230 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  88 "   -0.032 5.00e-02 4.00e+02   4.89e-02 3.83e+00
        pdb=" N   PRO B  89 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO B  89 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B  89 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  88 "    0.031 5.00e-02 4.00e+02   4.76e-02 3.62e+00
        pdb=" N   PRO A  89 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A  89 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A  89 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1339 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 463
        2.73 -     3.27: 8434
        3.27 -     3.81: 13029
        3.81 -     4.36: 15043
        4.36 -     4.90: 23143
  Nonbonded interactions: 60112
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 149 "
            pdb=" OG1 THR B 153 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" O   PRO A 322 "
            pdb=" OG1 THR A 325 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OE2 GLU A 312 "
            pdb=" NZ  LYS A 475 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" O   PRO B 456 "
            pdb=" N   GLY B 458 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" O   SER A  44 "
            pdb=" OG1 THR A  47 "
     model   vdw
     2.234 3.040
  ... (remaining 60107 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 'B'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
Set refine NCS operators
  NCS operators will be refined.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.400
  Find NCS groups from input model:        0.110
  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:             0.010
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7246
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7482  Z= 0.160
  Angle     :  0.862  12.226  10196  Z= 0.486
  Chirality :  0.040   0.189   1158
  Planarity :  0.006   0.063   1342
  Dihedral  : 13.606  88.100   2766
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 21.41
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.47 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.07 (0.25), residues: 958
  helix: -0.56 (0.27), residues: 304
  sheet: -1.72 (0.40), residues: 142
  loop : -1.77 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 404 
 TYR   0.012   0.002   TYR B  93 
 PHE   0.011   0.001   PHE A 385 
 TRP   0.016   0.001   TRP B 379 
 HIS   0.006   0.001   HIS B 455 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.16 ( 7482)
  covalent geometry    : angle       0.86247 /  0.49 (10196)
  hydrogen bonds       : bond        0.24073 / 15.37 (  283)
  hydrogen bonds       : angle       9.40233 /  6.54 (  783)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A   75 TRP cc_start: 0.9520 (t60) cc_final: 0.9203 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.1005
  time to fit residues: 4.5606
Evaluate side-chains
  20 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.0000
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    0.0570
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0270
   overall best weight:    0.2560
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.056648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.043161 restraints weight = 34695.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.044388 restraints weight = 25899.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.045286 restraints weight = 20541.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.046014 restraints weight = 17072.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.046554 restraints weight = 14784.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6591
moved from start:          0.6392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075   7482  Z= 0.154
  Angle     :  0.810  11.749  10196  Z= 0.393
  Chirality :  0.045   0.176   1158
  Planarity :  0.006   0.058   1342
  Dihedral  :  5.671  21.340   1058
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 17.94
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.64 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.02 (0.25), residues: 958
  helix: -0.54 (0.27), residues: 336
  sheet: -1.10 (0.38), residues: 162
  loop : -2.03 (0.26), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.001   ARG A 126 
 TYR   0.013   0.002   TYR B 284 
 PHE   0.007   0.001   PHE A 389 
 TRP   0.009   0.001   TRP B 379 
 HIS   0.003   0.001   HIS A 455 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.15 ( 7482)
  covalent geometry    : angle       0.80975 /  0.39 (10196)
  hydrogen bonds       : bond        0.06113 /  3.67 (  283)
  hydrogen bonds       : angle       7.17141 /  4.87 (  783)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A  268 LEU cc_start: 0.9222 (tp) cc_final: 0.8820 (tp)
REVERT: A  360 GLU cc_start: 0.9064 (pm20) cc_final: 0.8729 (pp20)
REVERT: A  401 LEU cc_start: 0.9675 (tp) cc_final: 0.9329 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.0527
  time to fit residues: 3.1318
Evaluate side-chains
  24 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 67 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 44 optimal weight:    9.9990
   chunk 74 optimal weight:    8.9990
   chunk 73 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 94 optimal weight:   50.0000
   overall best weight:    1.7990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.055377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.042573 restraints weight = 36649.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.043747 restraints weight = 27095.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.044653 restraints weight = 21365.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.045296 restraints weight = 17711.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.045820 restraints weight = 15316.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6661
moved from start:          0.6649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   7482  Z= 0.152
  Angle     :  0.755  12.305  10196  Z= 0.369
  Chirality :  0.042   0.147   1158
  Planarity :  0.006   0.046   1342
  Dihedral  :  5.535  22.223   1058
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 21.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.13 (0.25), residues: 958
  helix: -0.83 (0.27), residues: 332
  sheet: -0.72 (0.42), residues: 150
  loop : -2.08 (0.25), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG B 126 
 TYR   0.005   0.001   TYR A 398 
 PHE   0.005   0.001   PHE A  33 
 TRP   0.007   0.001   TRP A 437 
 HIS   0.003   0.001   HIS A 315 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.15 ( 7482)
  covalent geometry    : angle       0.75503 /  0.37 (10196)
  hydrogen bonds       : bond        0.05682 /  3.51 (  283)
  hydrogen bonds       : angle       6.74928 /  4.59 (  783)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A  159 MET cc_start: 0.8476 (tpp) cc_final: 0.8201 (tpp)
REVERT: A  360 GLU cc_start: 0.9072 (pm20) cc_final: 0.8778 (pp20)
REVERT: A  401 LEU cc_start: 0.9661 (tp) cc_final: 0.9416 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0530
  time to fit residues: 2.7943
Evaluate side-chains
  24 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 8 optimal weight:    0.0050
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 56 optimal weight:    0.0770
   chunk 92 optimal weight:   10.0000
   chunk 34 optimal weight:    9.9990
   chunk 25 optimal weight:    6.9990
   chunk 65 optimal weight:    0.5980
   chunk 69 optimal weight:    0.0270
   chunk 17 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.7412
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.056405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.043386 restraints weight = 34649.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.044599 restraints weight = 25266.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.045558 restraints weight = 19825.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.046234 restraints weight = 16318.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.046788 restraints weight = 14009.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6648
moved from start:          0.6865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7482  Z= 0.125
  Angle     :  0.734  11.957  10196  Z= 0.353
  Chirality :  0.043   0.169   1158
  Planarity :  0.006   0.045   1342
  Dihedral  :  5.366  22.099   1058
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 17.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.92 (0.25), residues: 958
  helix: -0.69 (0.27), residues: 338
  sheet: -0.59 (0.41), residues: 144
  loop : -1.94 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 126 
 TYR   0.008   0.001   TYR B 398 
 PHE   0.012   0.001   PHE A 389 
 TRP   0.005   0.001   TRP B 426 
 HIS   0.004   0.001   HIS A 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.12 ( 7482)
  covalent geometry    : angle       0.73412 /  0.35 (10196)
  hydrogen bonds       : bond        0.04792 /  2.98 (  283)
  hydrogen bonds       : angle       6.34024 /  4.32 (  783)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: A  258 PHE cc_start: 0.8144 (t80) cc_final: 0.7068 (t80)
REVERT: A  360 GLU cc_start: 0.9106 (pm20) cc_final: 0.8771 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.0574
  time to fit residues: 3.1944
Evaluate side-chains
  26 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0980
   chunk 40 optimal weight:    5.9990
   chunk 63 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 90 optimal weight:    0.0770
   chunk 24 optimal weight:    7.9990
   chunk 39 optimal weight:    0.4980
   chunk 42 optimal weight:    8.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    0.4738
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.057571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.045029 restraints weight = 37191.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.046236 restraints weight = 27431.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.047068 restraints weight = 21613.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.047811 restraints weight = 17964.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.048344 restraints weight = 15467.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6633
moved from start:          0.7149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7482  Z= 0.125
  Angle     :  0.742  10.752  10196  Z= 0.353
  Chirality :  0.042   0.150   1158
  Planarity :  0.005   0.044   1342
  Dihedral  :  5.132  21.568   1058
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 16.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.92 (0.25), residues: 958
  helix: -0.81 (0.27), residues: 342
  sheet: -0.53 (0.41), residues: 150
  loop : -1.87 (0.26), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 126 
 TYR   0.017   0.002   TYR B 248 
 PHE   0.012   0.001   PHE A 258 
 TRP   0.007   0.001   TRP B 426 
 HIS   0.004   0.001   HIS B 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.12 ( 7482)
  covalent geometry    : angle       0.74157 /  0.35 (10196)
  hydrogen bonds       : bond        0.04469 /  2.80 (  283)
  hydrogen bonds       : angle       6.08578 /  4.15 (  783)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A  171 VAL cc_start: 0.8152 (t) cc_final: 0.7948 (t)
REVERT: A  201 TYR cc_start: 0.9200 (m-80) cc_final: 0.8999 (m-80)
REVERT: A  258 PHE cc_start: 0.8187 (t80) cc_final: 0.7160 (t80)
REVERT: A  360 GLU cc_start: 0.9070 (pm20) cc_final: 0.8738 (pp20)
REVERT: A  362 LEU cc_start: 0.9222 (tt) cc_final: 0.8958 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.0618
  time to fit residues: 3.1233
Evaluate side-chains
  25 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 42 optimal weight:    0.5980
   chunk 87 optimal weight:    0.2980
   chunk 88 optimal weight:    0.3980
   chunk 82 optimal weight:    6.9990
   chunk 58 optimal weight:    8.9990
   chunk 94 optimal weight:    7.9990
   chunk 41 optimal weight:    0.0170
   chunk 83 optimal weight:    0.0060
   chunk 91 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 1 optimal weight:    0.3980
   overall best weight:    0.2234
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  98 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.057821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.044469 restraints weight = 35277.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.045807 restraints weight = 25343.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.046744 restraints weight = 19605.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.047513 restraints weight = 16030.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.048077 restraints weight = 13721.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6630
moved from start:          0.7389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7482  Z= 0.122
  Angle     :  0.747  11.162  10196  Z= 0.353
  Chirality :  0.043   0.157   1158
  Planarity :  0.005   0.043   1342
  Dihedral  :  5.093  22.658   1058
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 16.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.88 (0.25), residues: 958
  helix: -0.75 (0.26), residues: 356
  sheet: -0.41 (0.40), residues: 150
  loop : -1.93 (0.27), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 126 
 TYR   0.007   0.001   TYR A 284 
 PHE   0.014   0.002   PHE B 258 
 TRP   0.007   0.001   TRP B 426 
 HIS   0.005   0.001   HIS B 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.12 ( 7482)
  covalent geometry    : angle       0.74734 /  0.35 (10196)
  hydrogen bonds       : bond        0.04231 /  2.63 (  283)
  hydrogen bonds       : angle       5.95154 /  4.04 (  783)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.145 
Fit side-chains
REVERT: A  258 PHE cc_start: 0.8150 (t80) cc_final: 0.7263 (t80)
REVERT: A  360 GLU cc_start: 0.9008 (pm20) cc_final: 0.8680 (pp20)
REVERT: A  362 LEU cc_start: 0.9172 (tt) cc_final: 0.8941 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.0630
  time to fit residues: 3.1796
Evaluate side-chains
  26 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 41 optimal weight:    0.4980
   chunk 76 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 91 optimal weight:    5.9990
   chunk 78 optimal weight:    2.9990
   chunk 27 optimal weight:    9.9990
   chunk 85 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0000
   chunk 89 optimal weight:    0.0370
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.4262
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.058512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.045774 restraints weight = 35537.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.047053 restraints weight = 25510.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.047921 restraints weight = 19747.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.048640 restraints weight = 16247.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.049199 restraints weight = 13884.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6636
moved from start:          0.7571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   7482  Z= 0.120
  Angle     :  0.733   9.548  10196  Z= 0.347
  Chirality :  0.042   0.171   1158
  Planarity :  0.005   0.042   1342
  Dihedral  :  4.944  21.472   1058
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 15.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.85 (0.25), residues: 958
  helix: -0.77 (0.26), residues: 358
  sheet: -0.26 (0.40), residues: 150
  loop : -1.93 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 126 
 TYR   0.012   0.001   TYR B 248 
 PHE   0.014   0.001   PHE A 258 
 TRP   0.008   0.001   TRP B 426 
 HIS   0.004   0.001   HIS B 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.12 ( 7482)
  covalent geometry    : angle       0.73319 /  0.35 (10196)
  hydrogen bonds       : bond        0.04099 /  2.57 (  283)
  hydrogen bonds       : angle       5.80015 /  3.94 (  783)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A  258 PHE cc_start: 0.8154 (t80) cc_final: 0.7231 (t80)
REVERT: A  370 MET cc_start: 0.9649 (tpt) cc_final: 0.9284 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.0646
  time to fit residues: 3.2465
Evaluate side-chains
  26 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 25 optimal weight:    0.3980
   chunk 22 optimal weight:    6.9990
   chunk 51 optimal weight:    0.4980
   chunk 39 optimal weight:    0.0000
   chunk 95 optimal weight:    5.9990
   chunk 44 optimal weight:    0.0970
   chunk 4 optimal weight:    0.1980
   chunk 64 optimal weight:    0.0010
   chunk 65 optimal weight:    0.0070
   chunk 18 optimal weight:    0.0370
   chunk 1 optimal weight:    0.0170
   overall best weight:    0.0124
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.059209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.046385 restraints weight = 36551.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.047604 restraints weight = 26583.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.048475 restraints weight = 20886.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.049144 restraints weight = 17415.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.049451 restraints weight = 15155.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6626
moved from start:          0.7748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   7482  Z= 0.127
  Angle     :  0.748   9.724  10196  Z= 0.356
  Chirality :  0.042   0.174   1158
  Planarity :  0.006   0.065   1342
  Dihedral  :  4.890  20.979   1058
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 14.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.89 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.66 (0.26), residues: 958
  helix: -0.69 (0.27), residues: 344
  sheet: -0.03 (0.41), residues: 150
  loop : -1.78 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 126 
 TYR   0.025   0.002   TYR B 201 
 PHE   0.012   0.002   PHE A 258 
 TRP   0.009   0.001   TRP B 426 
 HIS   0.005   0.001   HIS B 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.13 ( 7482)
  covalent geometry    : angle       0.74774 /  0.36 (10196)
  hydrogen bonds       : bond        0.04077 /  2.58 (  283)
  hydrogen bonds       : angle       5.79318 /  3.95 (  783)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
REVERT: A  258 PHE cc_start: 0.8147 (t80) cc_final: 0.7206 (t80)
REVERT: A  360 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8145 (mm-30)
REVERT: A  370 MET cc_start: 0.9638 (tpt) cc_final: 0.9381 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0605
  time to fit residues: 2.9206
Evaluate side-chains
  28 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 76 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0980
   chunk 80 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 73 optimal weight:    0.0970
   chunk 93 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 84 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0070
   chunk 68 optimal weight:    0.5980
   chunk 55 optimal weight:    8.9990
   overall best weight:    0.3396
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.058748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.046168 restraints weight = 38053.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.047459 restraints weight = 27298.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.048390 restraints weight = 21292.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.049007 restraints weight = 17635.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.049553 restraints weight = 15341.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6634
moved from start:          0.7815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7482  Z= 0.119
  Angle     :  0.739   9.737  10196  Z= 0.351
  Chirality :  0.042   0.159   1158
  Planarity :  0.005   0.043   1342
  Dihedral  :  4.878  20.906   1058
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.57 (0.26), residues: 958
  helix: -0.62 (0.27), residues: 344
  sheet:  0.08 (0.41), residues: 150
  loop : -1.74 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 126 
 TYR   0.011   0.001   TYR B 248 
 PHE   0.014   0.002   PHE B 389 
 TRP   0.015   0.001   TRP B  75 
 HIS   0.005   0.001   HIS B 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.12 ( 7482)
  covalent geometry    : angle       0.73886 /  0.35 (10196)
  hydrogen bonds       : bond        0.03889 /  2.51 (  283)
  hydrogen bonds       : angle       5.68196 /  3.85 (  783)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.118 
Fit side-chains
REVERT: A  258 PHE cc_start: 0.8023 (t80) cc_final: 0.7192 (t80)
REVERT: A  370 MET cc_start: 0.9641 (tpt) cc_final: 0.9384 (tpt)
REVERT: A  411 LEU cc_start: 0.9271 (pt) cc_final: 0.8835 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0629
  time to fit residues: 2.8873
Evaluate side-chains
  25 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0060
   chunk 34 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 80 optimal weight:    0.0570
   chunk 13 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.5918
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.058676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.046182 restraints weight = 38010.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.047460 restraints weight = 27145.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.048288 restraints weight = 21119.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.049073 restraints weight = 17609.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.049545 restraints weight = 15164.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6652
moved from start:          0.7933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7482  Z= 0.119
  Angle     :  0.728   8.623  10196  Z= 0.348
  Chirality :  0.042   0.163   1158
  Planarity :  0.006   0.048   1342
  Dihedral  :  4.790  20.428   1058
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 15.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.55 (0.26), residues: 958
  helix: -0.53 (0.28), residues: 332
  sheet:  0.01 (0.40), residues: 150
  loop : -1.73 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 126 
 TYR   0.008   0.001   TYR B 248 
 PHE   0.012   0.002   PHE A 258 
 TRP   0.013   0.001   TRP B  75 
 HIS   0.005   0.001   HIS B 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.12 ( 7482)
  covalent geometry    : angle       0.72849 /  0.35 (10196)
  hydrogen bonds       : bond        0.03922 /  2.57 (  283)
  hydrogen bonds       : angle       5.69517 /  3.86 (  783)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A  258 PHE cc_start: 0.8044 (t80) cc_final: 0.7187 (t80)
REVERT: A  362 LEU cc_start: 0.9401 (mp) cc_final: 0.8899 (mp)
REVERT: A  411 LEU cc_start: 0.9305 (pt) cc_final: 0.8865 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0669
  time to fit residues: 2.8244
Evaluate side-chains
  24 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 50 optimal weight:    8.9990
   chunk 54 optimal weight:    5.9990
   chunk 91 optimal weight:    0.0870
   chunk 9 optimal weight:    0.8980
   chunk 66 optimal weight:    6.9990
   chunk 81 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 86 optimal weight:   30.0000
   chunk 87 optimal weight:    0.0030
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.4968
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.058973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.046552 restraints weight = 36892.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.047802 restraints weight = 26748.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.048631 restraints weight = 21023.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.049356 restraints weight = 17612.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.049896 restraints weight = 15202.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6650
moved from start:          0.7967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7482  Z= 0.119
  Angle     :  0.740   8.659  10196  Z= 0.352
  Chirality :  0.042   0.165   1158
  Planarity :  0.006   0.045   1342
  Dihedral  :  4.829  20.467   1058
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 15.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.55 (0.26), residues: 958
  helix: -0.54 (0.28), residues: 332
  sheet: -0.23 (0.39), residues: 166
  loop : -1.68 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 126 
 TYR   0.009   0.001   TYR B 248 
 PHE   0.011   0.001   PHE A 258 
 TRP   0.014   0.001   TRP B  75 
 HIS   0.005   0.001   HIS B 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 ( 7482)
  covalent geometry    : angle       0.73951 /  0.35 (10196)
  hydrogen bonds       : bond        0.03839 /  2.54 (  283)
  hydrogen bonds       : angle       5.69081 /  3.87 (  783)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1099.15 seconds
wall clock time: 19 minutes 47.59 seconds (1187.59 seconds total)