Starting phenix.real_space_refine
on Fri Aug 22 19:45:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uqk_42472/08_2025/8uqk_42472.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uqk_42472/08_2025/8uqk_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uqk_42472/08_2025/8uqk_42472.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uqk_42472/08_2025/8uqk_42472.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uqk_42472/08_2025/8uqk_42472.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uqk_42472/08_2025/8uqk_42472.map"
  }
  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-2.0-5787/lib/python3.9/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: 1.58, per 1000 atoms: 0.22
  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: 0.43
  Conformation dependent library (CDL) restraints added in 286.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.26
  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: 1.06

  Time building geometry restraints manager: 0.59 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: 0.01
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:             1.060
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.930
  Find NCS groups from input model:        0.100
  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:1.220
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
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 aren 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
  covalent geometry    : bond        0.00294 ( 7482)
  covalent geometry    : angle       0.86247 (10196)
  hydrogen bonds       : bond        0.24073 (  283)
  hydrogen bonds       : angle       9.40233 (  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  : 0.143 
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: 0.1013
  time to fit residues: 4.5402
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  : 0.137 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
** 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: 0.6660
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 aren 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
  covalent geometry    : bond        0.00334 ( 7482)
  covalent geometry    : angle       0.80975 (10196)
  hydrogen bonds       : bond        0.06113 (  283)
  hydrogen bonds       : angle       7.17141 (  783)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 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  : 0.148 
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: 0.0603
  time to fit residues: 3.4854
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  : 0.103 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 77 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 44 optimal weight:    9.9990
   chunk 74 optimal weight:    0.0470
   chunk 73 optimal weight:    6.9990
   chunk 54 optimal weight:    0.3980
   chunk 33 optimal weight:    1.9990
   chunk 94 optimal weight:    0.3980
   overall best weight:    0.5280
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3473 r_free = 0.3473 target = 0.056996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.043768 restraints weight = 36062.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.045016 restraints weight = 26648.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.045954 restraints weight = 20978.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.046633 restraints weight = 17384.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.047170 restraints weight = 15021.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6671
moved from start:          0.6802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   7482  Z= 0.135
  Angle     :  0.743  12.044  10196  Z= 0.357
  Chirality :  0.042   0.150   1158
  Planarity :  0.006   0.044   1342
  Dihedral  :  5.290  23.217   1058
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 17.67
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.52 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  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 aren not related in a simple way.
  whole: -2.53 (0.25), residues: 958
  helix: -1.25 (0.26), residues: 344
  sheet: -0.85 (0.41), residues: 148
  loop : -2.29 (0.26), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 126 
 TYR   0.008   0.001   TYR A 201 
 PHE   0.008   0.001   PHE A 258 
 TRP   0.007   0.001   TRP A  75 
 HIS   0.003   0.001   HIS B 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 7482)
  covalent geometry    : angle       0.74268 (10196)
  hydrogen bonds       : bond        0.05351 (  283)
  hydrogen bonds       : angle       6.48288 (  783)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 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  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: A  159 MET cc_start: 0.8371 (tpp) cc_final: 0.8108 (tpp)
REVERT: A  258 PHE cc_start: 0.8184 (t80) cc_final: 0.7084 (t80)
REVERT: A  260 LEU cc_start: 0.9090 (mm) cc_final: 0.8398 (mm)
REVERT: A  360 GLU cc_start: 0.9008 (pm20) cc_final: 0.8682 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.0503
  time to fit residues: 2.8842
Evaluate side-chains
  27 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
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:    0.0040
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0040
   chunk 92 optimal weight:    8.9990
   chunk 34 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9990
   chunk 69 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9990
   chunk 80 optimal weight:    0.5980
   overall best weight:    0.4206
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3478 r_free = 0.3478 target = 0.057526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.044202 restraints weight = 34355.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.045437 restraints weight = 25249.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.046395 restraints weight = 19845.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.047120 restraints weight = 16408.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.047629 restraints weight = 14122.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6673
moved from start:          0.7025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   7482  Z= 0.124
  Angle     :  0.725  11.475  10196  Z= 0.347
  Chirality :  0.042   0.163   1158
  Planarity :  0.005   0.039   1342
  Dihedral  :  5.141  22.192   1058
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 16.18
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.10 %
    Favored  : 92.69 %
  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 aren not related in a simple way.
  whole: -2.48 (0.25), residues: 958
  helix: -1.29 (0.26), residues: 340
  sheet: -0.60 (0.40), residues: 150
  loop : -2.27 (0.25), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 126 
 TYR   0.011   0.001   TYR B 284 
 PHE   0.010   0.002   PHE B 389 
 TRP   0.007   0.001   TRP B 474 
 HIS   0.003   0.001   HIS B 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 7482)
  covalent geometry    : angle       0.72519 (10196)
  hydrogen bonds       : bond        0.04702 (  283)
  hydrogen bonds       : angle       6.16777 (  783)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 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  : 0.155 
Fit side-chains
REVERT: A  171 VAL cc_start: 0.8199 (t) cc_final: 0.7964 (t)
REVERT: A  258 PHE cc_start: 0.8167 (t80) cc_final: 0.7113 (t80)
REVERT: A  360 GLU cc_start: 0.9011 (pm20) cc_final: 0.8677 (pp20)
REVERT: A  362 LEU cc_start: 0.9303 (tt) cc_final: 0.8953 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0491
  time to fit residues: 2.6690
Evaluate side-chains
  27 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
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:    0.0980
   chunk 22 optimal weight:    0.7980
   chunk 40 optimal weight:    4.9990
   chunk 63 optimal weight:    0.0050
   chunk 3 optimal weight:    0.0770
   chunk 68 optimal weight:    3.9990
   chunk 90 optimal weight:    0.0980
   chunk 24 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0980
   chunk 87 optimal weight:    3.9990
   overall best weight:    0.0752
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3514 r_free = 0.3514 target = 0.058877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.045529 restraints weight = 34514.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.046768 restraints weight = 25056.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.047773 restraints weight = 19556.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.048431 restraints weight = 16114.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.048982 restraints weight = 13938.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6657
moved from start:          0.7376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   7482  Z= 0.123
  Angle     :  0.719  11.355  10196  Z= 0.343
  Chirality :  0.042   0.153   1158
  Planarity :  0.005   0.039   1342
  Dihedral  :  4.855  21.402   1058
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 15.22
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.72 %
    Favored  : 92.07 %
  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 aren not related in a simple way.
  whole: -2.48 (0.25), residues: 958
  helix: -1.46 (0.26), residues: 344
  sheet: -0.50 (0.40), residues: 150
  loop : -2.18 (0.26), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 126 
 TYR   0.009   0.001   TYR B 398 
 PHE   0.011   0.001   PHE B 258 
 TRP   0.008   0.001   TRP B 426 
 HIS   0.004   0.001   HIS B 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 7482)
  covalent geometry    : angle       0.71911 (10196)
  hydrogen bonds       : bond        0.04290 (  283)
  hydrogen bonds       : angle       5.92359 (  783)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A  258 PHE cc_start: 0.8214 (t80) cc_final: 0.7189 (t80)
REVERT: A  362 LEU cc_start: 0.9302 (tt) cc_final: 0.9095 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.0590
  time to fit residues: 2.8301
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  : 0.155 
-------------------------------------------------------------------------------
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:    0.0050
   chunk 87 optimal weight:    0.0870
   chunk 88 optimal weight:    0.1980
   chunk 82 optimal weight:   10.0000
   chunk 58 optimal weight:    1.9990
   chunk 94 optimal weight:    0.0470
   chunk 41 optimal weight:    0.9980
   chunk 83 optimal weight:    0.0980
   chunk 91 optimal weight:    7.9990
   chunk 65 optimal weight:    9.9990
   chunk 1 optimal weight:    0.0770
   overall best weight:    0.0628
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3532 r_free = 0.3532 target = 0.059575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.046189 restraints weight = 36179.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.047411 restraints weight = 26317.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.048417 restraints weight = 20631.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.049182 restraints weight = 16911.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.049716 restraints weight = 14559.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6654
moved from start:          0.7608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.053   7482  Z= 0.117
  Angle     :  0.727   9.646  10196  Z= 0.343
  Chirality :  0.042   0.156   1158
  Planarity :  0.005   0.040   1342
  Dihedral  :  4.765  20.393   1058
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.72 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  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 aren not related in a simple way.
  whole: -2.36 (0.25), residues: 958
  helix: -1.42 (0.26), residues: 342
  sheet: -0.55 (0.38), residues: 166
  loop : -2.02 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 126 
 TYR   0.008   0.001   TYR B 398 
 PHE   0.018   0.002   PHE B 389 
 TRP   0.009   0.001   TRP B 426 
 HIS   0.005   0.001   HIS B 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 7482)
  covalent geometry    : angle       0.72665 (10196)
  hydrogen bonds       : bond        0.04066 (  283)
  hydrogen bonds       : angle       5.72541 (  783)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 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  : 0.166 
Fit side-chains
REVERT: A  258 PHE cc_start: 0.8198 (t80) cc_final: 0.7484 (t80)
REVERT: A  370 MET cc_start: 0.9656 (tpt) cc_final: 0.9383 (tpt)
REVERT: A  411 LEU cc_start: 0.9265 (pt) cc_final: 0.8855 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.0547
  time to fit residues: 2.7772
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  : 0.140 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 41 optimal weight:    5.9990
   chunk 76 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 91 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 85 optimal weight:    0.0670
   chunk 8 optimal weight:    0.0370
   chunk 89 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.4796
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3518 r_free = 0.3518 target = 0.058807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.045478 restraints weight = 36211.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.046757 restraints weight = 26070.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.047725 restraints weight = 20344.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.048353 restraints weight = 16821.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.048882 restraints weight = 14623.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6673
moved from start:          0.7760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7482  Z= 0.117
  Angle     :  0.708   9.989  10196  Z= 0.336
  Chirality :  0.041   0.169   1158
  Planarity :  0.005   0.056   1342
  Dihedral  :  4.728  21.843   1058
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 15.97
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.35 %
    Favored  : 91.44 %
  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 aren not related in a simple way.
  whole: -2.45 (0.25), residues: 958
  helix: -1.48 (0.25), residues: 346
  sheet: -0.47 (0.40), residues: 166
  loop : -2.16 (0.27), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 126 
 TYR   0.011   0.002   TYR A 161 
 PHE   0.019   0.002   PHE A 258 
 TRP   0.008   0.001   TRP A 426 
 HIS   0.004   0.001   HIS B 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 7482)
  covalent geometry    : angle       0.70796 (10196)
  hydrogen bonds       : bond        0.03981 (  283)
  hydrogen bonds       : angle       5.73850 (  783)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 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  : 0.107 
Fit side-chains
REVERT: A  201 TYR cc_start: 0.9173 (m-80) cc_final: 0.8918 (m-80)
REVERT: A  258 PHE cc_start: 0.8262 (t80) cc_final: 0.7358 (t80)
REVERT: A  411 LEU cc_start: 0.9275 (pt) cc_final: 0.8878 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.0626
  time to fit residues: 3.1108
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  : 0.140 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 22 optimal weight:    0.5980
   chunk 51 optimal weight:    0.1980
   chunk 39 optimal weight:    0.0670
   chunk 95 optimal weight:    7.9990
   chunk 44 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   chunk 64 optimal weight:    0.2980
   chunk 65 optimal weight:    2.9990
   chunk 18 optimal weight:    8.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    0.4118
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3525 r_free = 0.3525 target = 0.058972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.045927 restraints weight = 36752.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.047164 restraints weight = 26877.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.048089 restraints weight = 21140.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.048698 restraints weight = 17560.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.049267 restraints weight = 15293.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6670
moved from start:          0.7919

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     :  0.721   9.773  10196  Z= 0.345
  Chirality :  0.041   0.162   1158
  Planarity :  0.005   0.040   1342
  Dihedral  :  4.729  21.009   1058
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 14.82
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.35 %
    Favored  : 91.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  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 aren not related in a simple way.
  whole: -2.49 (0.25), residues: 958
  helix: -1.68 (0.25), residues: 346
  sheet: -0.42 (0.40), residues: 166
  loop : -2.07 (0.27), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 288 
 TYR   0.010   0.002   TYR A 161 
 PHE   0.018   0.001   PHE B 258 
 TRP   0.008   0.001   TRP A 426 
 HIS   0.004   0.001   HIS B 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 7482)
  covalent geometry    : angle       0.72056 (10196)
  hydrogen bonds       : bond        0.03804 (  283)
  hydrogen bonds       : angle       5.67791 (  783)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 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  : 0.141 
Fit side-chains
REVERT: A  201 TYR cc_start: 0.9125 (m-80) cc_final: 0.8877 (m-80)
REVERT: A  258 PHE cc_start: 0.8191 (t80) cc_final: 0.7223 (t80)
REVERT: A  370 MET cc_start: 0.9663 (tpt) cc_final: 0.9454 (tpt)
REVERT: A  411 LEU cc_start: 0.9241 (pt) cc_final: 0.8844 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.0536
  time to fit residues: 2.7382
Evaluate side-chains
  27 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 65 optimal weight:    0.6980
   chunk 80 optimal weight:    0.4980
   chunk 62 optimal weight:    4.9990
   chunk 73 optimal weight:    5.9990
   chunk 93 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0000
   chunk 84 optimal weight:    0.9990
   chunk 16 optimal weight:    0.3980
   chunk 68 optimal weight:    0.8980
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.4784
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.059156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.046381 restraints weight = 38493.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.047656 restraints weight = 27816.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.048571 restraints weight = 21814.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.049126 restraints weight = 18105.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.049721 restraints weight = 15870.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6676
moved from start:          0.8024

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= 0.119
  Angle     :  0.718   9.296  10196  Z= 0.343
  Chirality :  0.041   0.163   1158
  Planarity :  0.005   0.058   1342
  Dihedral  :  4.809  20.996   1058
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 15.22
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.14 %
    Favored  : 91.65 %
  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 aren not related in a simple way.
  whole: -2.42 (0.25), residues: 958
  helix: -1.61 (0.25), residues: 332
  sheet: -0.57 (0.39), residues: 166
  loop : -1.95 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 126 
 TYR   0.010   0.002   TYR B 248 
 PHE   0.018   0.002   PHE B 258 
 TRP   0.018   0.001   TRP A  75 
 HIS   0.004   0.001   HIS B 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 7482)
  covalent geometry    : angle       0.71788 (10196)
  hydrogen bonds       : bond        0.03712 (  283)
  hydrogen bonds       : angle       5.63440 (  783)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 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  : 0.132 
Fit side-chains
REVERT: A  258 PHE cc_start: 0.8055 (t80) cc_final: 0.7267 (t80)
REVERT: A  370 MET cc_start: 0.9674 (tpt) cc_final: 0.9464 (tpt)
REVERT: A  411 LEU cc_start: 0.9228 (pt) cc_final: 0.8825 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0590
  time to fit residues: 2.8126
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  : 0.144 
-------------------------------------------------------------------------------
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:    0.0170
   chunk 54 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 60 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0980
   chunk 34 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 80 optimal weight:    0.4980
   chunk 13 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.4818
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3526 r_free = 0.3526 target = 0.059041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.046439 restraints weight = 38252.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.047682 restraints weight = 27724.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.048589 restraints weight = 21709.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.049214 restraints weight = 17998.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.049766 restraints weight = 15616.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6690
moved from start:          0.8061

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= 0.120
  Angle     :  0.728   9.151  10196  Z= 0.351
  Chirality :  0.042   0.157   1158
  Planarity :  0.006   0.064   1342
  Dihedral  :  4.767  20.528   1058
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 14.95
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.72 %
    Favored  : 92.07 %
  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 aren not related in a simple way.
  whole: -2.40 (0.25), residues: 958
  helix: -1.60 (0.25), residues: 332
  sheet: -0.78 (0.38), residues: 176
  loop : -1.84 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 126 
 TYR   0.010   0.001   TYR B 248 
 PHE   0.016   0.002   PHE B 258 
 TRP   0.015   0.001   TRP A  75 
 HIS   0.004   0.001   HIS B 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 7482)
  covalent geometry    : angle       0.72752 (10196)
  hydrogen bonds       : bond        0.03673 (  283)
  hydrogen bonds       : angle       5.72245 (  783)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 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  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: A  258 PHE cc_start: 0.8176 (t80) cc_final: 0.7293 (t80)
REVERT: A  411 LEU cc_start: 0.9272 (pt) cc_final: 0.8855 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0423
  time to fit residues: 2.1266
Evaluate side-chains
  27 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 50 optimal weight:    9.9990
   chunk 54 optimal weight:    3.9990
   chunk 91 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0060
   chunk 66 optimal weight:    0.0030
   chunk 81 optimal weight:    0.9990
   chunk 25 optimal weight:    8.9990
   chunk 86 optimal weight:    7.9990
   chunk 87 optimal weight:    0.0270
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.3064
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3547 r_free = 0.3547 target = 0.059168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.046986 restraints weight = 37337.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.048201 restraints weight = 27510.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.049051 restraints weight = 21756.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.049677 restraints weight = 18149.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.050190 restraints weight = 15774.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6677
moved from start:          0.8174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7482  Z= 0.119
  Angle     :  0.723   8.693  10196  Z= 0.343
  Chirality :  0.041   0.157   1158
  Planarity :  0.006   0.063   1342
  Dihedral  :  4.702  20.545   1058
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 13.32
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.52 %
    Favored  : 92.28 %
  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 aren not related in a simple way.
  whole: -2.37 (0.25), residues: 958
  helix: -1.65 (0.25), residues: 332
  sheet: -0.72 (0.38), residues: 176
  loop : -1.79 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 126 
 TYR   0.007   0.001   TYR B 284 
 PHE   0.014   0.001   PHE A 258 
 TRP   0.016   0.001   TRP A  75 
 HIS   0.005   0.001   HIS B 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 7482)
  covalent geometry    : angle       0.72330 (10196)
  hydrogen bonds       : bond        0.03688 (  283)
  hydrogen bonds       : angle       5.61499 (  783)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 957.38 seconds
wall clock time: 17 minutes 13.76 seconds (1033.76 seconds total)