Starting phenix.real_space_refine
on Sun May 11 03:23:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uqk_42472/05_2025/8uqk_42472.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uqk_42472/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uqk_42472/05_2025/8uqk_42472.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uqk_42472/05_2025/8uqk_42472.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uqk_42472/05_2025/8uqk_42472.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uqk_42472/05_2025/8uqk_42472.cif"
  }
  resolution = 4.61
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.009
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.76, per 1000 atoms: 0.65
  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: 1.84
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.81
  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: 1.91

  Time building geometry restraints manager: 2.16 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: 0.04
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:             1.330
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.740
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  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:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.400
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.016   0.001   TRP B 379 
 HIS   0.006   0.001   HIS B 455 
 PHE   0.011   0.001   PHE A 385 
 TYR   0.012   0.002   TYR B  93 
 ARG   0.006   0.001   ARG B 404 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24073 (  283)
  hydrogen bonds       : angle       9.40233 (  783)
  covalent geometry    : bond        0.00294 ( 7482)
  covalent geometry    : angle       0.86247 (10196)

*********************** 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  : 0.374 
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: 0.2238
  time to fit residues: 10.1634
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  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    0.3980
   chunk 72 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0970
   chunk 24 optimal weight:    4.9990
   chunk 49 optimal weight:    0.4980
   chunk 38 optimal weight:    8.9990
   chunk 75 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0570
   chunk 87 optimal weight:    0.8980
   overall best weight:    0.3696
-------------------------------------------------------------------------------
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 = 0.3454 r_free = 0.3454 target = 0.056336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.043201 restraints weight = 34257.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.044338 restraints weight = 25659.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.045246 restraints weight = 20380.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6696
moved from start:          0.6330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   7482  Z= 0.153
  Angle     :  0.802  11.596  10196  Z= 0.390
  Chirality :  0.045   0.177   1158
  Planarity :  0.006   0.071   1342
  Dihedral  :  5.669  21.375   1058
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 18.55
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.64 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.70 %
    Favored  : 90.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.25), residues: 958
  helix: -0.40 (0.28), residues: 312
  sheet: -0.80 (0.41), residues: 142
  loop : -2.06 (0.24), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 379 
 HIS   0.003   0.001   HIS A 455 
 PHE   0.007   0.001   PHE B 258 
 TYR   0.012   0.002   TYR A 284 
 ARG   0.031   0.001   ARG A 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06538 (  283)
  hydrogen bonds       : angle       7.25351 (  783)
  covalent geometry    : bond        0.00330 ( 7482)
  covalent geometry    : angle       0.80162 (10196)

*********************** 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
  42 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.405 
Fit side-chains
REVERT: A  268 LEU cc_start: 0.9217 (tp) cc_final: 0.8779 (tp)
REVERT: A  360 GLU cc_start: 0.9125 (pm20) cc_final: 0.8785 (pp20)
REVERT: A  401 LEU cc_start: 0.9682 (tp) cc_final: 0.9327 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1401
  time to fit residues: 7.7990
Evaluate side-chains
  23 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 42 optimal weight:    0.0870
   chunk 68 optimal weight:    0.0970
   chunk 94 optimal weight:    0.0670
   chunk 32 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 23 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9990
   chunk 34 optimal weight:    8.9990
   chunk 91 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.4096
-------------------------------------------------------------------------------
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 = 0.3472 r_free = 0.3472 target = 0.057124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.043867 restraints weight = 34254.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.045097 restraints weight = 25282.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.046000 restraints weight = 19949.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6695
moved from start:          0.6810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   7482  Z= 0.133
  Angle     :  0.751  12.422  10196  Z= 0.358
  Chirality :  0.043   0.150   1158
  Planarity :  0.006   0.049   1342
  Dihedral  :  5.283  23.490   1058
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 16.99
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.31 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.57 (0.25), residues: 958
  helix: -1.32 (0.26), residues: 344
  sheet: -0.78 (0.41), residues: 148
  loop : -2.32 (0.26), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 426 
 HIS   0.003   0.001   HIS A 168 
 PHE   0.008   0.001   PHE A 155 
 TYR   0.008   0.001   TYR B 398 
 ARG   0.015   0.001   ARG A 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05329 (  283)
  hydrogen bonds       : angle       6.42103 (  783)
  covalent geometry    : bond        0.00295 ( 7482)
  covalent geometry    : angle       0.75081 (10196)

*********************** 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  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: A  360 GLU cc_start: 0.9035 (pm20) cc_final: 0.8701 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1200
  time to fit residues: 7.0394
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  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 81 optimal weight:    0.2980
   chunk 10 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   chunk 55 optimal weight:    0.0010
   chunk 22 optimal weight:   40.0000
   chunk 47 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 33 optimal weight:    0.2980
   overall best weight:    0.9190
-------------------------------------------------------------------------------
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 = 0.3461 r_free = 0.3461 target = 0.057225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.044295 restraints weight = 35948.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.045474 restraints weight = 26044.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.046426 restraints weight = 20451.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6734
moved from start:          0.7072

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= 0.126
  Angle     :  0.715  11.333  10196  Z= 0.345
  Chirality :  0.042   0.161   1158
  Planarity :  0.005   0.039   1342
  Dihedral  :  5.167  22.111   1058
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 17.26
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.72 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.43 (0.25), residues: 958
  helix: -1.28 (0.27), residues: 328
  sheet: -0.60 (0.41), residues: 150
  loop : -2.20 (0.25), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 426 
 HIS   0.003   0.001   HIS B 451 
 PHE   0.010   0.001   PHE A 389 
 TYR   0.020   0.002   TYR B 201 
 ARG   0.012   0.001   ARG B 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04731 (  283)
  hydrogen bonds       : angle       6.25405 (  783)
  covalent geometry    : bond        0.00273 ( 7482)
  covalent geometry    : angle       0.71484 (10196)

*********************** 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
  36 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.383 
Fit side-chains
REVERT: A  258 PHE cc_start: 0.8199 (t80) cc_final: 0.7109 (t80)
REVERT: A  360 GLU cc_start: 0.9060 (pm20) cc_final: 0.8718 (pp20)
REVERT: A  362 LEU cc_start: 0.9270 (tt) cc_final: 0.8913 (mp)
REVERT: A  370 MET cc_start: 0.9669 (tpt) cc_final: 0.9447 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.1116
  time to fit residues: 5.6462
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  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 82 optimal weight:    8.9990
   chunk 66 optimal weight:    6.9990
   chunk 39 optimal weight:    6.9990
   chunk 68 optimal weight:    2.9990
   chunk 76 optimal weight:    6.9990
   chunk 70 optimal weight:    0.0010
   chunk 58 optimal weight:    0.0370
   chunk 23 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    1.8070
-------------------------------------------------------------------------------
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 = 0.3414 r_free = 0.3414 target = 0.055382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.043039 restraints weight = 38082.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.044290 restraints weight = 26967.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.045114 restraints weight = 20842.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6799
moved from start:          0.7215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7482  Z= 0.140
  Angle     :  0.712  11.144  10196  Z= 0.347
  Chirality :  0.041   0.155   1158
  Planarity :  0.005   0.037   1342
  Dihedral  :  5.061  20.835   1058
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 19.44
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.56 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.24), residues: 958
  helix: -1.50 (0.25), residues: 332
  sheet: -0.68 (0.40), residues: 150
  loop : -2.25 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  75 
 HIS   0.003   0.001   HIS B 451 
 PHE   0.010   0.001   PHE A 258 
 TYR   0.006   0.001   TYR B 398 
 ARG   0.009   0.001   ARG A 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04434 (  283)
  hydrogen bonds       : angle       6.18280 (  783)
  covalent geometry    : bond        0.00303 ( 7482)
  covalent geometry    : angle       0.71246 (10196)

*********************** 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
  35 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.440 
Fit side-chains
REVERT: A  258 PHE cc_start: 0.8168 (t80) cc_final: 0.7096 (t80)
REVERT: A  360 GLU cc_start: 0.9154 (pm20) cc_final: 0.8841 (pp20)
REVERT: A  401 LEU cc_start: 0.9597 (tp) cc_final: 0.9295 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.1213
  time to fit residues: 5.9364
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  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 73 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0020
   chunk 36 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0070
   chunk 20 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.5206
-------------------------------------------------------------------------------
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 = 0.3447 r_free = 0.3447 target = 0.056675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.044143 restraints weight = 37385.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.045368 restraints weight = 26561.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.046211 restraints weight = 20688.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6773
moved from start:          0.7393

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= 0.125
  Angle     :  0.735   9.985  10196  Z= 0.347
  Chirality :  0.042   0.160   1158
  Planarity :  0.005   0.038   1342
  Dihedral  :  5.021  20.436   1058
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 16.92
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  9.39 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.54 (0.24), residues: 958
  helix: -1.39 (0.25), residues: 340
  sheet: -0.62 (0.40), residues: 150
  loop : -2.28 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 426 
 HIS   0.004   0.001   HIS B 451 
 PHE   0.015   0.002   PHE A 258 
 TYR   0.013   0.001   TYR A 248 
 ARG   0.012   0.001   ARG A 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04280 (  283)
  hydrogen bonds       : angle       5.91233 (  783)
  covalent geometry    : bond        0.00287 ( 7482)
  covalent geometry    : angle       0.73455 (10196)

*********************** 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
  39 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A  258 PHE cc_start: 0.8141 (t80) cc_final: 0.7209 (t80)
REVERT: A  360 GLU cc_start: 0.9174 (pm20) cc_final: 0.8829 (pp20)
REVERT: A  401 LEU cc_start: 0.9618 (tp) cc_final: 0.9418 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.1401
  time to fit residues: 7.2080
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  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 72 optimal weight:    7.9990
   chunk 17 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 63 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 77 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0970
   chunk 46 optimal weight:   10.0000
   overall best weight:    0.9582
-------------------------------------------------------------------------------
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 = 0.3448 r_free = 0.3448 target = 0.056349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.043991 restraints weight = 37021.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.045181 restraints weight = 26573.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.046086 restraints weight = 20678.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6783
moved from start:          0.7466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7482  Z= 0.123
  Angle     :  0.727  10.407  10196  Z= 0.349
  Chirality :  0.042   0.169   1158
  Planarity :  0.005   0.038   1342
  Dihedral  :  5.013  21.966   1058
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 16.45
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.35 %
    Favored  : 91.44 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.47 (0.25), residues: 958
  helix: -1.31 (0.25), residues: 346
  sheet: -0.68 (0.40), residues: 150
  loop : -2.22 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 167 
 HIS   0.004   0.001   HIS B 451 
 PHE   0.016   0.002   PHE A 258 
 TYR   0.007   0.001   TYR A 398 
 ARG   0.011   0.001   ARG B 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04105 (  283)
  hydrogen bonds       : angle       5.81169 (  783)
  covalent geometry    : bond        0.00272 ( 7482)
  covalent geometry    : angle       0.72728 (10196)

*********************** 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
  37 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: A  258 PHE cc_start: 0.8115 (t80) cc_final: 0.7168 (t80)
REVERT: A  268 LEU cc_start: 0.9214 (tp) cc_final: 0.8311 (tt)
REVERT: A  360 GLU cc_start: 0.9198 (pm20) cc_final: 0.8993 (mm-30)
REVERT: A  370 MET cc_start: 0.9712 (tpt) cc_final: 0.9404 (tpt)
REVERT: A  401 LEU cc_start: 0.9587 (tp) cc_final: 0.9381 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1470
  time to fit residues: 7.2927
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  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 64 optimal weight:    0.2980
   chunk 65 optimal weight:    8.9990
   chunk 51 optimal weight:    0.0670
   chunk 16 optimal weight:    0.2980
   chunk 44 optimal weight:    0.6980
   chunk 81 optimal weight:    0.0770
   chunk 91 optimal weight:    0.0370
   chunk 67 optimal weight:    0.0010
   chunk 38 optimal weight:    0.8980
   chunk 75 optimal weight:    4.9990
   overall best weight:    0.0960
-------------------------------------------------------------------------------
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 = 0.057584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.044820 restraints weight = 36716.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.046071 restraints weight = 26329.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.047066 restraints weight = 20487.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6765
moved from start:          0.7706

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= 0.123
  Angle     :  0.745   8.898  10196  Z= 0.354
  Chirality :  0.043   0.172   1158
  Planarity :  0.005   0.040   1342
  Dihedral  :  4.827  21.294   1058
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.98 %
    Favored  : 90.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.52 (0.24), residues: 958
  helix: -1.46 (0.25), residues: 346
  sheet: -0.61 (0.40), residues: 150
  loop : -2.18 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 167 
 HIS   0.005   0.001   HIS B 451 
 PHE   0.010   0.001   PHE A 258 
 TYR   0.009   0.001   TYR B 248 
 ARG   0.010   0.001   ARG A 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03911 (  283)
  hydrogen bonds       : angle       5.74271 (  783)
  covalent geometry    : bond        0.00270 ( 7482)
  covalent geometry    : angle       0.74526 (10196)

*********************** 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  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: A  258 PHE cc_start: 0.8121 (t80) cc_final: 0.7126 (t80)
REVERT: A  360 GLU cc_start: 0.9081 (pm20) cc_final: 0.8836 (mm-30)
REVERT: A  401 LEU cc_start: 0.9541 (tp) cc_final: 0.9335 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.1406
  time to fit residues: 7.0135
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  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 53 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 41 optimal weight:    0.2980
   chunk 65 optimal weight:    0.4980
   chunk 47 optimal weight:    5.9990
   chunk 17 optimal weight:    0.4980
   chunk 63 optimal weight:    0.1980
   chunk 66 optimal weight:    5.9990
   chunk 88 optimal weight:    0.0470
   chunk 54 optimal weight:    6.9990
   chunk 87 optimal weight:    0.0570
   overall best weight:    0.2196
-------------------------------------------------------------------------------
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 = 0.3491 r_free = 0.3491 target = 0.058033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.045432 restraints weight = 36505.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.046623 restraints weight = 26485.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.047605 restraints weight = 20793.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6762
moved from start:          0.7832

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= 0.119
  Angle     :  0.723   9.649  10196  Z= 0.343
  Chirality :  0.042   0.164   1158
  Planarity :  0.005   0.040   1342
  Dihedral  :  4.787  20.908   1058
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.14 %
    Favored  : 91.65 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.51 (0.24), residues: 958
  helix: -1.53 (0.24), residues: 346
  sheet: -0.50 (0.40), residues: 150
  loop : -2.14 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 426 
 HIS   0.005   0.001   HIS B 451 
 PHE   0.019   0.002   PHE B 389 
 TYR   0.007   0.001   TYR B 398 
 ARG   0.009   0.000   ARG A 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03865 (  283)
  hydrogen bonds       : angle       5.58456 (  783)
  covalent geometry    : bond        0.00259 ( 7482)
  covalent geometry    : angle       0.72291 (10196)

*********************** 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
  37 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
REVERT: A  258 PHE cc_start: 0.8110 (t80) cc_final: 0.7295 (t80)
REVERT: A  370 MET cc_start: 0.9721 (tpt) cc_final: 0.9519 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1468
  time to fit residues: 7.1754
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  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   chunk 78 optimal weight:    5.9990
   chunk 83 optimal weight:    0.4980
   chunk 54 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 95 optimal weight:    0.3980
   chunk 80 optimal weight:    0.0670
   chunk 41 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0040
   overall best weight:    0.5932
-------------------------------------------------------------------------------
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 = 0.3479 r_free = 0.3479 target = 0.057670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.045659 restraints weight = 36295.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.046870 restraints weight = 25913.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.047812 restraints weight = 20047.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6768
moved from start:          0.7891

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= 0.118
  Angle     :  0.729   9.763  10196  Z= 0.349
  Chirality :  0.042   0.162   1158
  Planarity :  0.005   0.040   1342
  Dihedral  :  4.777  20.176   1058
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 15.56
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.35 %
    Favored  : 91.44 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.44 (0.24), residues: 958
  helix: -1.44 (0.25), residues: 346
  sheet: -0.35 (0.42), residues: 140
  loop : -2.14 (0.26), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 426 
 HIS   0.005   0.001   HIS B 451 
 PHE   0.009   0.001   PHE B 389 
 TYR   0.011   0.001   TYR B 248 
 ARG   0.010   0.001   ARG B 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03822 (  283)
  hydrogen bonds       : angle       5.70166 (  783)
  covalent geometry    : bond        0.00262 ( 7482)
  covalent geometry    : angle       0.72917 (10196)

********************** 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
  38 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
REVERT: A  258 PHE cc_start: 0.8136 (t80) cc_final: 0.7241 (t80)
REVERT: A  411 LEU cc_start: 0.9289 (pt) cc_final: 0.8880 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.1376
  time to fit residues: 6.9548
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  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0670
   chunk 17 optimal weight:    0.0070
   chunk 13 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 46 optimal weight:    6.9990
   chunk 90 optimal weight:   10.0000
   overall best weight:    0.4736
-------------------------------------------------------------------------------
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 = 0.3484 r_free = 0.3484 target = 0.057856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.045479 restraints weight = 36548.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.046701 restraints weight = 26490.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.047567 restraints weight = 20738.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6770
moved from start:          0.7991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7482  Z= 0.116
  Angle     :  0.719  10.031  10196  Z= 0.342
  Chirality :  0.041   0.157   1158
  Planarity :  0.005   0.040   1342
  Dihedral  :  4.680  19.617   1058
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 15.22
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.35 %
    Favored  : 91.44 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.46 (0.25), residues: 958
  helix: -1.51 (0.24), residues: 346
  sheet: -0.82 (0.39), residues: 160
  loop : -1.97 (0.27), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 426 
 HIS   0.005   0.001   HIS B 451 
 PHE   0.010   0.001   PHE A 389 
 TYR   0.011   0.001   TYR B 248 
 ARG   0.009   0.001   ARG A 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03938 (  283)
  hydrogen bonds       : angle       5.56299 (  783)
  covalent geometry    : bond        0.00254 ( 7482)
  covalent geometry    : angle       0.71882 (10196)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1881.33 seconds
wall clock time: 33 minutes 47.86 seconds (2027.86 seconds total)