Starting phenix.real_space_refine
on Tue Mar 11 18:20:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jda_36076/03_2025/8jda_36076_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jda_36076/03_2025/8jda_36076.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jda_36076/03_2025/8jda_36076.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jda_36076/03_2025/8jda_36076.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jda_36076/03_2025/8jda_36076_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jda_36076/03_2025/8jda_36076_neut.cif"
  }
  resolution = 3.67
  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=   0.001 sd=   0.065
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      26      5.16       5
     C    4322      2.51       5
     N    1042      2.21       5
     O    1136      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6526
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 424, 3263
          Classifications: {'peptide': 424}
          Link IDs: {'PTRANS': 8, 'TRANS': 415}
    Chain: "B"
      Number of atoms: 3263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 424, 3263
          Classifications: {'peptide': 424}
          Link IDs: {'PTRANS': 8, 'TRANS': 415}
  Time building chain proxies: 4.68, per 1000 atoms: 0.72
  Number of scatterers: 6526
  At special positions: 0
  Unit cell: (68.04, 106.92, 66.96, 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      26     16.00
     O    1136      8.00
     N    1042      7.00
     C    4322      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: 1.76
  Conformation dependent library (CDL) restraints added in 918.5 milliseconds
  

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1540

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 0 sheets defined
      80.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 54
      removed outlier: 4.161A  pdb=" N   VAL A  37 " --> pdb=" O   PRO A  33 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   LEU A  44 " --> pdb=" O   VAL A  40 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   VAL A  45 " --> pdb=" O   GLY A  41 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   SER A  50 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 77
      removed outlier: 3.938A  pdb=" N   ALA A  64 " --> pdb=" O   PRO A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 95
      removed outlier: 3.783A  pdb=" N   GLU A  95 " --> pdb=" O   ARG A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 116
      removed outlier: 4.059A  pdb=" N   LEU A 102 " --> pdb=" O   PRO A  98 " (cutoff:3.500A)
      Proline residue:  A 107  - end of helix
      removed outlier: 4.339A  pdb=" N   GLU A 112 " --> pdb=" O   ALA A 108 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   SER A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 138
      removed outlier: 3.649A  pdb=" N   LEU A 132 " --> pdb=" O   GLN A 128 " (cutoff:3.500A)
      Proline residue:  A 135  - end of helix
    Processing helix  chain 'A' and resid 139 through 152
      removed outlier: 3.594A  pdb=" N   VAL A 148 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 169
      removed outlier: 4.123A  pdb=" N   LEU A 164 " --> pdb=" O   THR A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 181
    Processing helix  chain 'A' and resid 188 through 204
      removed outlier: 3.971A  pdb=" N   SER A 197 " --> pdb=" O   ILE A 193 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LEU A 198 " --> pdb=" O   GLU A 194 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   MET A 199 " --> pdb=" O   GLY A 195 " (cutoff:3.500A)
      removed outlier: 5.225A  pdb=" N   GLY A 202 " --> pdb=" O   LEU A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 217
      removed outlier: 4.595A  pdb=" N   PHE A 211 " --> pdb=" O   VAL A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 232
    Processing helix  chain 'A' and resid 235 through 254
    Processing helix  chain 'A' and resid 257 through 278
      removed outlier: 3.533A  pdb=" N   ILE A 266 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   PHE A 271 " --> pdb=" O   ALA A 267 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   TYR A 274 " --> pdb=" O   TYR A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 298
      removed outlier: 3.685A  pdb=" N   THR A 287 " --> pdb=" O   SER A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 339
      removed outlier: 4.218A  pdb=" N   LYS A 309 " --> pdb=" O   GLY A 305 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   SER A 310 " --> pdb=" O   ASP A 306 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   HIS A 313 " --> pdb=" O   LYS A 309 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   GLU A 316 " --> pdb=" O   HIS A 312 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLY A 331 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 352
      removed outlier: 4.130A  pdb=" N   TRP A 351 " --> pdb=" O   GLN A 347 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   ARG A 352 " --> pdb=" O   GLY A 348 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 347 through 352'
    Processing helix  chain 'A' and resid 353 through 378
      removed outlier: 3.651A  pdb=" N   VAL A 371 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU A 372 " --> pdb=" O   VAL A 368 " (cutoff:3.500A)
      Proline residue:  A 374  - end of helix
      removed outlier: 3.924A  pdb=" N   ARG A 378 " --> pdb=" O   PRO A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 392
    Processing helix  chain 'A' and resid 398 through 410
    Processing helix  chain 'A' and resid 418 through 451
      removed outlier: 3.561A  pdb=" N   THR A 423 " --> pdb=" O   LYS A 419 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   LEU A 424 " --> pdb=" O   GLU A 420 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU A 426 " --> pdb=" O   GLY A 422 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   PHE A 434 " --> pdb=" O   GLY A 430 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ASN A 440 " --> pdb=" O   THR A 436 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   GLY A 441 " --> pdb=" O   LEU A 437 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 54
      removed outlier: 3.789A  pdb=" N   LEU B  38 " --> pdb=" O   VAL B  34 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   PHE B  39 " --> pdb=" O   ASP B  35 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU B  44 " --> pdb=" O   VAL B  40 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   VAL B  45 " --> pdb=" O   GLY B  41 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   ILE B  48 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 77
      removed outlier: 4.122A  pdb=" N   ALA B  64 " --> pdb=" O   PRO B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 93
    Processing helix  chain 'B' and resid 97 through 105
      removed outlier: 3.653A  pdb=" N   ALA B 103 " --> pdb=" O   GLU B  99 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   PHE B 105 " --> pdb=" O   LEU B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 110
    Processing helix  chain 'B' and resid 111 through 116
    Processing helix  chain 'B' and resid 125 through 138
      Proline residue:  B 135  - end of helix
    Processing helix  chain 'B' and resid 139 through 152
      removed outlier: 3.744A  pdb=" N   LEU B 147 " --> pdb=" O   CYS B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 168
      removed outlier: 3.830A  pdb=" N   LEU B 164 " --> pdb=" O   THR B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 183
      removed outlier: 3.707A  pdb=" N   VAL B 176 " --> pdb=" O   ASP B 172 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   LEU B 183 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 204
      removed outlier: 3.591A  pdb=" N   LEU B 198 " --> pdb=" O   GLU B 194 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   MET B 199 " --> pdb=" O   GLY B 195 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   GLY B 202 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 218
      removed outlier: 4.307A  pdb=" N   PHE B 211 " --> pdb=" O   VAL B 207 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLN B 218 " --> pdb=" O   MET B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 232
      removed outlier: 3.620A  pdb=" N   ILE B 225 " --> pdb=" O   ASP B 221 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ILE B 226 " --> pdb=" O   TRP B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 254
    Processing helix  chain 'B' and resid 257 through 281
      removed outlier: 4.011A  pdb=" N   PHE B 271 " --> pdb=" O   ALA B 267 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   TYR B 274 " --> pdb=" O   TYR B 270 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   TRP B 279 " --> pdb=" O   THR B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 299
    Processing helix  chain 'B' and resid 304 through 339
      removed outlier: 4.077A  pdb=" N   LYS B 309 " --> pdb=" O   GLY B 305 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   SER B 310 " --> pdb=" O   ASP B 306 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   HIS B 312 " --> pdb=" O   GLN B 308 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   HIS B 313 " --> pdb=" O   LYS B 309 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   GLU B 316 " --> pdb=" O   HIS B 312 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   MET B 317 " --> pdb=" O   HIS B 313 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ILE B 328 " --> pdb=" O   THR B 324 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   GLY B 331 " --> pdb=" O   PHE B 327 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ILE B 334 " --> pdb=" O   SER B 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 377
      removed outlier: 3.786A  pdb=" N   VAL B 371 " --> pdb=" O   VAL B 367 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   LEU B 372 " --> pdb=" O   VAL B 368 " (cutoff:3.500A)
      Proline residue:  B 374  - end of helix
    Processing helix  chain 'B' and resid 384 through 392
    Processing helix  chain 'B' and resid 398 through 411
      removed outlier: 3.584A  pdb=" N   LEU B 402 " --> pdb=" O   GLY B 398 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 439
    Processing helix  chain 'B' and resid 439 through 451
      removed outlier: 3.683A  pdb=" N   ARG B 449 " --> pdb=" O   GLN B 445 " (cutoff:3.500A)

    430 hydrogen bonds defined for protein.
    1290 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: 1.84

  Time building geometry restraints manager: 2.06 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1972
        1.34 -     1.46: 1133
        1.46 -     1.57: 3519
        1.57 -     1.69: 0
        1.69 -     1.81: 46
  Bond restraints: 6670
  Sorted by residual:
  bond pdb=" C   VAL A 134 "
       pdb=" N   PRO A 135 "
    ideal  model  delta    sigma   weight residual
    1.335  1.354 -0.019 9.40e-03 1.13e+04 4.23e+00
  bond pdb=" C   VAL B 134 "
       pdb=" N   PRO B 135 "
    ideal  model  delta    sigma   weight residual
    1.335  1.354 -0.019 9.40e-03 1.13e+04 4.05e+00
  bond pdb=" C   TYR A 373 "
       pdb=" N   PRO A 374 "
    ideal  model  delta    sigma   weight residual
    1.335  1.354 -0.019 1.38e-02 5.25e+03 1.87e+00
  bond pdb=" CA  ILE A 438 "
       pdb=" C   ILE A 438 "
    ideal  model  delta    sigma   weight residual
    1.523  1.539 -0.016 1.27e-02 6.20e+03 1.66e+00
  bond pdb=" CG1 ILE B 193 "
       pdb=" CD1 ILE B 193 "
    ideal  model  delta    sigma   weight residual
    1.513  1.464  0.049 3.90e-02 6.57e+02 1.58e+00
  ... (remaining 6665 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 8703
        1.71 -     3.42: 291
        3.42 -     5.12: 45
        5.12 -     6.83: 17
        6.83 -     8.54: 6
  Bond angle restraints: 9062
  Sorted by residual:
  angle pdb=" N   LEU A 132 "
        pdb=" CA  LEU A 132 "
        pdb=" C   LEU A 132 "
      ideal   model   delta    sigma   weight residual
     114.75  107.72    7.03 1.26e+00 6.30e-01 3.11e+01
  angle pdb=" N   VAL B 207 "
        pdb=" CA  VAL B 207 "
        pdb=" C   VAL B 207 "
      ideal   model   delta    sigma   weight residual
     112.80  107.59    5.21 1.15e+00 7.56e-01 2.05e+01
  angle pdb=" N   ILE B 139 "
        pdb=" CA  ILE B 139 "
        pdb=" C   ILE B 139 "
      ideal   model   delta    sigma   weight residual
     111.90  108.56    3.34 8.10e-01 1.52e+00 1.71e+01
  angle pdb=" C   VAL B 232 "
        pdb=" N   ALA B 233 "
        pdb=" CA  ALA B 233 "
      ideal   model   delta    sigma   weight residual
     121.54  129.08   -7.54 1.91e+00 2.74e-01 1.56e+01
  angle pdb=" N   GLY A  84 "
        pdb=" CA  GLY A  84 "
        pdb=" C   GLY A  84 "
      ideal   model   delta    sigma   weight residual
     111.21  114.91   -3.70 1.04e+00 9.25e-01 1.26e+01
  ... (remaining 9057 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.40: 3364
       14.40 -    28.81: 313
       28.81 -    43.21: 136
       43.21 -    57.61: 17
       57.61 -    72.01: 10
  Dihedral angle restraints: 3840
    sinusoidal: 1428
      harmonic: 2412
  Sorted by residual:
  dihedral pdb=" CA  LEU A 198 "
           pdb=" C   LEU A 198 "
           pdb=" N   MET A 199 "
           pdb=" CA  MET A 199 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.80   28.20     0      5.00e+00 4.00e-02 3.18e+01
  dihedral pdb=" CA  GLU B  99 "
           pdb=" C   GLU B  99 "
           pdb=" N   LEU B 100 "
           pdb=" CA  LEU B 100 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.00   22.00     0      5.00e+00 4.00e-02 1.94e+01
  dihedral pdb=" CA  LEU B 131 "
           pdb=" C   LEU B 131 "
           pdb=" N   LEU B 132 "
           pdb=" CA  LEU B 132 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.17   21.83     0      5.00e+00 4.00e-02 1.91e+01
  ... (remaining 3837 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 958
       0.064 -    0.128: 129
       0.128 -    0.192: 6
       0.192 -    0.255: 0
       0.255 -    0.319: 1
  Chirality restraints: 1094
  Sorted by residual:
  chirality pdb=" CB  ILE A 438 "
            pdb=" CA  ILE A 438 "
            pdb=" CG1 ILE A 438 "
            pdb=" CG2 ILE A 438 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.32 2.00e-01 2.50e+01 2.55e+00
  chirality pdb=" CB  ILE A 417 "
            pdb=" CA  ILE A 417 "
            pdb=" CG1 ILE A 417 "
            pdb=" CG2 ILE A 417 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 7.08e-01
  chirality pdb=" CA  ASN A 256 "
            pdb=" N   ASN A 256 "
            pdb=" C   ASN A 256 "
            pdb=" CB  ASN A 256 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.59e-01
  ... (remaining 1091 not shown)

  Planarity restraints: 1088
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 233 "    0.021 2.00e-02 2.50e+03   4.24e-02 1.80e+01
        pdb=" C   ALA B 233 "   -0.073 2.00e-02 2.50e+03
        pdb=" O   ALA B 233 "    0.027 2.00e-02 2.50e+03
        pdb=" N   LEU B 234 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  97 "   -0.037 5.00e-02 4.00e+02   5.63e-02 5.07e+00
        pdb=" N   PRO B  98 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO B  98 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B  98 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 373 "    0.030 5.00e-02 4.00e+02   4.59e-02 3.38e+00
        pdb=" N   PRO A 374 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 374 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 374 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1085 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 288
        2.72 -     3.27: 7176
        3.27 -     3.81: 10998
        3.81 -     4.36: 13750
        4.36 -     4.90: 22530
  Nonbonded interactions: 54742
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 274 "
            pdb=" OD1 ASP B  35 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" O   LYS A 309 "
            pdb=" ND1 HIS A 313 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" OD1 ASP A  35 "
            pdb=" OH  TYR B 274 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OH  TYR B  77 "
            pdb=" ND2 ASN B  94 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" O   GLY A  47 "
            pdb=" OG  SER A  50 "
     model   vdw
     2.224 3.040
  ... (remaining 54737 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     19.610
  Find NCS groups from input model:        0.230
  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:             0.010
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6883
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      :  0.004   0.049   6670  Z= 0.240
  Angle     :  0.779   8.539   9062  Z= 0.441
  Chirality :  0.043   0.319   1094
  Planarity :  0.005   0.056   1088
  Dihedral  : 14.021  72.012   2300
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.69 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  1.14 %
    Favored  : 98.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.29), residues: 844
  helix: -0.57 (0.21), residues: 618
  sheet:  None (None), residues: 0
  loop : -1.67 (0.40), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 156 
 HIS   0.003   0.001   HIS B 416 
 PHE   0.021   0.002   PHE A 425 
 TYR   0.025   0.002   TYR A 273 
 ARG   0.003   0.000   ARG A 378 

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 117
  time to evaluate  : 0.770 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 118
  average time/residue: 0.1477
  time to fit residues: 24.9576
Evaluate side-chains
  99 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 35 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 34 optimal weight:    4.9990
   chunk 65 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 76 optimal weight:    6.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 440 ASN
B 362 GLN
** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.214997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.198240 restraints weight = 7374.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.201676 restraints weight = 9079.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.201057 restraints weight = 5621.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.4406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6786
moved from start:          0.1244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6670  Z= 0.231
  Angle     :  0.680   8.729   9062  Z= 0.345
  Chirality :  0.042   0.195   1094
  Planarity :  0.004   0.053   1088
  Dihedral  :  5.124  28.510    899
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  9.71 %
    Favored  : 88.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.29), residues: 844
  helix: -0.18 (0.21), residues: 638
  sheet:  None (None), residues: 0
  loop : -1.59 (0.43), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 158 
 HIS   0.003   0.001   HIS B  88 
 PHE   0.027   0.002   PHE B 298 
 TYR   0.012   0.001   TYR B 273 
 ARG   0.002   0.000   ARG B 397 

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
  outliers start: 14
  outliers final: 9
  residues processed: 124
  average time/residue: 0.1453
  time to fit residues: 25.9381
Evaluate side-chains
  109 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  318 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   chunk 78 optimal weight:    0.6980
   chunk 72 optimal weight:    0.5980
   chunk 41 optimal weight:    4.9990
   chunk 82 optimal weight:    0.6980
   chunk 5 optimal weight:    0.4980
   chunk 55 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 349 ASN
B 218 GLN
B 362 GLN
** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.216175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.199123 restraints weight = 7422.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.202711 restraints weight = 9261.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.202190 restraints weight = 5763.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.4415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6763
moved from start:          0.1748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6670  Z= 0.194
  Angle     :  0.628   8.387   9062  Z= 0.317
  Chirality :  0.040   0.195   1094
  Planarity :  0.004   0.047   1088
  Dihedral  :  4.806  23.493    896
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.71 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.65 (0.29), residues: 844
  helix:  0.00 (0.21), residues: 648
  sheet:  None (None), residues: 0
  loop : -1.54 (0.43), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 156 
 HIS   0.003   0.001   HIS B  88 
 PHE   0.029   0.001   PHE B 298 
 TYR   0.015   0.001   TYR A 273 
 ARG   0.003   0.000   ARG B 300 

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.744 
Fit side-chains
REVERT: A  256 ASN cc_start: 0.7130 (p0) cc_final: 0.6863 (p0)
  outliers start: 17
  outliers final: 10
  residues processed: 127
  average time/residue: 0.1417
  time to fit residues: 26.0525
Evaluate side-chains
  114 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain B residue   42 MET
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  318 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 17 optimal weight:    0.0970
   chunk 23 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 39 optimal weight:    0.3980
   chunk 63 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
A 313 HIS
** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4541 r_free = 0.4541 target = 0.216167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.198991 restraints weight = 7537.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.202531 restraints weight = 9404.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.201976 restraints weight = 5866.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.4415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6753
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6670  Z= 0.185
  Angle     :  0.620   8.690   9062  Z= 0.311
  Chirality :  0.040   0.200   1094
  Planarity :  0.004   0.047   1088
  Dihedral  :  4.683  21.535    896
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 17.43 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.30), residues: 844
  helix:  0.10 (0.21), residues: 650
  sheet:  None (None), residues: 0
  loop : -1.38 (0.44), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 156 
 HIS   0.011   0.001   HIS A 313 
 PHE   0.022   0.001   PHE B 298 
 TYR   0.011   0.001   TYR B 273 
 ARG   0.002   0.000   ARG B 300 

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.745 
Fit side-chains
REVERT: B   42 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7475 (ttp)
  outliers start: 17
  outliers final: 8
  residues processed: 123
  average time/residue: 0.1408
  time to fit residues: 24.9903
Evaluate side-chains
  116 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain B residue   42 MET
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  318 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   chunk 23 optimal weight:    0.2980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 218 GLN
B 414 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.214971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.198064 restraints weight = 7458.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.201409 restraints weight = 9069.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.200869 restraints weight = 6175.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.4405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6763
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6670  Z= 0.191
  Angle     :  0.628   8.225   9062  Z= 0.313
  Chirality :  0.041   0.209   1094
  Planarity :  0.004   0.050   1088
  Dihedral  :  4.625  20.421    896
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 18.29 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.30), residues: 844
  helix:  0.11 (0.21), residues: 656
  sheet:  None (None), residues: 0
  loop : -1.36 (0.44), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 156 
 HIS   0.002   0.001   HIS B  88 
 PHE   0.015   0.001   PHE B 298 
 TYR   0.012   0.001   TYR B 273 
 ARG   0.001   0.000   ARG B 397 

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.666 
Fit side-chains
  outliers start: 18
  outliers final: 12
  residues processed: 114
  average time/residue: 0.1438
  time to fit residues: 23.6059
Evaluate side-chains
  116 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  218 GLN
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  336 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 80 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0170
   chunk 35 optimal weight:    6.9990
   overall best weight:    0.7420

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

Flipped N/Q/H residues before XYZ refinement:
B 218 GLN
B 362 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.214932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.194790 restraints weight = 7362.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.194455 restraints weight = 9749.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.195641 restraints weight = 8909.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.4322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6860
moved from start:          0.2460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6670  Z= 0.203
  Angle     :  0.636   8.265   9062  Z= 0.317
  Chirality :  0.041   0.223   1094
  Planarity :  0.004   0.051   1088
  Dihedral  :  4.618  21.098    896
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 19.43 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.30), residues: 844
  helix:  0.19 (0.21), residues: 656
  sheet:  None (None), residues: 0
  loop : -1.35 (0.45), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 156 
 HIS   0.002   0.001   HIS B  88 
 PHE   0.025   0.001   PHE A 434 
 TYR   0.013   0.001   TYR B 273 
 ARG   0.001   0.000   ARG B 365 

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.733 
Fit side-chains
REVERT: A  351 TRP cc_start: 0.5774 (t-100) cc_final: 0.5387 (t60)
  outliers start: 21
  outliers final: 14
  residues processed: 127
  average time/residue: 0.1461
  time to fit residues: 26.8645
Evaluate side-chains
  119 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  218 GLN
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  218 GLN
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  336 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 35 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0980
   chunk 54 optimal weight:    0.0170
   chunk 14 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 362 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.216499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.199255 restraints weight = 7382.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.202381 restraints weight = 9109.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.202096 restraints weight = 6415.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.4412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6754
moved from start:          0.2625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6670  Z= 0.182
  Angle     :  0.645   9.665   9062  Z= 0.317
  Chirality :  0.041   0.222   1094
  Planarity :  0.004   0.049   1088
  Dihedral  :  4.558  20.810    896
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 21.29 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.30), residues: 844
  helix:  0.24 (0.21), residues: 658
  sheet:  None (None), residues: 0
  loop : -1.30 (0.44), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 156 
 HIS   0.002   0.001   HIS B  88 
 PHE   0.020   0.001   PHE B 298 
 TYR   0.015   0.001   TYR A 360 
 ARG   0.001   0.000   ARG B 300 

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.742 
Fit side-chains
REVERT: A  351 TRP cc_start: 0.5773 (t-100) cc_final: 0.5529 (t60)
  outliers start: 21
  outliers final: 15
  residues processed: 126
  average time/residue: 0.1469
  time to fit residues: 26.6659
Evaluate side-chains
  116 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  218 GLN
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  336 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0670
   chunk 44 optimal weight:    0.0980
   chunk 28 optimal weight:    0.6980
   chunk 64 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 54 optimal weight:    0.0170
   chunk 16 optimal weight:    2.9990
   chunk 73 optimal weight:    0.0020
   chunk 31 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.1764

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

Flipped N/Q/H residues before XYZ refinement:
** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 349 ASN
B 218 GLN
B 362 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.221228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.205038 restraints weight = 7281.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.206948 restraints weight = 8791.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4450 r_free = 0.4450 target = 0.207264 restraints weight = 6143.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.4463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6658
moved from start:          0.2861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6670  Z= 0.160
  Angle     :  0.641   9.905   9062  Z= 0.320
  Chirality :  0.041   0.210   1094
  Planarity :  0.004   0.049   1088
  Dihedral  :  4.500  22.248    896
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 22.71 %
    Favored  : 75.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.30), residues: 844
  helix:  0.38 (0.21), residues: 656
  sheet:  None (None), residues: 0
  loop : -1.31 (0.44), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 156 
 HIS   0.005   0.001   HIS A  52 
 PHE   0.021   0.001   PHE B 298 
 TYR   0.014   0.001   TYR B 273 
 ARG   0.003   0.000   ARG B 300 

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.824 
Fit side-chains
REVERT: A  105 PHE cc_start: 0.7838 (m-10) cc_final: 0.7618 (m-10)
REVERT: A  256 ASN cc_start: 0.6849 (p0) cc_final: 0.6639 (p0)
REVERT: A  351 TRP cc_start: 0.5833 (t-100) cc_final: 0.5615 (t60)
  outliers start: 14
  outliers final: 9
  residues processed: 117
  average time/residue: 0.1488
  time to fit residues: 25.1255
Evaluate side-chains
  117 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  336 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 73 optimal weight:    0.5980
   chunk 80 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0470
   chunk 6 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 35 optimal weight:    7.9990
   chunk 41 optimal weight:    8.9990
   overall best weight:    0.6280

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 GLN
B 362 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.218567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.200984 restraints weight = 7442.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.204600 restraints weight = 9482.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.204064 restraints weight = 5730.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.4426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6727
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6670  Z= 0.196
  Angle     :  0.657  10.711   9062  Z= 0.326
  Chirality :  0.041   0.221   1094
  Planarity :  0.004   0.048   1088
  Dihedral  :  4.502  21.568    896
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 23.86 %
    Favored  : 73.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.30), residues: 844
  helix:  0.38 (0.21), residues: 656
  sheet:  None (None), residues: 0
  loop : -1.34 (0.44), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 156 
 HIS   0.003   0.001   HIS A  52 
 PHE   0.021   0.001   PHE A 434 
 TYR   0.024   0.001   TYR A 154 
 ARG   0.004   0.000   ARG B 300 

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.755 
Fit side-chains
REVERT: A  256 ASN cc_start: 0.6976 (p0) cc_final: 0.6757 (p0)
REVERT: A  351 TRP cc_start: 0.5820 (t-100) cc_final: 0.5596 (t60)
REVERT: B  416 HIS cc_start: 0.5551 (OUTLIER) cc_final: 0.3984 (p-80)
  outliers start: 16
  outliers final: 12
  residues processed: 115
  average time/residue: 0.1386
  time to fit residues: 23.3620
Evaluate side-chains
  118 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  336 GLU
Chi-restraints excluded: chain B residue  416 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B 218 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.198214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.170287 restraints weight = 7635.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.171124 restraints weight = 7523.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.172638 restraints weight = 8193.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.4058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6889
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6670  Z= 0.229
  Angle     :  0.683  10.467   9062  Z= 0.341
  Chirality :  0.043   0.257   1094
  Planarity :  0.004   0.048   1088
  Dihedral  :  4.587  21.563    896
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 23.71 %
    Favored  : 74.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.30), residues: 844
  helix:  0.30 (0.21), residues: 658
  sheet:  None (None), residues: 0
  loop : -1.38 (0.44), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 393 
 HIS   0.003   0.001   HIS A  52 
 PHE   0.015   0.001   PHE A 105 
 TYR   0.021   0.002   TYR B 360 
 ARG   0.002   0.000   ARG B 300 

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.749 
Fit side-chains
REVERT: A  256 ASN cc_start: 0.7364 (p0) cc_final: 0.7134 (p0)
REVERT: A  351 TRP cc_start: 0.5949 (t-100) cc_final: 0.5524 (t60)
REVERT: B  416 HIS cc_start: 0.5673 (OUTLIER) cc_final: 0.3892 (p-80)
  outliers start: 16
  outliers final: 11
  residues processed: 117
  average time/residue: 0.1352
  time to fit residues: 23.3010
Evaluate side-chains
  114 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  336 GLU
Chi-restraints excluded: chain B residue  416 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    0.2980
   chunk 17 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 0 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9980
   chunk 83 optimal weight:   10.0000
   chunk 39 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 73 optimal weight:    9.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.199071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.171452 restraints weight = 7658.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.173706 restraints weight = 7413.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.175282 restraints weight = 7363.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.4091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6847
moved from start:          0.2997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6670  Z= 0.213
  Angle     :  0.684  11.524   9062  Z= 0.344
  Chirality :  0.042   0.258   1094
  Planarity :  0.004   0.049   1088
  Dihedral  :  4.555  21.529    896
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 24.14 %
    Favored  : 73.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.30), residues: 844
  helix:  0.31 (0.21), residues: 658
  sheet:  None (None), residues: 0
  loop : -1.41 (0.44), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 393 
 HIS   0.003   0.001   HIS A  52 
 PHE   0.021   0.001   PHE A 434 
 TYR   0.020   0.001   TYR B 360 
 ARG   0.003   0.000   ARG B 300 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1933.66 seconds
wall clock time: 34 minutes 25.85 seconds (2065.85 seconds total)